diff --git a/R/biblioshiny.R b/R/biblioshiny.R
index 57f8437a..12e36ec1 100644
--- a/R/biblioshiny.R
+++ b/R/biblioshiny.R
@@ -29,4 +29,8 @@ biblioshiny <- function(host = "127.0.0.1", port = NULL,
shinyOptions(maxUploadSize = maxUploadSize)
runApp(system.file("biblioshiny",package="bibliometrix"),launch.browser = launch.browser, port = port, host = getOption("shiny.host", host))
+
+ #remove utils functions from global environment
+ rm(ValueBoxes, countryCollab, pos = ".GlobalEnv")
+
}
diff --git a/inst/biblioshiny/server.R b/inst/biblioshiny/server.R
index eb6f9591..1bbab25a 100644
--- a/inst/biblioshiny/server.R
+++ b/inst/biblioshiny/server.R
@@ -1,8476 +1,8461 @@
-#### SERVER ####
-
-server <- function(input, output,session){
- session$onSessionEnded(stopApp)
- ##
-
- ## suppress warnings
- options(warn = -1)
- ##
-
- ## file upload max size
- maxUploadSize <- 200 # default value
- maxUploadSize <- getShinyOption("maxUploadSize", maxUploadSize)
- options(shiny.maxRequestSize=maxUploadSize*1024^2)
-
- ## initial values
- data("logo",package="bibliometrix",envir=environment())
- values = reactiveValues()
- values$logo <- logo
- values$logoGrid <- grid::rasterGrob(logo,interpolate = TRUE)
- values$h <- 7
- values$w <- 14
- values$results <- list("NA")
- values$log <- "working..."
- values$load="FALSE"
- values$field = values$cocngrams = "NA"
- values$citField=values$colField=values$citSep="NA"
- values$NetWords=values$NetRefs=values$ColNetRefs=matrix(NA,1,1)
- values$Title="Network"
- values$Histfield="NA"
- values$histlog="working..."
- values$kk=0
- #values$MRWremove.terms=NULL
- values$M=data.frame(PY=0)
- values$histsearch="NA"
- values$citShortlabel="NA"
- values$S=list("NA")
- values$GR="NA"
- values$dsToken <- "Wrong account or password"
- values$dsSample <- 0
- values$dsQuery <- ""
- values$pmQuery <- " "
- values$pmSample <- 0
- values$ApiOk <- 0
- values$checkControlBar <-FALSE
-
- ## NOTIFICATION ITEM ----
-
- output$notificationMenu <- renderMenu({
-
- notifTot <- notifications()
-
- values$nots <- apply(notifTot, 1, function(row) {
-
- ## extract href from messages
- if (is.na(row[["href"]])){href <- NULL
- }else{
- href <- paste("javascript:void(window.open('",row[["href"]],"', '_blank'))", sep="")
- }
-
- ## add bold to new messages and split the long ones in two rows
- if (row[["status"]]=="danger"){ ### new messages
- textRows <- paste("tags$strong('",row[["nots"]],"')", sep="")
- textRows <- strsplit(substr(textRows,1,85), "(?<=.{48})", perl = TRUE)[[1]]
- if (length(textRows)>1){
- textRows <- paste("tags$div(",textRows[1],"',tags$br(),'",textRows[2],")", sep="")
- }else{
- textRows <- paste("tags$div(",textRows,")", sep="")
- }
- }else{ ## old messages
- textRows <- strsplit(substr(row[["nots"]],1,70), "(?<=.{35})", perl = TRUE)[[1]]
- if (length(textRows)>1){
- textRows <- paste("tags$div('",textRows[1],"',tags$br(),'",textRows[2],"')", sep="")
- }else{
- textRows <- paste("tags$div('",textRows,"')", sep="")
- }
- }
-
-
-
- notificationItem(
- #text = row[["nots"]],
- text = eval(parse(text=textRows)),
- icon = if (row[["status"]]=="danger") {fa_i(name ="envelope")}else{fa_i(name ="envelope-open")},
- status = row[["status"]],
- href = href
- )
- })
-
- if ("danger" %in% notifTot[["status"]]){
- badge = "danger"
- icon_name ="envelope"
- } else {
- badge = NULL
- icon_name ="envelope-open"
- }
-
- dropdownMenu(type = "notifications",
- .list = values$nots,
- headerText ="",
- badgeStatus = NULL,
- icon = fa_i(name = icon_name)
- #icon = icon_color
- )
- })
-
- ###Menu sidebar ----
-
- # Apply Data----
- observe({
- toggleElement(
- id ="rest_of_sidebar",
- condition = input[["applyLoad"]]
- )
- })
-
- output$rest_of_sidebar <- renderMenu({
- sidebarMenu(
- menuItem("Filters",tabName = "filters",icon = fa_i(name ="filter")),
- menuItem("Overview",tabName = "overview",icon=fa_i(name = "table"),startExpanded = FALSE,
- menuSubItem("Main Information",tabName="mainInfo",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Annual Scientific Production",tabName = "annualScPr",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Average Citations per Year",tabName = "averageCitPerYear",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Three-Field Plot", tabName ="threeFieldPlot",icon = icon("chevron-right",lib = "glyphicon"))),
- menuItem("Sources", tabName = "sources",icon = fa_i(name ="book"), startExpanded = FALSE,
- menuSubItem("Most Relevant Sources", tabName = "relevantSources",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Most Local Cited Sources",tabName = "localCitedSources",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Bradford's Law",tabName = "bradford",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Source Impact",tabName = "sourceImpact",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Source Dynamics",tabName = "sourceDynamics",icon = icon("chevron-right",lib = "glyphicon"))),
- menuItem("Authors", tabName = "authors",icon = fa_i(name="user"),startExpanded = FALSE,
- "Authors",
- menuSubItem("Most Relevant Authors", tabName = "mostRelAuthors",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Local Cited Authors",tabName = "mostLocalCitedAuthors",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Authors' Production over Time",tabName = "authorsProdOverTime",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Lotka's Law",tabName = "lotka",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Author Impact",tabName = "authorImpact",icon = icon("chevron-right", lib = "glyphicon")),
- "Affiliations",
- menuSubItem("Most Relevant Affiliations",tabName = "mostRelAffiliations",icon = icon("chevron-right", lib = "glyphicon")),
- "Countries",
- menuSubItem("Corresponding Author's Country",tabName = "correspAuthorCountry",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Country Scientific Production",tabName = "countryScientProd",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Cited Countries",tabName = "mostCitedCountries",icon = icon("chevron-right", lib = "glyphicon"))
- ),
- menuItem("Documents", tabName = "documents",icon = fa_i(name="layer-group"), startExpanded = FALSE,
- "Documents",
- menuSubItem("Most Global Cited Documents",tabName = "mostGlobalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Local Cited Documents",tabName = "mostLocalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
- "Cited Refereces",
- menuSubItem("Most Local Cited References",tabName = "mostLocalCitRef",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Reference Spectroscopy",tabName = "ReferenceSpect",icon = icon("chevron-right", lib = "glyphicon")),
- "Words",
- menuSubItem("Most Frequent Words",tabName = "mostFreqWords",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("WordCloud", tabName = "wcloud",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("TreeMap",tabName = "treemap",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Word Dynamics",tabName = "wordDynamics",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Trend Topics",tabName = "trendTopic",icon = icon("chevron-right", lib = "glyphicon"))
- ),
- menuItem("Clustering", tabName = "clustering",icon = fa_i(name ="spinner"),startExpanded = FALSE,
- menuSubItem("Clustering by Coupling",tabName = "coupling",icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Conceptual Structure",tabName = "concepStructure",icon = fa_i(name="spell-check"),startExpanded = FALSE,
- "Network Approach",
- menuSubItem("Co-occurence Network",tabName = "coOccurenceNetwork",icon = icon("chevron-right", lib = "glyphicon") ),
- menuSubItem("Thematic Map",tabName = "thematicMap", icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Thematic Evolution",tabName = "thematicEvolution", icon = icon("chevron-right", lib = "glyphicon")),
- "Factorial Approach",
- menuSubItem("Factorial Analysis", tabName = "factorialAnalysis", icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Intellectual Structure",tabName = "intStruct",icon = fa_i(name="gem"), startExpanded = FALSE,
- menuSubItem("Co-citation Network",tabName = "coCitationNetwork", icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Historiograph",tabName = "historiograph", icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Social Structure",tabName = "socialStruct", icon = fa_i("users"),startExpanded = FALSE,
- menuSubItem("Collaboration Network",tabName = "collabNetwork",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Collaboration WorldMap", tabName = "collabWorldMap",icon = icon("chevron-right", lib = "glyphicon")))
- )
- })
-
- # Apply API ----
- observe({
- toggleElement(
- id ="rest_of_sidebar",
- condition = input[["apiApply"]]
- )
- })
-
- output$rest_of_sidebar <- renderMenu({
- sidebarMenu(
- menuItem("Filters",tabName = "filters",icon = fa_i(name ="filter")),
- menuItem("Overview",tabName = "overview",icon=fa_i(name = "table"),startExpanded = FALSE,
- menuSubItem("Main Information",tabName="mainInfo",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Annual Scientific Production",tabName = "annualScPr",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Average Citations per Year",tabName = "averageCitPerYear",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Three-Field Plot", tabName ="threeFieldPlot",icon = icon("chevron-right",lib = "glyphicon"))),
- menuItem("Sources", tabName = "sources",icon = fa_i(name ="book"), startExpanded = FALSE,
- menuSubItem("Most Relevant Sources", tabName = "relevantSources",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Most Local Cited Sources",tabName = "localCitedSources",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Bradford's Law",tabName = "bradford",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Source Impact",tabName = "sourceImpact",icon = icon("chevron-right",lib = "glyphicon")),
- menuSubItem("Source Dynamics",tabName = "sourceDynamics",icon = icon("chevron-right",lib = "glyphicon"))),
- menuItem("Authors", tabName = "authors",icon = fa_i(name="user"),startExpanded = FALSE,
- "Authors",
- menuSubItem("Most Relevant Authors", tabName = "mostRelAuthors",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Local Cited Authors",tabName = "mostLocalCitedAuthors",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Authors' Production over Time",tabName = "authorsProdOverTime",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Lotka's Law",tabName = "lotka",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Author Impact",tabName = "authorImpact",icon = icon("chevron-right", lib = "glyphicon")),
- "Affiliations",
- menuSubItem("Most Relevant Affiliations",tabName = "mostRelAffiliations",icon = icon("chevron-right", lib = "glyphicon")),
- "Countries",
- menuSubItem("Corresponding Author's Country",tabName = "correspAuthorCountry",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Country Scientific Production",tabName = "countryScientProd",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Cited Countries",tabName = "mostCitedCountries",icon = icon("chevron-right", lib = "glyphicon"))
- ),
- menuItem("Documents", tabName = "documents",icon = fa_i(name="layer-group"), startExpanded = FALSE,
- "Documents",
- menuSubItem("Most Global Cited Documents",tabName = "mostGlobalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Most Local Cited Documents",tabName = "mostLocalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
- "Cited Refereces",
- menuSubItem("Most Local Cited References",tabName = "mostLocalCitRef",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Reference Spectroscopy",tabName = "ReferenceSpect",icon = icon("chevron-right", lib = "glyphicon")),
- "Words",
- menuSubItem("Most Frequent Words",tabName = "mostFreqWords",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("WordCloud", tabName = "wcloud",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("TreeMap",tabName = "treemap",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Word Dynamics",tabName = "wordDynamics",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Trend Topics",tabName = "trendTopic",icon = icon("chevron-right", lib = "glyphicon"))
- ),
- menuItem("Clustering", tabName = "clustering",icon = fa_i(name ="spinner"),startExpanded = FALSE,
- menuSubItem("Clustering by Coupling",tabName = "coupling",icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Conceptual Structure",tabName = "concepStructure",icon = fa_i(name="spell-check"),startExpanded = FALSE,
- "Network Approach",
- menuSubItem("Co-occurence Network",tabName = "coOccurenceNetwork",icon = icon("chevron-right", lib = "glyphicon") ),
- menuSubItem("Thematic Map",tabName = "thematicMap", icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Thematic Evolution",tabName = "thematicEvolution", icon = icon("chevron-right", lib = "glyphicon")),
- "Factorial Approach",
- menuSubItem("Factorial Analysis", tabName = "factorialAnalysis", icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Intellectual Structure",tabName = "intStruct",icon = fa_i(name="gem"), startExpanded = FALSE,
- menuSubItem("Co-citation Network",tabName = "coCitationNetwork", icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Historiograph",tabName = "historiograph", icon = icon("chevron-right", lib = "glyphicon"))),
- menuItem("Social Structure",tabName = "socialStruct", icon = fa_i("users"),startExpanded = FALSE,
- menuSubItem("Collaboration Network",tabName = "collabNetwork",icon = icon("chevron-right", lib = "glyphicon")),
- menuSubItem("Collaboration WorldMap", tabName = "collabWorldMap",icon = icon("chevron-right", lib = "glyphicon")))
- )
- })
-
- # observe({
- # toggleElement(
- # id = "rest_of_sidebar",
- # condition = input[["applyLoad"]]
- # )
- # })
- #
- # # menuItem("Quit", tabName = "quit",icon=icon("off",lib = "glyphicon")),
- # # menuItem("K-Synth", icon = icon("globe",lib = "glyphicon"), badgeLabel = "Link", badgeColor = "blue",
- # # href = "https://www.k-synth.unina.it")
-
-
-
-
- ## LOAD MENU ----
- format <- function(obj){
- ext<- sub('.*\\.', '', obj[1])
- switch(ext,
- txt ={
- format <- "plaintext"
- },
- csv ={
- format <- "csv"
- },
- bib ={
- format <- "bibtex"
- },
- ciw ={
- format <- "endnote"
- },
- xlsx={
- format <- "excel"
- }
- )
- return(format)
- }
-
- ## smart_load function ----
- smart_load <- function(file){
- var <- load(file)
- n <- length(var)
- if (!"M" %in% var){
- if (n == 1) {
- eval(parse(text = paste0("M <- ", var)))
- } else {
- stop("I could not find bibliometrixDB object in your data file: ", file)
- }
- }
- rm(list = var[var != "M"])
- if ( ("M" %in% ls()) & inherits(M, "bibliometrixDB") ){
- return(M)
- } else {
- stop("Please make sure your RData/Rda file contains a bibliometrixDB object (M).")
- }
- }
-
- DATAloading<- eventReactive(input$applyLoad,{
- # input$file1 will be NULL initially. After the user selects
- # and uploads a file, it will be a data frame with 'name',
- # 'size', 'type', and 'datapath' columns. The 'datapath'
- # column will contain the local filenames where the data can
- # be found.
- if (input$load=="demo"){
- data(management, package="bibliometrixData")
- values = initial(values)
- row.names(management) <- management$SR
- values$M <- management
- values$Morig = management
- values$Histfield = "NA"
- values$results = list("NA")
- return()
- }
- inFile <- input$file1
-
- if (!is.null(inFile) & input$load=="import") {
- ext <- getFileNameExtension(inFile$datapath)
- switch(
- input$dbsource,
- isi = {
- switch(ext,
- ### WoS ZIP Files
- zip = {
- D <- unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(D,
- dbsource = input$dbsource,
- format = format(D))
- })
- },
- ### WoS Txt/Bib Files
- {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = format(inFile$datapath))
- })
- })
- },
- scopus = {
- switch(ext,
- ### Scopus ZIP Files
- zip = {
- D <- unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(D,
- dbsource = input$dbsource,
- format = format(D))
- })
- },
- ### Scopus CSV/Bib Files
- csv = {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = "csv")
- })
- },
- bib = {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = "bibtex")
- })
- })
-
- },
- lens = {
- switch(ext,
- ### Lens.org ZIP Files
- zip = {
- D <- unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(D,
- dbsource = input$dbsource,
- format = format(D))
- })
- },
- ### Lens.org CSV Files
- {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = format(inFile$datapath))
- })
- })
- },
- cochrane = {
- switch(ext,
- ### Cochrane ZIP Files
- zip = {
- D <- unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(D,
- dbsource = input$dbsource,
- format = format(D))
- })
- },
- ### Cochrane txt files
- {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = "plaintext")
- })
- })
-
- },
- pubmed = {
- switch(ext,
- ### Pubmed ZIP Files
- zip = {
- D <- unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(D,
- dbsource = input$dbsource,
- format = "pubmed")
- })
- },
- ### Pubmed txt Files
- txt = {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <- convert2df(inFile$datapath,
- dbsource = input$dbsource,
- format = "pubmed")
- })
- })
- },
- dimensions = {
- switch(ext,
- ### Dimensions ZIP Files
- zip = {
- D = unzip(inFile$datapath)
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <-
- convert2df(D,
- dbsource = input$dbsource,
- format = format(D))
- })
- },
- ### Dimensions Xlsx/csv Files
- xlsx = {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <-
- convert2df(
- inFile$datapath,
- dbsource = "dimensions",
- format = "excel"
- )
- })
- },
- csv = {
- withProgress(message = 'Conversion in progress',
- value = 0, {
- M <-
- convert2df(
- inFile$datapath,
- dbsource = "dimensions",
- format = "csv"
- )
- })
- })
-
- }
- )
-
- } else if (!is.null(inFile) & input$load=="load") {
- ext <- tolower(getFileNameExtension(inFile$datapath))
- #print(ext)
- switch(ext,
- ### excel format
- xlsx={
- #M <- rio::import(inFile$datapath)
- M <- readxl::read_excel(inFile$datapath) %>% as.data.frame(stringsAsFactors=FALSE)
- class(M) <- c("bibliometrixDB", "data.frame")
- ### M row names
- ### identify duplicated SRs
- SR=M$SR
- tab=table(SR)
- tab2=table(tab)
- ind=as.numeric(names(tab2))
- ind=ind[which(ind>1)]
- if (length(ind)>0){
- for (i in ind){
- indice=names(which(tab==i))
- for (j in indice){
- indice2=which(SR==j)
- SR[indice2]=paste(SR[indice2],as.character(1:length(indice2)),sep=" ")
- }
- }
- }
-
- row.names(M) <- SR
- },
- ### RData format
- rdata={
- M <- smart_load(inFile$datapath)
- },
- rda={
- M <- smart_load(inFile$datapath)
- },
- rds={
- M <- readRDS(inFile$datapath)
- })
- } else if (is.null(inFile)) {return(NULL)}
-
- values = initial(values)
- values$M <- M
- values$Morig = M
- values$Histfield = "NA"
- values$results = list("NA")
-
-
- })
- output$contents <- DT::renderDT({
- DATAloading()
- MData = as.data.frame(apply(values$M, 2, function(x) {
- substring(x, 1, 150)
- }), stringsAsFactors = FALSE)
- MData$DOI <-
- paste0(
- '',
- MData$DI,
- ''
- )
- nome = c("DOI", names(MData)[-length(names(MData))])
- MData = MData[nome]
- DT::datatable(MData,escape = FALSE,rownames = FALSE, extensions = c("Buttons"),
- options = list(
- pageLength = 10,
- dom = 'Bfrtip',
- buttons = list(list(extend = 'pageLength'),
- list(extend = 'print')),
- lengthMenu = list(c(10, 25, 50, -1),
- c('10 rows', '25 rows', '50 rows', 'Show all')),
- columnDefs = list(list(
- className = 'dt-center', targets = 0:(length(names(MData)) - 1)
- ))
- ),
- class = 'cell-border compact stripe'
- ) %>%
- formatStyle(
- names(MData),
- backgroundColor = 'white',
- textAlign = 'center',
- fontSize = '70%'
- )
- })
-
- ## export functions ----
- output$collection.save <- downloadHandler(
- filename = function() {
-
- paste("Bibliometrix-Export-File-", Sys.Date(), ".",input$save_file, sep="")
- },
- content <- function(file) {
- switch(input$save_file,
- #xlsx={suppressWarnings(rio::export(values$M, file=file))},
- xlsx={suppressWarnings(openxlsx::write.xlsx(values$M, file=file))},
- RData={
- M=values$M
- save(M, file=file)
- })
-
- },
- contentType = input$save_file
- )
-
- output$collection.save_api <- downloadHandler(
- filename = function() {
-
- paste("Bibliometrix-Export-File-", Sys.Date(), ".",input$save_file_api, sep="")
- },
- content <- function(file) {
- switch(input$save_file_api,
- #xlsx={suppressWarnings(rio::export(values$M, file=file))},
- xlsx={suppressWarnings(openxlsx::write.xlsx(values$M, file=file))},
- RData={
- M=values$M
- save(M, file=file)
- })
-
- },
- contentType = input$save_file_api
- )
-
- output$textLog <- renderUI({
- k=dim(values$M)[1]
- if (k==1){k=0}
- log=paste("Number of Documents ",k)
- textInput("textLog", "Conversion results",
- value=log)
- })
-
- dsModal <- function(failed = FALSE) {
- modalDialog(
- title = "Dimensions API",
- size = "l",
-
- h4(em(
- strong("1) Get a token using your Dimensions credentials")
- )),
- textInput(
- "dsAccount",
- "Account",
- "",
- width = NULL,
- placeholder = NULL
- ),
- passwordInput("dsPassword",
- "Password",
- "",
- width = NULL,
- placeholder = NULL),
-
- actionButton("dsToken", "Get a token "),
- h5(tags$b("Token")),
- verbatimTextOutput("tokenLog", placeholder = FALSE),
- tags$hr(),
- h4(em(strong("2) Create a query"))),
- textInput(
- "dsWords",
- "Words",
- "",
- width = NULL,
- placeholder = NULL
- ),
- selectInput(
- "dsFullsearch",
- label = "search field",
- choices = c("Title and Abstract only" = FALSE,
- "Full text" = TRUE),
- selected = FALSE
- ),
- textInput(
- "dsCategories",
- "Science Categories",
- "",
- width = NULL,
- placeholder = NULL
- ),
- numericInput("dsStartYear", "Start Year", value = 1990),
- numericInput("dsEndYear", "End Year", value = as.numeric(substr(Sys.time(), 1, 4))),
-
-
- actionButton("dsQuery", "Create the query "),
-
- h5(tags$b("Your query")),
- verbatimTextOutput("queryLog", placeholder = FALSE),
- h5(tags$b("Documents returned using your query")),
- verbatimTextOutput("sampleLog", placeholder = FALSE),
-
-
- uiOutput("sliderLimit"),
-
- footer = tagList(
- modalButton("Cancel"),
- actionButton("dsok", "OK")
- )
- )
- }
-
- ### Show Dimensions modal when button is clicked.
- observeEvent(input$dsShow, {
- showModal(dsModal())
- })
-
- observeEvent(input$dsok, {
- removeModal()
- values$M <- data.frame(Message="Waiting for data")
- })
-
- output$tokenLog <- renderText({
- input$dsToken
- isolate({
- capture.output(Token <- dsAuth(username = input$dsAccount, password = input$dsPassword))
- #Token <- dsAuth(username = input$dsAccount, password = input$dsPassword)
- if (Token==1){
- values$dsToken <- "Wrong account or password"
- }else{
- values$dsToken <- Token
- }
- values$dsToken
-
- })
- })
-
- DSQUERYload<- eventReactive(input$dsQuery,{
- values$dsQuery <- dsQueryBuild(item = "publications",
- words = input$dsWords,
- full.search = input$dsFullsearch,
- type = "article",
- categories = input$dsCategories,
- start_year = input$dsStartYear, end_year = input$dsEndYear)
- dsSample <- 0
- capture.output(dsSample <- dsApiRequest(token = values$dsToken, query = values$dsQuery, limit = 0))
- if (class(dsSample)=="numeric"){
- values$dsSample <- 0
- }else{values$dsSample <- dsSample$total_count}
- })
-
- output$queryLog <- renderText({
-
- DSQUERYload()
- values$dsQuery
-
- })
-
- output$queryLog2 <- renderText({
- DSQUERYload()
- values$dsQuery
- })
-
- output$sampleLog <- renderText({
- DSQUERYload()
- mes <- paste("Dimensions returns ",values$dsSample, " documents", collapse="",sep="")
- mes
- })
-
- output$sampleLog2 <- renderText({
-
- if (nrow(values$M)<2) {n <- 0}else{n <- nrow(values$M)}
- mes <- paste("Dimensions API returns ",n, " documents", collapse="",sep="")
- values$ApiOk <- 0
- return(mes)
- })
-
- output$sliderLimit <- renderUI({
-
- sliderInput("sliderLimit", "Total document to download", min = 1,
- max = values$dsSample, value = values$dsSample, step = 1)
- })
-
- ### API MENU: PubMed ----
- ### PubMed modal
- pmModal <- function(failed = FALSE) {
- modalDialog(
- title = "PubMed API",
- size = "l",
- h4(em(strong(
- "1) Generate a valid query"
- ))),
- textInput(
- "pmQueryText",
- "Search terms",
- " ",
- width = NULL,
- placeholder = NULL
- ),
- numericInput("pmStartYear", "Start Year", value = 1990),
- numericInput("pmEndYear", "End Year", value = as.numeric(substr(Sys.time(
- ), 1, 4))),
- actionButton("pmQuery", "Try the query "),
- h5(tags$b("Query Translation")),
- verbatimTextOutput("pmQueryLog", placeholder = FALSE),
- #h5(tags$b("Generated query")),
- h5(tags$b("Documents returned using your query")),
- verbatimTextOutput("pmSampleLog", placeholder = FALSE),
- tags$hr(),
- h4(em(
- strong("2) Choose how many documents to download")
- )),
-
- uiOutput("pmSliderLimit"),
-
- footer = tagList(
- modalButton("Cancel"),
- actionButton("pmok", "OK")
- )
- )
- }
-
- # Show modal when button is clicked.
- observeEvent(input$pmShow, {
- showModal(pmModal())
- })
-
- observeEvent(input$pmok, {
- removeModal()
- })
-
- pmQUERYLOAD <- eventReactive(input$pmQuery,{
-
- query = paste(input$pmQueryText,"[Title/Abstract] AND english[LA] AND Journal Article[PT] AND "
- ,input$pmStartYear,":",input$pmEndYear,"[DP]", sep="")
- res <- pmQueryTotalCount(query = query, api_key = NULL)
- if (class(res)=="list"){
- values$pmSample <- res$total_count
- values$pmQuery <- res$query_translation}
- values$pmQuery <- res$query_translation
-
- })
- output$pmQueryLog <- renderText({
- pmQUERYLOAD()
- values$pmQuery
- })
-
- output$pmQueryLog2 <- renderText({
- pmQUERYLOAD()
- values$pmQuery
- })
-
- output$pmSampleLog <- renderText({
- pmQUERYLOAD()
- mes <- paste("PubMed returns ",values$pmSample, " documents", collapse="",sep="")
- mes
-
- })
- output$pmSampleLog2 <- renderText({
- if (nrow(values$M)<2) {n <- 0}else{n <- nrow(values$M)}
-
- mes <- paste("PubMed API returns ",n, " documents", collapse="",sep="")
- values$ApiOk <- 0
- return(mes)
- })
-
- output$pmSliderLimit <- renderUI({
- sliderInput("pmSliderLimit", "Total document to download", min = 1,
- max = values$pmSample, value = values$pmSample, step = 1)
- })
- ### API MENU: Content Download ----
- APIDOWNLOAD <- eventReactive(input$apiApply,{
- values = initial(values)
- values$M <- data.frame(Message="Waiting for data")
-
- switch(input$dbapi,
- ds={
- if (input$dsWords!="") {
- #capture.output(
- D <-
- dsApiRequest(
- token = values$dsToken,
- query = values$dsQuery,
- limit = input$sliderLimit
- )
- #)
- M <- convert2df(D, "dimensions", "api")
- values$ApiOk <- 1
- values$M <- M
- values$Morig = M
-
- values$Histfield = "NA"
- values$results = list("NA")
-
- contentTable(values)
- }
- },
- pubmed={
- #if (exists("input$pmQueryText")){
- if (input$pmQueryText !=" ") {
- #capture.output(
- D <-
- pmApiRequest(
- query = values$pmQuery,
- limit = input$pmSliderLimit,
- api_key = NULL
- )
- #)
- M <- convert2df(D, "pubmed", "api")
- values$ApiOk <- 1
- values$M <- M
- values$Morig = M
-
- values$Histfield = "NA"
- values$results = list("NA")
-
- #contentTable(values)
- }
-
- })
- })
-
-
-
- output$apiContents <- DT::renderDT({
- APIDOWNLOAD()
- contentTable(values)
- #}
-
- })
-
- ### function returns a formatted data.frame ----
- contentTable <- function(values){
- MData = as.data.frame(apply(values$M, 2, function(x) {
- substring(x, 1, 150)
- }), stringsAsFactors = FALSE)
- MData$DOI <-
- paste0(
- '',
- MData$DI,
- ''
- )
- nome = c("DOI", names(MData)[-length(names(MData))])
- MData = MData[nome]
- DT::datatable(MData,escape = FALSE,rownames = FALSE, extensions = c("Buttons"),
- options = list(
- pageLength = 10,
- dom = 'Bfrtip',
- buttons = list(list(extend = 'pageLength'),
- list(extend = 'print')),
- lengthMenu = list(c(10, 25, 50, -1),
- c('10 rows', '25 rows', '50 rows', 'Show all')),
- columnDefs = list(list(
- className = 'dt-center', targets = 0:(length(names(MData)) - 1)
- ))
- ),
- class = 'cell-border compact stripe'
- ) %>%
- formatStyle(
- names(MData),
- backgroundColor = 'white',
- textAlign = 'center',
- fontSize = '70%'
- )
- }
-
- output$textDim <- renderUI({
- str1=paste("Documents ",dim(values$M)[1]," of ",dim(values$Morig)[1])
- str2=paste("Sources ",length(unique(values$M$SO))," of ", length(unique(values$Morig$SO)))
- str3=paste("Authors ",length(unique(unlist(strsplit(values$M$AU,";"))))," of ", length(unique(unlist(strsplit(values$Morig$AU,";")))))
- HTML(paste("",str1, str2, str3, sep = '
'))
- })
-
- output$selectType <- renderUI({
-
- artType=sort(unique(values$Morig$DT))
- selectInput("selectType", "Document Type",
- choices = artType,
- selected = artType,
- multiple =TRUE )
- })
- output$selectLA <- renderUI({
-
- if ("LA" %in% names(values$Morig)){
- LA <- sort(unique(values$Morig$LA))} else {
- values$Morig$LA <- "N.A."
- LA <- "N.A."
- }
- selectInput("selectLA", "Language",
- choices = LA,
- selected = LA,
- multiple =TRUE )
- })
-
- output$sliderPY <- renderUI({
-
- sliderInput("sliderPY", "Publication Year", min = min(values$Morig$PY,na.rm=T),sep="",
- max = max(values$Morig$PY,na.rm=T), value = c(min(values$Morig$PY,na.rm=T),max(values$Morig$PY,na.rm=T)))
- })
-
- output$selectSource <- renderUI({
- SO=sort(unique(values$Morig$SO))
- selectInput("selectSource", "Source",
- choices = SO,
- selected = SO,
- multiple = TRUE)
-
- })
-
- output$sliderTCpY <- renderUI({
- Y <- as.numeric(substr(Sys.time(),1,4))
- values$Morig <- values$Morig %>%
- mutate(Age = Y - .data$PY+1,
- TCpY = round(.data$TC/Age,2)) %>%
- group_by(.data$PY) %>%
- mutate(NTC = .data$TC/mean(.data$TC, na.rm=T)) %>%
- as.data.frame()
- sliderInput("sliderTCpY", "Average Citation per Year", min = floor(min(values$Morig$TCpY, na.rm=T)),
- max = ceiling(max(values$Morig$TCpY,na.rm=T)), step=0.1,
- value = c(floor(min(values$Morig$TCpY, na.rm=T)),ceiling(max(values$Morig$TCpY,na.rm=T))))
- })
-
- ## Update filtered data ----
-
- DTfiltered <- eventReactive(input$applyFilter,{
- M <- values$Morig
- B <- bradford(M)$table
- M <- subset(M, M$PY>=input$sliderPY[1] & M$PY<=input$sliderPY[2])
- M <- subset(M, M$TCpY>=input$sliderTCpY[1] & M$TCpY<=input$sliderTCpY[2])
- M <- subset(M, M$DT %in% input$selectType)
- M <- subset(M, M$LA %in% input$selectLA)
- switch(input$bradfordSources,
- "core"={
- SO=B$SO[B$Zone %in% "Zone 1"]
- },
- "zone2"={
- SO=B$SO[B$Zone %in% c("Zone 1", "Zone 2")]
- },
- "all"={SO=B$SO})
- M=M[M$SO %in% SO,]
- values<-initial(values)
- values$M=M
- Mdisp=as.data.frame(apply(values$M,2,function(x){substring(x,1,150)}),stringsAsFactors = FALSE)
- if (dim(Mdisp)[1]>0){
- DT::datatable(Mdisp, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Filtered_DataTable',
- title = "My Title",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Filtered_DataTable',
- title = "My Title",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(Mdisp))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(Mdisp), backgroundColor = 'white',textAlign = 'center', fontSize = '70%')
- }else{Mdisp=data.frame(Message="Empty collection",stringsAsFactors = FALSE, row.names = " ")}
- })
-
- output$dataFiltered <- DT::renderDT({
-
- DTfiltered()
-
- })
-
- ## Main Info ----
- output$MainInfo <- DT::renderDT({
- res <- descriptive(values,type="tab1")
- values <- res$values
- values$TABdesc <- res$TAB
-
- DT::datatable(values$TABdesc, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 50, dom = 'Bfrtip',ordering=F,
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Main_Information',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Main_Information',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Main_Information',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- #lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- #columnDefs = list(list(className = 'dt-center', targets = "_all"),
- # list(width = '50px', targets = 0)),
- columnDefs = list(list(className = 'dt-center', targets = "_all"),
- list(width = '350px', targets = 0))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$TABdesc)[1], backgroundColor = 'white',textAlign = 'left', fontSize = '110%') %>%
- formatStyle(names(values$TABdescb)[2], backgroundColor = 'white',textAlign = 'right', fontSize = '110%')
- })
-
-
- #box1 ---------------
- output$Timespan <- renderValueBox({
-
- #TAB <- res$TAB
- TAB <- ValueBoxes(values$M)
- values$TABvb <- TAB
- valueBox(value = p(TAB[TAB$Description=="Timespan", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong((TAB[TAB$Description=="Timespan", 2])), style = 'font-size:36px;color:white;', align="center"),
- icon = fa_i(name="hourglass"), color = "blue",
- width = NULL
- )
- })
- #box2 ---------------
- output$au <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Authors", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Authors", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="user"), color = "light-blue",
- width = NULL)
- })
-
-
- #box3 ------------
- output$kw <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Author's Keywords (DE)", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Author's Keywords (DE)", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="spell-check"), color = "aqua",
- width = NULL)
- })
- #box4 ---------------
- output$so <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p("Sources", style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Sources (Journals, Books, etc)", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name ="book"), color = "blue",
- width = NULL)
- })
-
- #box5 --------------------
- output$auS1 <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Authors of single-authored docs", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Authors of single-authored docs", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="pen-fancy"), color = "light-blue",
- width = NULL)
- })
-
- #box6 -------------
-
- output$cr <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="References", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="References", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="file"), color = "aqua",
- width = NULL)
- })
-
- #box7 ----------------
-
- output$doc <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Documents", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Documents", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="layer-group"), color = "blue",
- width = NULL)
- })
- #box8 ---------------
-
- output$col <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(strong("International Co-Authorship"), style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="International co-authorships %", 2]," %"), style = 'font-size:36px;color:white;',align="center"),
- icon = icon("globe",lib = "glyphicon"), color = "light-blue",
- width = NULL)
- })
-
-
- #box9 ---------------
- output$agePerDoc <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Document Average Age", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Document Average Age", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="calendar"), color = "aqua",
- width = NULL)
- })
- #box10 ------------------
- output$cagr <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(strong("Annual Growth Rate"), style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Annual Growth Rate %", 2]," %"), style = 'font-size:36px;color:white;',align="center"),
- icon = icon("arrow-up", lib="glyphicon"), color = "blue",
- width = NULL)
- })
-
- #box11 ------
- output$coAuPerDoc <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Co-Authors per Doc", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Co-Authors per Doc", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = fa_i(name="users"), color = "light-blue",
- width = NULL)
- })
-
- #box12 -------
- output$tc <- renderValueBox({
- TAB <- values$TABvb
- valueBox(value = p(TAB[TAB$Description=="Average citations per doc", 1], style = 'font-size:16px;color:white;'),
- subtitle = p(strong(TAB[TAB$Description=="Average citations per doc", 2]), style = 'font-size:36px;color:white;',align="center"),
- icon = icon("volume-up", lib = "glyphicon"), color = "aqua",
- width = NULL)
- })
-
-
- ## Annual Production ----
- output$CAGR <- renderText({
- # Y=table(values$M$PY)
- # ny=dim(Y)[1]
- # values$GR<-round(((Y[ny]/Y[1])^(1/(ny-1))-1)*100,2)
- paste0(values$GR," %")
- })
-
- output$AnnualProdPlot <- renderPlotly({
- res <- descriptive(values,type="tab2")
- values <-res$values
- Y <- values$TAB
-
- names(Y)=c("Year","Freq")
- x <- c(max(Y$Year)-0.02-diff(range(Y$Year))*0.125, max(Y$Year)-0.02)+1
- y <- c(min(Y$Freq),min(Y$Freq)+diff(range(Y$Freq))*0.125)
-
-
- g=ggplot2::ggplot(Y, aes(x = .data$Year, y = .data$Freq, text=paste("Year: ",.data$Year,"\nN .of Documents: ",.data$Freq))) +
- geom_line(aes(group="NA")) +
- geom_area(aes(group="NA"),fill = 'grey90', alpha = .5) +
- labs(x = 'Year'
- , y = 'Articles'
- , title = "Annual Scientific Production") +
- scale_x_continuous(breaks= (Y$Year[seq(1,length(Y$Year),by=2)])) +
- theme(text = element_text(color = "#444444")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 0)
- ,axis.title.x = element_text(hjust = 0)
- ,axis.text.x = element_text(vjust = 1, angle = 90)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) +
- annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
- values$ASPplot <- g
-
- #'#EFEFEF'
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.7, size=0.10)
- })#, height = 500, width =900)
-
- output$ASPplot.save <- downloadHandler(
- filename = function() {
-
- paste("AnnualScientificProduction-", Sys.Date(), ".png", sep="")
- },
-
- content <- function(file) {
- ggsave(filename = file, plot = values$ASPplot, dpi = as.numeric(input$ASPdpi), height = input$ASPh, width = input$ASPh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$AnnualProdTable <- DT::renderDT({
- TAB <- values$TAB
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Annual_Production',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Annual_Production',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Annual_Production',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
-
- ## Annual Citation per Year ----
- output$AnnualTotCitperYearPlot <- renderPlotly({
-
- if (values$results[[1]]=="NA"){
- values$results=biblioAnalysis(values$M)}
- x=values$results
-
- # Total Citation Plot
- Table2=aggregate(x$TotalCitation,by=list(x$Years),length)
- Table2$xx=aggregate(x$TotalCitation,by=list(x$Years),mean)$x
- Table2$Annual=NA
- d=date()
- d=as.numeric(substring(d,nchar(d)-3,nchar(d)))
- Table2$Years=d-Table2$Group.1
- Table2$Annual=Table2$xx/Table2$Years
- names(Table2)=c("Year","N","MeanTCperArt","MeanTCperYear","CitableYears")
-
- ## inserting missing years
- YY=setdiff(seq(min(x$Years,na.rm=TRUE),max(x$Years,na.rm=TRUE)),Table2$Year)
- if (length(YY>0)){
- YY=data.frame(YY,0,0,0,0)
- names(YY)=c("Year","N","MeanTCperArt","MeanTCperYear","CitableYears")
- Table2=rbind(Table2,YY)
- Table2=Table2[order(Table2$Year),]
- row.names(Table2)=Table2$Year}
-
- values$AnnualTotCitperYear=Table2
- Table2$group="A"
-
- x <- c(max(Table2$Year)-0.02-diff(range(Table2$Year))*0.125, max(Table2$Year)-0.02)+1
- y <- c(min(Table2$MeanTCperYear),min(Table2$MeanTCperYear)+diff(range(Table2$MeanTCperYear))*0.125)
-
- g <- ggplot(Table2, aes(x = .data$Year, y =.data$MeanTCperYear,text=paste("Year: ",.data$Year,"\nAverage Citations per Year: ",round(.data$MeanTCperYear,1)))) +
- geom_line(aes(x = .data$Year, y = .data$MeanTCperYear, group=.data$group)) +
- geom_area(aes(x = .data$Year, y = .data$MeanTCperYear, group=.data$group),fill = 'grey90', alpha = .5) +
- labs(x = 'Year'
- , y = 'Citations'
- , title = "Average Article Citations per Year")+
- scale_x_continuous(breaks= (Table2$Year[seq(1,length(Table2$Year),by=2)])) +
- theme(text = element_text(color = "#444444")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 0)
- ,axis.title.x = element_text(hjust = 0)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) +
- annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
- values$ACpYplot <- g
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.7, size=0.10)
- })
-
- output$ACpYplot.save <- downloadHandler(
- filename = function() {
-
- paste("AverageArticleCitationPerYear-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$ACpYplot, dpi = as.numeric(input$ACpYdpi), height = input$ACpYh, width = input$ACpYh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$AnnualTotCitperYearTable <- DT::renderDT({
-
- TAB <- values$AnnualTotCitperYear
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Annual_Total_Citation_per_Year',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Annual_Total_Citation_per_Year',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Annual_Total_Citation_per_Year',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[c(3:4)], digits=2)
-
- })
-
- ## Three Fields Plot ----
- TFP <- eventReactive(input$apply3F,{
- fields=c(input$LeftField, input$CentralField, input$RightField)
- threeFieldsPlot(values$M, fields=fields,n=c(input$LeftFieldn, input$CentralFieldn,input$RightFieldn))
- })
-
- output$ThreeFieldsPlot <- renderPlotly({
- TFP()
- })
-
- # SOURCES MENU ----
- ## Most Relevant Sources ----
- MRSources <- eventReactive(input$applyMRSources,{
- res <- descriptive(values,type="tab7")
- values <-res$values
- values$TABSo<-values$TAB
- #xx=as.data.frame(values$results$Sources)
- xx<- values$TAB
- if (input$MostRelSourcesK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelSourcesK}
- xx <- xx %>%
- slice_head(n=k)
- #xx=xx[1:k,]
- #xx=subset(xx, row.names(xx) %in% row.names(xx)[1:k])
- #xx$Articles=as.numeric(xx$Articles)
- xx$Sources=substr(xx$Sources,1,50)
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Sources", textLabx = "N. of Documents", title = "Most Relevant Sources")
-
- values$MRSplot <- g
- return(g)
- })
-
- output$MRSplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostRelevantSources-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MRSplot, dpi = as.numeric(input$MRSdpi), height = input$MRSh, width = input$MRSh*2, bg="white")
- },
- contentType = "png"
- )
-
-
- output$MostRelSourcesPlot <- renderPlotly({
- g <- MRSources()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.1, size=0.10)
- })#, height = 500, width =900)
-
-
- output$MostRelSourcesTable <- DT::renderDT({
-
- g <- MRSources()
-
- TAB <- values$TABSo
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Relevant_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Relevant_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Relevant_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
-
- ## Most Local Cited Sources ----
- MLCSources <- eventReactive(input$applyMLCSources,{
- values$M=metaTagExtraction(values$M,"CR_SO")
- TAB=tableTag(values$M,"CR_SO")
- TAB=data.frame(Sources=names(TAB),Articles=as.numeric(TAB),stringsAsFactors = FALSE)
- values$TABSoCit<-TAB
- #xx=as.data.frame(values$results$Sources)
- xx<- TAB
- if (input$MostRelCitSourcesK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelCitSourcesK}
- #xx=xx[1:k,]
- xx=subset(xx, row.names(xx) %in% row.names(xx)[1:k])
- xx$Articles=as.numeric(xx$Articles)
- xx$Sources=substr(xx$Sources,1,50)
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Cited Sources", textLabx = "N. of Local Citations", title = "Most Local Cited Sources")
-
- values$MLCSplot <- g
- return(g)
- })
-
- output$MLCSplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostLocalCitedSources-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MLCSplot, dpi = as.numeric(input$MLCSdpi), height = input$MLCSh, width = input$MLCSh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostRelCitSourcesPlot <- renderPlotly({
-
- g <- MLCSources()
-
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
- })#, height = 500, width =900)
-
- output$MostRelCitSourcesTable <- DT::renderDT({
-
- g <- MLCSources()
- TAB <- values$TABSoCit
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Cited_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Cited_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Cited_Sources',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
- ## Bradford's Law ----
- output$bradfordPlot <- renderPlotly({
-
- values$bradford=bradford(values$M)
- plot.ly(values$bradford$graph,flip=FALSE, side="r", aspectratio=1.6, size=0.15)
-
- })#,height = 600)
-
- output$BLplot.save <- downloadHandler(
- filename = function() {
-
- paste("BradfordLaws-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$bradford$graph, dpi = as.numeric(input$BLdpi), height = input$BLh, width = input$BLh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$bradfordTable <- DT::renderDT({
-
- DT::datatable(values$bradford$table, rownames = FALSE,
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Bradford_Law',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Bradford_Law',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Bradford_Law',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$bradford$table))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$bradford$table), backgroundColor = 'white',textAlign = 'center')
- })
- ## Sources' Impact ----
- Hsource <- eventReactive(input$applyHsource,{
- withProgress(message = 'Calculation in progress',
- value = 0, {
- res <- Hindex_plot(values,type="source")
- })
- values$SIplot <- res$g
- plot.ly(res$g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
- })
-
- output$SIplot.save <- downloadHandler(
- filename = function() {
-
- paste("SourceImpact-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$SIplot, dpi = as.numeric(input$SIdpi), height = input$SIh, width = input$SIh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$SourceHindexPlot <- renderPlotly({
- Hsource()
- })#, height = 500, width =900)
-
- output$SourceHindexTable <- DT::renderDT({
-
- DT::datatable(values$H, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Source_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Source_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Source_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$H))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$H), backgroundColor = 'white',textAlign = 'center') %>%
- formatRound(names(values$H)[4], digits=3)
-
- })
- ## Source Growth ----
- SOGrowth <- eventReactive(input$applySOGrowth,{
- #if (input$SOse=="Yes"){se=TRUE}else{se=FALSE}
-
- if (input$cumSO=="Cum"){
- cdf=TRUE
- laby="Cumulate occurrences"
- }else{
- cdf=FALSE
- laby="Annual occurrences"}
-
- values$PYSO=sourceGrowth(values$M,input$topSO[2], cdf=cdf)
- if (input$topSO[1]>1){
- values$PYSO <- values$PYSO[-c(2:(input$topSO[1]))]
- }
-
- term=names(values$PYSO)[-1]
-
- term=rep(term,each=dim(values$PYSO)[1])
- n=dim(values$PYSO)[1]*(dim(values$PYSO)[2]-1)
- freq=matrix(as.matrix(values$PYSO[,-1]),n,1)
- values$SODF=data.frame(Year=rep(values$PYSO$Year,(dim(values$PYSO)[2]-1)),Source=term, Freq=freq, stringsAsFactors = TRUE)
-
- Text <- paste(values$SODF$Source," (",values$SODF$Year,") ",values$SODF$Freq, sep="")
-
- width_scale <- 1.7 * 26 / length(unique(values$SODF$Source))
-
- x <- c(max(values$SODF$Year)-0.02-diff(range(values$SODF$Year))*0.15, max(values$SODF$Year)-0.02)+1
- y <- c(min(values$SODF$Freq),min(values$SODF$Freq)+diff(range(values$SODF$Freq))*0.15)
-
- g=ggplot(values$SODF, aes(x=values$SODF$Year,y=values$SODF$Freq, group=values$SODF$Source, color=values$SODF$Source, text=Text))+
- geom_line()+
- labs(x = 'Year'
- , y = laby
- , title = "Source Growth") +
- scale_x_continuous(breaks= (values$PYSO$Year[seq(1,length(values$PYSO$Year),by=ceiling(length(values$PYSO$Year)/20))])) +
- geom_hline(aes(yintercept=0), alpha=0.1)+
- labs(color = "Source")+
- #guides(fill = guide_legend(nrow = 5))+
- theme(text = element_text(color = "#444444"),
- legend.text=ggplot2::element_text(size=width_scale),
- legend.box.margin = margin(6, 6, 6, 6),
- legend.title=ggplot2::element_text(size=1.5*width_scale,face="bold"),
- legend.position="bottom",
- legend.direction = "vertical",
- legend.key.size = grid::unit(width_scale/50, "inch"),
- legend.key.width = grid::unit(width_scale/50, "inch")
- ,plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 90)
- ,axis.title.x = element_text(hjust = 0.95, angle = 0)
- ,axis.text.x = element_text(size=10, angle = 90)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) + annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
-
- values$SDplot <- g
- return(g)
- #suppressWarnings(plot(g))
- })
-
- output$SDplot.save <- downloadHandler(
- filename = function() {
-
- paste("SourceDynamics-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$SDplot, dpi = as.numeric(input$SDdpi), height = input$SDh, width = input$SDh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$soGrowthPlot <- renderPlotly({
-
- g <- SOGrowth()
-
- leg <- list(
- orientation = 'h',
- y = -0.15,
- font = list(
- family = "sans-serif",
- size = 10,
- color = "#000"),
- bgcolor = "#FFFFFF",
- bordercolor = "#FFFFFF",
- borderwidth = 2)
-
- plot.ly(g, flip=FALSE, side="r", aspectratio=1.8, size=0.10) %>%
- layout(legend = leg) %>%
- config(displaylogo = FALSE,
- modeBarButtonsToRemove = c(
- 'sendDataToCloud',
- 'pan2d',
- 'select2d',
- 'lasso2d',
- 'toggleSpikelines'
- )) %>%
- layout(hovermode = 'compare')
- #suppressWarnings(plot(g))
-
-
- #}, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 600, width = 900)
- })
-
- output$soGrowthtable <- DT::renderDT({
-
- g <- SOGrowth()
-
- soData=values$PYSO
-
- DT::datatable(soData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Source_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Source_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Source_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(soData))-1))))) %>%
- formatStyle(names(soData), backgroundColor = 'white')
- #return(Data)
- })
-
- # AUTHORS MENU ----
- ## Most Relevant Authors ----
- MRAuthors <- eventReactive(input$applyMRAuthors,{
- res <- descriptive(values,type="tab3")
- values <-res$values
- values$TABAu<-values$TAB
-
- #xx=as.data.frame(values$results$Authors, stringsAsFactors = FALSE)
- xx=values$TABAu
- switch(input$AuFreqMeasure,
- t={
- lab="N. of Documents"
- xx=xx[,1:2]
- },
- p={xx=xx[,1:2]
- xx[,2]=as.numeric(xx[,2])/dim(values$M)[1]*100
- lab="N. of Documents (in %)"
- },
- f={
- xx=xx[,c(1,3)]
- lab="N. of Documents (Fractionalized)"
- })
-
- xx[,2]=as.numeric(xx[,2])
-
- if (input$MostRelAuthorsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelAuthorsK}
-
- xx=xx[1:k,]
- xx[,2]=round(xx[,2],1)
-
- xx <- xx[order(-xx[,2]),]
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Authors", textLabx = lab, title = "Most Relevant Authors")
-
- values$MRAplot <- g
- return(g)
- })
-
- output$MRAplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostRelevantAuthors-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MRAplot, dpi = as.numeric(input$MRAdpi), height = input$MRAh, width = input$MRAh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostRelAuthorsPlot <- renderPlotly({
-
- g <- MRAuthors()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
- })#, height = 500, width =900)
-
- output$MostRelAuthorsTable <- DT::renderDT({
-
- TAB <- values$TABAu
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Local_Cited_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Local_Cited_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Relevant_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[3], digits=2)
-
- })
- ## Most Cited Authors ----
- MLCAuthors <- eventReactive(input$applyMLCAuthors,{
- res <- descriptive(values,type="tab13")
- values <-res$values
- values$TABAuCit<-values$TAB
-
- #xx=as.data.frame(values$results$Authors, stringsAsFactors = FALSE)
- xx <- values$TABAuCit
- lab <- "Local Citations"
- xx[,2]=as.numeric(xx[,2])
-
- if (input$MostCitAuthorsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostCitAuthorsK}
-
- xx=xx[1:k,]
- xx[,2]=round(xx[,2],1)
-
- xx <- xx[order(-xx[,2]),]
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Authors", textLabx = lab, title = "Most Local Cited Authors")
-
- values$MLCAplot <- g
- return(g)
- })
-
- output$MLCAplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostLocalCitedAuthors-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MLCAplot, dpi = as.numeric(input$MLCAdpi), height = input$MLCAh, width = input$MLCAh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostCitAuthorsPlot <- renderPlotly({
-
- g <- MLCAuthors()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
- })#, height = 500, width =900)
-
- output$MostCitAuthorsTable <- DT::renderDT({
-
- TAB <- values$TABAuCit
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Local_Cited_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Local_Cited_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Relevant_Authors',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
- ## Authors' Impact ----
- HAuthors <- eventReactive(input$applyHAuthors,{
- withProgress(message = 'Calculation in progress',
- value = 0, {
- res <- Hindex_plot(values,type="author")
- })
- values$AIplot <- res$g
- return(res)
- })
-
- output$AIplot.save <- downloadHandler(
- filename = function() {
-
- paste("AuthorImpact-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$AIplot, dpi = as.numeric(input$AIdpi), height = input$AIh, width = input$AIh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$AuthorHindexPlot <- renderPlotly({
-
- res <- HAuthors()
- plot.ly(res$g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
-
- })#, height = 500, width =900)
-
- output$AuthorHindexTable <- DT::renderDT({
-
- DT::datatable(values$H, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Author_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Author_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Author_Impact',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$H))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$H), backgroundColor = 'white',textAlign = 'center') %>%
- formatRound(names(values$H)[4], 3)
-
- })
- ## Authors Production Over Time ----
- AUoverTime <- eventReactive(input$applyAUoverTime,{
- values$AUProdOverTime <- authorProdOverTime(values$M, k=input$TopAuthorsProdK, graph=FALSE)
- })
-
- output$APOTplot.save <- downloadHandler(
- filename = function() {
-
- paste("AuthorsProductionOverTime-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$AUProdOverTime$graph, dpi = as.numeric(input$APOTdpi), height = input$APOTh, width = input$APOTh*2.5, bg="white")
- },
- contentType = "png"
- )
-
- output$TopAuthorsProdPlot <- renderPlotly({
- AUoverTime()
-
- plot.ly(values$AUProdOverTime$graph, flip=TRUE, side="l", aspectratio=1)
-
-
- })#, height = 550, width =1100)
-
- output$TopAuthorsProdTable <- DT::renderDT({
- AUoverTime()
-
- TAB <- values$AUProdOverTime$dfAU
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Author_Production_Over_Time',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Author_Production_Over_Time',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Author_Production_Over_Time',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[dim(TAB)[2]], 3)
-
- })
-
- output$TopAuthorsProdTablePapers <- DT::renderDT({
- AUoverTime()
- TAB <- values$AUProdOverTime$dfPapersAU
- TAB$DOI=paste0('',TAB$DOI,'')
- DT::datatable(TAB, rownames = FALSE, escape = FALSE,extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Author_Production_Over_Time_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Author_Production_Over_Time_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Author_Production_Over_Time_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[dim(TAB)[2]], 3)
-
- })
- ## Lotka Law ----
- output$lotkaPlot <- renderPlotly({
-
- values$lotka=lotka(biblioAnalysis(values$M))
- AuProd=values$lotka$AuthorProd
- AuProd$Theoretical=10^(log10(values$lotka$C)-2*log10(AuProd[,1]))
- AuProd$Theoretical=AuProd$Theoretical/sum(AuProd$Theoretical)
-
- x <- c(max(AuProd$N.Articles)-0.02-diff(range(AuProd$N.Articles))*0.125, max(AuProd$N.Articles)-0.02)+1
- y <- c(min(AuProd$Freq*100),min(AuProd$Freq*100)+diff(range(AuProd$Freq*100))*0.125)
-
- g=ggplot2::ggplot(AuProd, aes(x = .data$N.Articles, y = .data$Freq*100, text=paste("N.Articles: ",.data$N.Articles,"\n% of production: ",round(.data$Freq*100,1)))) +
- geom_line(aes(group="NA")) +
- geom_area(aes(group="NA"),fill = 'grey90', alpha = .5) +
- geom_line(data=AuProd, aes(y=.data$Theoretical*100, group="NA"),linetype = "dashed",color="black",alpha=0.8)+
- xlim(0,max(AuProd$N.Articles)+1)+
- labs(x = 'Documents written'
- , y = '% of Authors'
- , title = "The Frequency Distribution of Scientific Productivity") +
- #scale_x_continuous(breaks= (Y$Year[seq(1,length(Y$Year),by=2)])) +
- theme(text = element_text(color = "#444444")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 0)
- ,axis.title.x = element_text(hjust = 0)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) +
- annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
- values$LLplot <- g
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.4, size=0.10)
-
- })#,height = 600)
-
- output$LLplot.save <- downloadHandler(
- filename = function() {
-
- paste("LotkaLaw-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$LLplot, dpi = as.numeric(input$LLdpi), height = input$LLh, width = input$LLh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$lotkaTable <- DT::renderDT({
- names(values$lotka$AuthorProd)=c("Documents written","N. of Authors","Proportion of Authors")
- DT::datatable(values$lotka$AuthorProd, rownames = FALSE,
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Lotka_Law',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Lotka_Law',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Lotka_Law',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$lotka$AuthorProd))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$lotka$AuthorProd), backgroundColor = 'white',textAlign = 'center') %>%
- formatRound(names(values$lotka$AuthorProd)[3], 3)
- })
-
-
- # Affiliations ----
- ## Most Relevant Affliations ----
- MRAffiliations <- eventReactive(input$applyMRAffiliations,{
- if (input$disAff=="Y"){
- res <- descriptive(values,type="tab11")
- }else{
- res <- descriptive(values,type="tab12")
- }
- xx=values$TAB
- names(xx)=c("AFF","Freq")
- values <-res$values
- values$TABAff <- values$TAB
-
-
- if (input$MostRelAffiliationsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelAffiliationsK}
-
- xx=xx[1:k,]
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Affiliations", textLabx = "Articles", title = "Most Relevant Affiliations")
-
- values$AFFplot <- g
- return(g)
- })
-
- output$AFFplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostRelevantAffiliations-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$AFFplot, dpi = as.numeric(input$AFFdpi), height = input$AFFh, width = input$AFFh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostRelAffiliationsPlot <- renderPlotly({
-
- g <- MRAffiliations()
-
- plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.15)
- })#, height = 500, width =900)
-
- output$MostRelAffiliationsTable <- DT::renderDT({
- g <- MRAffiliations()
-
- TAB <- values$TABAff
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Relevant_Affiliations',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Relevant_Affiliations',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Relevant_Affiliations',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
-
-
- # Countries ----
- ## Country by Corresponding Authors ----
- CAUCountries <- eventReactive(input$applyCAUCountries,{
- res <- descriptive(values,type="tab5")
- values <-res$values
- values$TABCo <- values$TAB
-
- k=input$MostRelCountriesK
- xx <- values$TABCo %>% slice_head(n=k) %>%
- select(.data$Country,.data$SCP,.data$MCP)
- xx=xx[order(-(xx$SCP+xx$MCP)),]
- xx1=cbind(xx[,1:2],rep("SCP",k))
- names(xx1)=c("Country","Freq","Collaboration")
- xx2=cbind(xx[,c(1,3)],rep("MCP",k))
- names(xx2)=c("Country","Freq","Collaboration")
- xx=rbind(xx2,xx1)
- xx$Country=factor(xx$Country,levels=xx$Country[1:dim(xx2)[1]])
-
- xx2 <- xx %>% dplyr::group_by(.data$Country) %>%
- dplyr::summarize(Freq = sum(.data$Freq))
-
- #x <- c(length(levels(xx2$Country))*(1-0.125)-0.02, length(levels(xx2$Country))-0.02)
- x <- c(0.5,0.5+length(levels(xx2$Country))*0.125)+1
- y <- c(max(xx2$Freq)-0.02-diff(range(xx2$Freq))*0.125,max(xx2$Freq)-0.02)
-
- g=suppressWarnings(ggplot2::ggplot(data=xx, aes(x=.data$Country, y=.data$Freq,fill=.data$Collaboration, text=paste("Country: ",.data$Country,"\nN.of Documents: ",.data$Freq))) +
- geom_bar(aes(group="NA"),stat="identity")+
- scale_x_discrete(limits = rev(levels(xx$Country)))+
- scale_fill_discrete(name="Collaboration",
- breaks=c("SCP","MCP"))+
- labs(title = "Corresponding Author's Country", x = "Countries", y = "N. of Documents",
- caption = "SCP: Single Country Publications, MCP: Multiple Country Publications")+
- #theme_minimal()
- theme(plot.caption = element_text(size = 9, hjust = 0.5,
- color = "blue", face = "italic")
- ,panel.background = element_rect(fill = '#FFFFFF')
- #,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major.y = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 0)
- ,axis.title.x = element_text(hjust = 0)
- ,axis.line.x = element_line(color="black",size=0.5)
- #,axis.line.y = element_line(color="black",size=0.5)
- )+
- coord_flip()) +
- annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
-
- values$MRCOplot <- g
- return(g)
- })
-
- output$MRCOplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostRelevantCountries-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MRCOplot, dpi = as.numeric(input$MRCOdpi), height = input$MRCOh, width = input$MRCOh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostRelCountriesPlot <- renderPlotly({
-
- g <- CAUCountries()
-
- plot.ly(g,flip=T, side="r", aspectratio=1.4, size=0.10, data.type=1)
-
- })#, height = 500, width =900)
-
- output$MostRelCountriesTable <- DT::renderDT({
- g <- CAUCountries()
-
- TAB <- values$TABCo
- # TAB=format(TAB,justify="left",digits=3)
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Relevant_Countries_By_Corresponding_Author',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Relevant_Countries_By_Corresponding_Author',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Relevant_Countries_By_Corresponding_Author',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[5], digits=3) %>%
- formatRound(names(TAB)[6], digits=3)
-
- })
-
- ## Country Production ----
- output$countryProdPlot <- renderPlotly({
- values$mapworld<-mapworld(values$M)
- plot.ly(values$mapworld$g,flip=FALSE, side="r", aspectratio=1.7, size=0.07, data.type=1,height=15)
- })#, height = 500, width =900)
-
- output$CSPplot.save <- downloadHandler(
- filename = function() {
-
- paste("CountryScientificProduction-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$mapworld$g, dpi = as.numeric(input$CSPdpi), height = input$CSPh, width = input$CSPh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$countryProdTable <- DT::renderDT({
-
- TAB <- values$mapworld$tab
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Country_Production',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Country_Production',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Country_Production',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
- ## Most Cited Country ----
- MCCountries <- eventReactive(input$applyMCCountries,{
- res <- descriptive(values,type="tab6")
- values <-res$values
- values$TABCitCo <- values$TAB
-
- xx=values$TAB
- xx[,2]=as.numeric(xx[,2])
- xx[,3]=as.numeric(xx[,3])
- if (input$MostCitCountriesK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelAffiliationsK}
- if (input$CitCountriesMeasure=="TC"){
- xx=xx[1:k,c(1,2)]
- laby="N. of Citations"
- } else {
- xx=xx[order(-xx[,3]),]
- xx=xx[1:k,c(1,3)]
- laby="N. of Citations per Year"
- }
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Countries", textLabx = laby, title = "Most Cited Countries")
-
- values$MCCplot <- g
- return(g)
- })
-
- output$MCCplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostCitedCountries-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MCCplot, dpi = as.numeric(input$MCCdpi), height = input$MCCh, width = input$MCCh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostCitCountriesPlot <- renderPlotly({
- g <- MCCountries()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
- })#, height = 500, width =900)
-
- output$MostCitCountriesTable <- DT::renderDT({
- g <- MCCountries()
- TAB <- values$TABCitCo
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Cited_Countries',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Cited_Countries',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Cited_Countries',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[3], 2)
-
- })
-
-
- # DOCUMENTS MENU ----
- ## Most Global Cited Documents ----
-
- MGCDocuments <- eventReactive(input$applyMGCDocuments,{
- res <- descriptive(values,type="tab4")
- values <-res$values
- values$TABGlobDoc <- values$TAB
-
- if (input$CitDocsMeasure=="TC"){
- xx <- values$TABGlobDoc %>% select(1,3)
- lab="Global Citations"} else {
- xx <- values$TABGlobDoc %>% select(1,4)
- lab="Global Citations per Year"
- }
-
- if (input$MostCitDocsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostCitDocsK}
-
- xx=xx[1:k,]
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "Documents", textLabx = lab, title = "Most Global Cited Documents")
-
- values$MGCDplot <- g
- return(g)
- })
-
- output$MGCDplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostGlobalCitedDocuments-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MGCDplot, dpi = as.numeric(input$MGCDdpi), height = input$MGCDh, width = input$MGCDh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostCitDocsPlot <- renderPlotly({
-
- g <- MGCDocuments()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.10)
- })#, height = 500, width =900)
-
- output$MostCitDocsTable <- DT::renderDT({
- g <- MGCDocuments()
- TAB <- values$TABGlobDoc
- TAB$DOI<- paste0('',TAB$DOI,'')
- DT::datatable(TAB, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Global_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Global_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Global_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[4], 2) %>%
- formatRound(names(TAB)[5], 2)
-
- })
- ## Most Local Cited Documents ----
- MLCDocuments <- eventReactive(input$applyMLCDocuments,{
- withProgress(message = 'Calculation in progress',
- value = 0, {
- TAB <-localCitations(values$M, fast.search=FALSE, sep = input$LocCitSep)$Paper
- TAB <- TAB %>%
- group_by(.data$Year) %>%
- mutate(Ratio = .data$LCS/.data$GCS*100,
- NLCS = .data$LCS/mean(.data$LCS),
- NGCS = .data$GCS/mean(.data$GCS)) %>%
- ungroup() %>%
- as.data.frame()
-
- })
-
- xx=data.frame(Document=as.character(TAB[,1]), DOI=as.character(TAB[,2]), Year=TAB[,3],
- "Local Citations"=TAB[,4], "Global Citations"=TAB[,5],"LC/GC Ratio"=TAB[6],
- "Normalized Local Citations"=TAB[,7],"Normalized Global Citations"=TAB[,8], stringsAsFactors = FALSE)
- values$TABLocDoc=xx
-
- if (input$MostLocCitDocsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostLocCitDocsK}
-
- xx=xx[1:k,]
-
- g <- freqPlot(xx,x=4,y=1, textLaby = "Documents", textLabx = "Local Citations", title = "Most Local Cited Documents")
-
- values$MLCDplot <- g
- return(g)
- })
-
- output$MLCDplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostLocalCitedDocuments-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MLCDplot, dpi = as.numeric(input$MLCDdpi), height = input$MLCDh, width = input$MLCDh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostLocCitDocsPlot <- renderPlotly({
-
- g <- MLCDocuments()
- plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.10)
- })#, height = 500, width =900)
-
- output$MostLocCitDocsTable <- DT::renderDT({
-
- TAB <- values$TABLocDoc
- TAB$DOI <- paste0('',TAB$DOI,'')
-
- names(TAB)[4:8] <- c("Local Citations", "Global Citations","LC/GC Ratio (%)", "Normalized Local Citations","Normalized Global Citations")
- DT::datatable(TAB, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Local_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Local_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Local_Cited_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
- formatRound(names(TAB)[c(6:8)], digits=2)
-
- })
-
- ## Most Local Cited References ----
- MLCReferences <- eventReactive(input$applyMLCReferences,{
- CR=citations(values$M,sep=input$CitRefsSep)$Cited
- TAB=data.frame(names(CR),as.numeric(CR),stringsAsFactors = FALSE)
- names(TAB)=c("Cited References", "Citations")
- values$TABCitRef=TAB
-
- xx=values$TABCitRef
- if (input$MostCitRefsK>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostCitRefsK}
-
- xx=xx[1:k,]
- #xx[,1]=substr(xx[,1],1,50)
-
- g <- freqPlot(xx,x=2,y=1, textLaby = "References", textLabx = "Local Citations", title = "Most Local Cited References")
-
- values$MLCRplot <- g
- return(g)
- })
-
- output$MLCRplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostLocalCitedReferences-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MLCRplot, dpi = as.numeric(input$MLCRdpi), height = input$MLCRh, width = input$MLCRh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostCitRefsPlot <- renderPlotly({
-
- g <- MLCReferences()
- plot.ly(g,flip=FALSE, side="r", aspectratio=0.6, size=0.20)
- })#, height = 500, width =900)
-
- output$MostCitRefsTable <- DT::renderDT({
- g <- MLCReferences()
- TAB <- values$TABCitRef
-
- TAB$link <- trimES(gsub("[[:punct:]]" , " ",reduceRefs(TAB[,1])))
-
-
- TAB$link <- paste0('','link','')
-
- TAB=TAB[,c(3,1,2)]
- names(TAB)[1]="Google Scholar"
- DT::datatable(TAB, rownames = FALSE, escape=FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Local_Cited_References',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Local_Cited_References',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Local_Cited_References',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
- ## Reference Spectroscopy ----
- RPYS <- eventReactive(input$applyRPYS,{
-
- timespan <- c(-Inf,Inf)
- if (!is.na(input$rpysMinYear)){
- timespan[1] <- input$rpysMinYear
- }
- if (!is.na(input$rpysMaxYear)){
- timespan[2] <- input$rpysMaxYear
- }
- values$res <- rpys(values$M, sep=input$rpysSep, timespan=timespan, graph=FALSE)
- })
-
- output$RSplot.save <- downloadHandler(
- filename = function() {
-
- paste("ReferenceSpectroscopy-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$res$spectroscopy, dpi = as.numeric(input$RSdpi), height = input$RSh, width = input$RSh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$rpysPlot <- renderPlotly({
-
- RPYS()
- plot.ly(values$res$spectroscopy, side="l", aspectratio = 1.3, size=0.10)
-
- })#,height = 600, width = 900)
-
- output$rpysTable <- DT::renderDT({
- RPYS()
- rpysData=values$res$rpysTable
-
- DT::datatable(rpysData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'RPYS',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'RPYS',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'RPYS',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(rpysData))-1))))) %>%
- formatStyle(names(rpysData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$crTable <- DT::renderDT({
- RPYS()
- crData=values$res$CR
- crData$link <- paste0('','link','')
-
- crData=crData[order(-as.numeric(crData$Year),-crData$Freq),]
- names(crData)=c("Year", "Reference", "Local Citations", "Google link")
- crData <- crData[,c(1,4,2,3)]
- DT::datatable(crData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'RPYS_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'RPYS_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'RPYS_Documents',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(crData))-1))))) %>%
- formatStyle(names(crData), backgroundColor = 'white')
- #return(Data)
-
- })
-
-
- # Words ----
- ## Most Frequent Words ----
- MFWords <- eventReactive(input$applyMFWords,{
- if (input$MostRelWords %in% c("TI","AB")){
- ngrams <- as.numeric(input$MRWngrams)
- }else{
- ngrams <- 1
- }
-
- ### load file with terms to remove
- if (input$MostRelWordsStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$MostRelWordsStop, sep=input$MostRelWordsSep))
- }else{remove.terms <- NULL}
- values$MRWremove.terms <- remove.terms
- ### end of block
-
- ### load file with synonyms
- if (input$MRWSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$MRWSyn, sep=input$MRWSynSep))
- }else{synonyms <- NULL}
- values$MRWsyn.terms <- synonyms
- ### end of block
-
- WR=wordlist(values$M,Field=input$MostRelWords,n=Inf,measure="identity", ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)$v
-
- TAB=data.frame(names(WR),as.numeric(WR),stringsAsFactors = FALSE)
- names(TAB)=c("Words", "Occurrences")
- values$TABWord=TAB
-
- xx=values$TABWord
- if (input$MostRelWordsN>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=input$MostRelWordsN}
-
- xx=xx[1:k,]
- switch(input$MostRelWords,
- ID={lab="Keywords Plus"},
- DE={lab="Author's Keywords"},
- TI={lab="Title's Words"},
- AB={lab="Abstract's Words"})
-
- g <- freqPlot(xx,x=2,y=1, textLaby = lab, textLabx = "Occurrences", title = "Most Relevant Words")
-
- values$MRWplot <- g
- return(g)
-
- })
-
- output$MostRelWordsStopPreview <- renderUI({
-
- if (!is.null(values$MRWremove.terms) | exists("values$MRWremove.terms")){
- strPreview(values$MRWremove.terms, input$MostRelWordsSep)
- }else{
- strPreview(" ", input$MostRelWordsSep)
- }
- })
-
- output$MRWSynPreview <- renderUI({
-
- if (!is.null(values$MRWsyn.terms) | exists("values$MRWsyn.terms")){
- strSynPreview(values$MRWsyn.terms)
- }else{
- strSynPreview(" ; ")
- }
- })
-
- output$MRWplot.save <- downloadHandler(
- filename = function() {
-
- paste("MostRelevantWords-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$MRWplot, dpi = as.numeric(input$MRWdpi), height = input$MRWh, width = input$MRWh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$MostRelWordsPlot <- renderPlotly({
- g <- MFWords()
- plot.ly(g, side="r", aspectratio = 1.3, size=0.10)
- })#, height = 500, width =900)
-
- output$MostRelWordsTable <- DT::renderDT({
- g <- MFWords()
-
- TAB <- values$TABWord
-
- DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
-
- })
- ## WordCloud ----
- WordCloud <- eventReactive(input$applyWordCloud,{
-
- if (input$summaryTerms %in% c("TI","AB")){
- ngrams <- as.numeric(input$summaryTermsngrams)
- }else{
- ngrams <- 1
- }
-
- ### load file with terms to remove
- if (input$WCStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$WCStop, sep=input$WCSep))
- }else{remove.terms <- NULL}
- values$WCremove.terms <- remove.terms
- ### end of block
-
- ### load file with synonyms
- if (input$WCSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$WCSyn, sep=input$WCSynSep))
- }else{synonyms <- NULL}
- values$WCsyn.terms <- synonyms
- ### end of block
- print(values$WCsyn.terms )
-
- resW=wordlist(M=values$M, Field=input$summaryTerms, n=input$n_words, measure=input$measure, ngrams=ngrams, remove.terms = remove.terms, synonyms = values$WCsyn.terms)
-
- W=resW$W
- values$Words=resW$Words
-
- wordcloud2::wordcloud2(W, size = input$scale, minSize = 0, gridSize = input$padding,
- fontFamily = input$font, fontWeight = 'normal',
- color = input$wcCol, backgroundColor = "white", #input$wcBGCol,
- minRotation = 0, maxRotation = input$rotate/10, shuffle = TRUE,
- rotateRatio = 0.7, shape = input$wcShape, ellipticity = input$ellipticity,
- widgetsize = NULL, figPath = NULL, hoverFunction = NULL)
- })
- output$wordcloud <- wordcloud2::renderWordcloud2({
-
- WordCloud()
- })
-
- ## TreeMap ----
- TreeMap <- eventReactive(input$applyTreeMap,{
- if (input$treeTerms %in% c("TI","AB")){
- ngrams <- as.numeric(input$treeTermsngrams)
- }else{
- ngrams <- 1
- }
- ### load file with terms to remove
- if (input$TreeMapStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$TreeMapStop, sep=input$TreeMapSep))
- }else{remove.terms <- NULL}
- values$TreeMapremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$TreeMapSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$TreeMapSyn, sep=input$TreeMapSynSep))
- }else{synonyms <- NULL}
- values$TreeMapsyn.terms <- synonyms
- ### end of block
-
- resW=wordlist(M=values$M, Field=input$treeTerms, n=input$treen_words, measure="identity", ngrams=ngrams, remove.terms=remove.terms, synonyms = synonyms)
-
- W=resW$W
- values$TreeMap <- plot_ly(
- type='treemap',
- labels=W[,1],
- parents="Tree",
- values= W[,2],
- textinfo="label+value+percent entry",
- domain=list(column=0))
-
- values$WordsT=resW$Words
- return(resW$Words)
-
- })
-
- output$treemap <- renderPlotly({
- TreeMap()
- values$TreeMap
- })
-
- output$TreeMapStopPreview <- renderUI({
-
- if (!is.null(values$TreeMapremove.terms) | exists("values$TreeMapremove.terms")){
- strPreview(values$TreeMapremove.terms, input$TreeMapSep)
- }else{
- strPreview(" ", input$TreeMapSep)
- }
- })
-
- output$TreeMapSynPreview <- renderUI({
-
- if (!is.null(values$TreeMapsyn.terms) | exists("values$TreeMapsyn.terms")){
- strSynPreview(values$TreeMapsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
-
- output$wordTable <- DT::renderDT({
- WordCloud()
-
- DT::datatable(values$Words, rownames = FALSE,
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$Words))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$Words), backgroundColor = 'white',textAlign = 'center')
- })
-
- output$treeTable <- DT::renderDT({
- WordsT <- TreeMap()
-
- DT::datatable(values$WordsT, rownames = FALSE,
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Most_Frequent_Words',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$WordsT))-1)))),
- class = 'cell-border compact stripe') %>%
- formatStyle(names(values$WordsT), backgroundColor = 'white',textAlign = 'center')
-
- },height = 600, width = 900)
- ## Word Dynamics ----
- WDynamics <- eventReactive(input$applyWD,{
- if (input$cumTerms=="Cum"){
- cdf=TRUE
- laby="Cumulate occurrences"
- }else{
- cdf=FALSE
- laby="Annual occurrences"}
- #if (input$se=="Yes"){se=TRUE}else{se=FALSE}
-
- ### load file with terms to remove
- if (input$WDStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$WDStop, sep=input$WDSep))
- }else{remove.terms <- NULL}
- values$WDremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$WDSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$WDSyn, sep=input$WDSynSep))
- }else{synonyms <- NULL}
- values$WDsyn.terms <- synonyms
- ### end of block
-
- switch(input$growthTerms,
- ID={
- KW=KeywordGrowth(values$M, Tag = "ID", sep = ";", top = input$topkw[2], cdf = cdf, remove.terms=remove.terms, synonyms = synonyms)
-
- },
- DE={
- KW=KeywordGrowth(values$M, Tag = "DE", sep = ";", top = input$topkw[2], cdf = cdf, remove.terms=remove.terms, synonyms = synonyms)
- },
- TI={
- #if (!("TI_TM" %in% names(values$M))){
- values$M=termExtraction(values$M,Field = "TI", verbose=FALSE, ngrams=as.numeric(input$growthTermsngrams), remove.terms=remove.terms, synonyms = synonyms)
- #}
- KW=KeywordGrowth(values$M, Tag = "TI_TM", sep = ";", top = input$topkw[2], cdf = cdf)
- },
- AB={
- #if (!("AB_TM" %in% names(values$M))){
- values$M=termExtraction(values$M,Field = "AB", verbose=FALSE, ngrams=as.numeric(input$growthTermsngrams), remove.terms=remove.terms, synonyms = synonyms)
- #}
- KW=KeywordGrowth(values$M, Tag = "AB_TM", sep = ";", top = input$topkw[2], cdf = cdf)
- }
- )
-
- values$KW=KW[,c(1,seq(input$topkw[1],input$topkw[2])+1)]
-
- term=names(values$KW)[-1]
- term=rep(term,each=dim(values$KW)[1])
- n=dim(values$KW)[1]*(dim(values$KW)[2]-1)
- freq=matrix(as.matrix(values$KW[,-1]),n,1)
- values$DF=data.frame(Year=rep(values$KW$Year,(dim(values$KW)[2]-1)),Term=term, Freq=freq, stringsAsFactors = TRUE)
-
- width_scale <- 2.5 * 26 / length(unique(values$DF$Term))
-
- Text <- paste(values$DF$Term," (",values$DF$Year,") ",values$DF$Freq, sep="")
-
- x <- c(max(values$DF$Year)-0.02-diff(range(values$SO$Year))*0.20, max(values$DF$Year)-0.02)-1
- y <- c(min(values$DF$Freq),min(values$DF$Freq)+diff(range(values$DF$Freq))*0.20)
-
- g <- ggplot(values$DF, aes(x=.data$Year,y=.data$Freq, group=.data$Term, color=.data$Term, text = Text))+
- geom_line()+
- labs(x = 'Year'
- , y = laby
- , title = "Word Growth") +
- #ylim(0, NA) +
- scale_x_continuous(breaks= (values$KW$Year[seq(1,length(values$KW$Year),by=ceiling(length(values$KW$Year)/20))])) +
- geom_hline(aes(yintercept=0), alpha=0.1)+
- labs(color = "Term")+
- #guides(fill = guide_legend(nrow = 5))+
- theme(text = element_text(color = "#444444"),
- legend.text=ggplot2::element_text(size=width_scale),
- legend.box.margin = margin(6, 6, 6, 6),
- legend.title=ggplot2::element_text(size=1.5*width_scale,face="bold"),
- legend.position="bottom",
- legend.direction = "vertical",
- legend.key.size = grid::unit(width_scale/50, "inch"),
- legend.key.width = grid::unit(width_scale/50, "inch")
- ,plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 90)
- ,axis.title.x = element_text(hjust = 0.95, angle = 0)
- ,axis.text.x = element_text(size=10, angle = 90)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) +
- annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
-
- values$WDplot <- g
- return(g)
- })
-
- output$WDStopPreview <- renderUI({
-
- if (!is.null(values$WDremove.terms) | exists("values$WDremove.terms")){
- strPreview(values$WDremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$WDSynPreview <- renderUI({
-
- if (!is.null(values$WDsyn.terms) | exists("values$WDsyn.terms")){
- strSynPreview(values$WDsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- output$WDplot.save <- downloadHandler(
- filename = function() {
-
- paste("WordDynamics-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$WDplot, dpi = as.numeric(input$WDdpi), height = input$WDh, width = input$WDh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$kwGrowthPlot <- renderPlotly({
-
- g <- WDynamics()
-
- leg <- list(
- orientation = 'h',
- y = -0.15,
- font = list(
- family = "sans-serif",
- size = 10,
- color = "#000"),
- bgcolor = "#FFFFFF",
- bordercolor = "#FFFFFF",
- borderwidth = 2)
-
- plot.ly(g, flip=FALSE, side="r", aspectratio=1.6, size=0.10) %>%
- layout(legend = leg) %>%
- config(displaylogo = FALSE,
- modeBarButtonsToRemove = c(
- 'sendDataToCloud',
- 'pan2d',
- 'select2d',
- 'lasso2d',
- 'toggleSpikelines'
- )) %>%
- layout(hovermode = 'compare')
-
- #}, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 600, width = 900)
- })
-
- output$kwGrowthtable <- DT::renderDT({
- g <- WDynamics()
- kwData=values$KW
-
- DT::datatable(kwData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Word_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Word_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Word_Dynamics',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(kwData))-1))))) %>%
- formatStyle(names(kwData), backgroundColor = 'white')
- #return(Data)
- })
-
- ## Trend Topics ----
- output$trendSliderPY <- renderUI({
-
- sliderInput("trendSliderPY", "Timespan", min = min(values$M$PY,na.rm=T),sep="",
- max = max(values$M$PY,na.rm=T), value = c(min(values$M$PY,na.rm=T),max(values$M$PY,na.rm=T)))
- })
-
- TrendTopics <- eventReactive(input$applyTrendTopics,{
-
- ### load file with terms to remove
- if (input$TTStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$TTStop, sep=input$TTSep))
- }else{remove.terms <- NULL}
- values$TTremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$TTSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$TTSyn, sep=input$TTSynSep))
- }else{synonyms <- NULL}
- values$TTsyn.terms <- synonyms
- ### end of block
-
- if (input$trendTerms %in% c("TI","AB")){
- values$M=termExtraction(values$M, Field = input$trendTerms, stemming = input$trendStemming, verbose = FALSE, ngrams=as.numeric(input$trendTermsngrams))
- field=paste(input$trendTerms,"_TM",sep="")
- } else {field=input$trendTerms}
- values$trendTopics <- fieldByYear(values$M, field = field, timespan = input$trendSliderPY, min.freq = input$trendMinFreq,
- n.items = input$trendNItems, remove.terms = remove.terms, synonyms = synonyms,
- dynamic.plot=TRUE, graph = FALSE)
- return(values$trendTopics$graph)
-
- })
-
- output$TTStopPreview <- renderUI({
-
- if (!is.null(values$TTremove.terms) | exists("values$TTremove.terms")){
- strPreview(values$TTremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$TTSynPreview <- renderUI({
-
- if (!is.null(values$TTsyn.terms) | exists("values$TTsyn.terms")){
- strSynPreview(values$TTsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- output$TTplot.save <- downloadHandler(
- filename = function() {
-
- paste("TrendTopics-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$trendTopics$graph, dpi = as.numeric(input$TTdpi), height = input$TTh, width = input$TTh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$trendTopicsPlot <- renderPlotly({
- g <- TrendTopics()
- plot.ly(g, flip=TRUE, side="r", size=0.1, aspectratio=1.3)
- })#, height = 500, width =900)
-
- # output$trendTopicsPlot <- renderPlot({
- #
- # TrendTopics()
- # plot(values$trendTopics$graph)
- #
- # }, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 700)
-
-
- output$trendTopicsTable <- DT::renderDT({
- TrendTopics()
- tpData=values$trendTopics$df_graph
-
- DT::datatable(tpData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Trend_Topics',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Trend_Topics',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Trend_Topics',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tpData))-1))))) %>%
- formatStyle(names(tpData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- # Coupling ----
-
- CMMAP <- eventReactive(input$applyCM,{
-
- values$CM <- couplingMap(values$M, analysis=input$CManalysis, field=input$CMfield,
- n=input$CMn, minfreq=input$CMfreq,
- ngrams=as.numeric(input$CMngrams),
- impact.measure=input$CMimpact,
- stemming=input$CMstemming, size=input$sizeCM,
- label.term = input$CMlabeling,
- n.labels=input$CMn.labels, repel=FALSE)
-
- validate(
- need(values$CM$nclust > 0, "\n\nNo clusters in one or more periods. Please select a different set of parameters.")
- )
- })
- output$CMPlot <- renderPlotly({
-
- CMMAP()
- plot.ly(values$CM$map, size=0.15, aspectratio = 1.3)
-
- })#, height = 650, width = 800)
-
- output$CMNetPlot <- renderVisNetwork({
- CMMAP()
- values$networkCM<-igraph2vis(g=values$CM$net$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$CM$net,shadow=FALSE)
-
- values$networkCM$VIS
-
- })
-
- output$CMplot.save <- downloadHandler(
- filename = function() {
-
- paste("CouplingMap-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$CM$map, dpi = as.numeric(input$CMdpi), height = input$CMh, width = input$CMh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$CMTable <- DT::renderDT({
- CMMAP()
- cmData=values$CM$data[,c(2,1,3,5)]
-
- DT::datatable(cmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CouplingMap',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CouplingMap',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CouplingMap',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cmData))-1))))) %>%
- formatStyle(names(cmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$CMTableCluster <- DT::renderDT({
- CMMAP()
- cmData=values$CM$clusters[,c(7,1:4,6)]
-
- DT::datatable(cmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CouplingMap_Clusters',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CouplingMap_Clusters',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CouplingMap_Clusters',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cmData))-1))))) %>%
- formatStyle(names(cmData), backgroundColor = 'white')
- #return(Data)
-
- })
- ### Conceptual Structure #####
-
- ### Co-occurrences network ----
- COCnetwork <- eventReactive(input$applyCoc,{
-
- values <- cocNetwork(input,values)
-
-
- values$network<-igraph2vis(g=values$cocnet$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$cocnet, shadow=(input$coc.shadow=="Yes"))
-
-
- })
-
- output$cocPlot <- renderVisNetwork({
-
- COCnetwork()
-
- values$network$VIS
-
- })
-
- output$COCStopPreview <- renderUI({
-
- if (!is.null(values$COCremove.terms) | exists("values$COCremove.terms")){
- strPreview(values$COCremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$COCSynPreview <- renderUI({
-
- if (!is.null(values$COCsyn.terms) | exists("values$COCsyn.terms")){
- strSynPreview(values$COCsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- # output$cocPlotComm <- renderVisNetwork({
- #
- # g <- splitCommunities(values$cocnet$graph, n=NULL)
- # igraph2vis(g=g,curved=(input$coc.curved=="Yes"),
- # labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- # shape=input$coc.shape, net=values$cocnet)$VIS
- #
- # })
-
- output$network.coc <- downloadHandler(
- filename = "Co_occurrence_network.net",
- content <- function(file) {
- igraph::write.graph(values$cocnet$graph_pajek,file=file, format="pajek")
-
- },
- contentType = "net"
- )
-
- ### save coc network image as html ####
- output$networkCoc.fig <- downloadHandler(
- filename = "network.html",
- content <- function(con) {
- savenetwork(con)
- },
- contentType = "html"
- )
-
- output$cocTable <- DT::renderDT({
- COCnetwork()
- cocData=values$cocnet$cluster_res
- names(cocData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
- DT::datatable(cocData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CoWord_Network_Analysis',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CoWord_Network_Analysis',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CoWord_Network_Analysis',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cocData))-1))))) %>%
- formatStyle(names(cocData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- ### Degree Plot Co-word analysis ####
- output$cocDegree <- renderPlotly({
- COCnetwork()
- p <- degreePlot(values$cocnet)
- plot.ly(p)
- })
-
-
- ### Correspondence Analysis ----
-
- CSfactorial <- eventReactive(input$applyCA,{
- values <- CAmap(input,values)
- })
-
- output$CSStopPreview <- renderUI({
-
- if (!is.null(values$CSremove.terms) | exists("values$CSremove.terms")){
- strPreview(values$CSremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$FASynPreview <- renderUI({
-
- if (!is.null(values$FAsyn.terms) | exists("values$FAsyn.terms")){
- strSynPreview(values$FAsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- output$FA1plot.save <- downloadHandler(
- filename = function() {
-
- paste("FactorialMap-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$CS$graph_terms, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
- },
- contentType = "png"
- )
- output$FA2plot.save <- downloadHandler(
- filename = function() {
-
- paste("Dendrogram-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$CS$graph_dendogram, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$FA3plot.save <- downloadHandler(
- filename = function() {
-
- paste("MostContribDocuments-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$CS$graph_documents_Contrib, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
- },
- contentType = "png"
- )
-
- output$FA4plot.save <- downloadHandler(
- filename = function() {
-
- paste("MostCitedDocuments-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$CS$graph_documents_TC, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
- },
- contentType = "png"
- )
-
- output$CSPlot1 <- renderPlot({
- CSfactorial()
- plot(values$CS$graph_terms)
-
- }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
- height = exprToFunction(as.numeric(input$dimension[2])*0.85),
- res = 150)
- #width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 650, width = 800)
-
- output$CSPlot2 <- renderPlot({
- CSfactorial()
- if (input$method!="MDS"){
-
- if (values$CS[[1]][1]!="NA"){
-
- plot(values$CS$graph_documents_Contrib)
- }else{
- emptyPlot("Selected field is not included in your data collection")
- }
- }else{
- emptyPlot("This plot is available only for CA or MCA analyses")
- }
-
- }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
- height = exprToFunction(as.numeric(input$dimension[2])*0.85),
- res = 150)
-
- output$CSPlot3 <- renderPlot({
- CSfactorial()
- if (input$method!="MDS"){
- if (values$CS[[1]][1]!="NA"){
- plot(values$CS$graph_documents_TC)
- }else{
- emptyPlot("Selected field is not included in your data collection")
- }
- }else{
- emptyPlot("This plot is available only for CA or MCA analyses")
- }
-
-
- }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
- height = exprToFunction(as.numeric(input$dimension[2])*0.85),
- res = 150)
-
- output$CSPlot4 <- renderPlot({
-
- CSfactorial()
- if (values$CS[[1]][1]!="NA"){
- plot(values$CS$graph_dendogram)
- }else{
- emptyPlot("Selected field is not included in your data collection")
- }
-
- }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
- height = exprToFunction(as.numeric(input$dimension[2])*0.85),
- res = 150)
-
- output$CSTableW <- DT::renderDT({
- CSfactorial()
- switch(input$method,
- CA={
- WData=data.frame(word=row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
- stringsAsFactors = FALSE)
- names(WData)[4]="cluster"
- },
- MCA={
- WData=data.frame(word=row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
- stringsAsFactors = FALSE)
- names(WData)[4]="cluster"
- },
- MDS={
- WData=data.frame(word=row.names(values$CS$res), values$CS$res,
- cluster=values$CS$km.res$cluster,stringsAsFactors = FALSE)
- })
-
- WData$Dim.1=round(WData$Dim.1,2)
- WData$Dim.2=round(WData$Dim.2,2)
-
- DT::datatable(WData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(WData))-1))))) %>%
- formatStyle(names(WData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$CSTableD <- DT::renderDT({
- CSfactorial()
- CSData=values$CS$docCoord
- CSData=data.frame(Documents=row.names(CSData),CSData,stringsAsFactors = FALSE)
- CSData$dim1=round(CSData$dim1,2)
- CSData$dim2=round(CSData$dim2,2)
- CSData$contrib=round(CSData$contrib,2)
- DT::datatable(CSData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(CSData))-1))))) %>%
- formatStyle(names(CSData), backgroundColor = 'white')
-
- })
-
- ### Thematic Map ----
- TMAP <- eventReactive(input$applyTM,{
-
- if (input$TMfield %in% c("TI","AB")){
- ngrams <- as.numeric(input$TMngrams)
- }else{
- ngrams <- 1
- }
-
- ### load file with terms to remove
- if (input$TMStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$TMStop, sep=input$TMSep))
- }else{remove.terms <- NULL}
- values$TMremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$TMapSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$TMapSyn, sep=input$TMapSynSep))
- }else{synonyms <- NULL}
- values$TMapsyn.terms <- synonyms
- ### end of block
-
- values$TM <- thematicMap(values$M, field=input$TMfield,
- n=input$TMn, minfreq=input$TMfreq, ngrams=ngrams,
- stemming=input$TMstemming, size=input$sizeTM,
- n.labels=input$TMn.labels, repel=FALSE, remove.terms=remove.terms, synonyms=synonyms)
-
- validate(
- need(values$TM$nclust > 0, "\n\nNo topics in one or more periods. Please select a different set of parameters.")
- )
- })
- output$TMPlot <- renderPlotly({
-
- TMAP()
- plot.ly(values$TM$map, size=0.07, aspectratio = 1.3)
-
- })#, height = 650, width = 800)
-
- output$NetPlot <- renderVisNetwork({
- TMAP()
- values$networkTM<-igraph2vis(g=values$TM$net$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$TM$net)
-
- values$networkTM$VIS
-
- })
-
- output$TMStopPreview <- renderUI({
-
- if (!is.null(values$TMremove.terms) | exists("values$TMremove.terms")){
- strPreview(values$TMremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$TMapSynPreview <- renderUI({
-
- if (!is.null(values$TMapsyn.terms) | exists("values$TMapsyn.terms")){
- strSynPreview(values$TMapsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- output$TMplot.save <- downloadHandler(
- filename = function() {
-
- paste("ThematicMap-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$TM$map, dpi = as.numeric(input$TMdpi), height = input$TMh, width = input$TMh*1.5, bg="white")
- },
- contentType = "png"
- )
-
- output$TMTable <- DT::renderDT({
- TMAP()
- tmData=values$TM$words[,-4]
-
-
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster <- DT::renderDT({
- TMAP()
- tmData <- values$TM$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- ### Thematic Evolution ----
- output$sliders <- renderUI({
- numSlices <- as.integer(input$numSlices)
- v=quantile(values$M$PY, seq(0,1,by=(1/(numSlices+1))), na.rm=TRUE)
- v=round(v[-c(1,length(v))],0)
- lapply(1:numSlices, function(i) {
- # sliderInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),
- # min=1990,max=2018,value=1990)
-
- numericInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),value=v[i],min=min(values$M$PY, na.rm = TRUE)+1,max=max(values$M$PY, na.rm = TRUE)-1, step=1)
- #numericInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),value=median(values$M$PY),min=min(values$M$PY)+1,max=max(values$M$PY)-1, step=1)
- })
- })
-
- TEMAP <- eventReactive(input$applyTE,{
- if (input$TEfield %in% c("TI","AB")){
- ngrams <- as.numeric(input$TEngrams)
- }else{
- ngrams <- 1
- }
-
- ### load file with terms to remove
- if (input$TEStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$TEStop, sep=input$TESep))
- }else{remove.terms <- NULL}
- values$TEremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$TESynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$TESyn, sep=input$TESynSep))
- }else{synonyms <- NULL}
- values$TEsyn.terms <- synonyms
- ### end of block
-
- values$yearSlices <- as.numeric()
- for (i in 1:as.integer(input$numSlices)){
- if (length(input[[paste0("Slice", i)]])>0){values$yearSlices=c(values$yearSlices,input[[paste0("Slice", i)]])}
- }
-
- if (length(values$yearSlices)>0){
- values$nexus <- thematicEvolution(values$M, field=input$TEfield, values$yearSlices, n = input$nTE, minFreq = input$fTE, size = input$sizeTE,
- n.labels=input$TEn.labels, repel=FALSE, ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)
-
- validate(
- need(values$nexus$check != FALSE, "\n\nNo topics in one or more periods. Please select a different set of parameters.")
- )
-
- plotThematicEvolution(Nodes = values$nexus$Nodes,Edges = values$nexus$Edges, measure = input$TEmeasure, min.flow = input$minFlowTE)
- }
- })
-
- output$TEPlot <- plotly::renderPlotly({
-
- TEMAP()
-
- })
-
- output$TEStopPreview <- renderUI({
-
- if (!is.null(values$TEremove.terms) | exists("values$TEremove.terms")){
- strPreview(values$TEremove.terms)
- }else{
- strPreview(" ")
- }
- })
-
- output$TESynPreview <- renderUI({
-
- if (!is.null(values$TEsyn.terms) | exists("values$TEsyn.terms")){
- strSynPreview(values$TEsyn.terms)
- }else{
- strSynPreview(" ")
- }
- })
-
- output$TETable <- DT::renderDT({
- TEMAP()
- TEData=values$nexus$Data
- TEData=TEData[TEData$Inc_index>0,-c(4,8)]
- names(TEData)=c("From", "To", "Words", "Weighted Inclusion Index", "Inclusion Index", "Occurrences", "Stability Index")
- DT::datatable(TEData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Evolution',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Evolution',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Evolution',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TEData))-1))))) %>%
- formatStyle(names(TEData), backgroundColor = 'white') %>%
- formatRound(names(TEData)[4], 2) %>%
- formatRound(names(TEData)[5], 2) %>%
- formatRound(names(TEData)[7], 2)
- #return(Data)
-
- })
-
- output$TMPlot1 <- renderPlotly({
- TEMAP()
- #input$applyTM
- if (length(values$nexus$TM)>=1){
- plot.ly(values$nexus$TM[[1]]$map, size=0.07, aspectratio = 1.3)
- } else {emptyPlot("You have selected fewer periods!")}
-
- })#, height = 650, width = 800)
-
- output$TMPlot2 <- renderPlotly({
- TEMAP()
- #input$applyTM
- if (length(values$nexus$TM)>=2){
- plot.ly(values$nexus$TM[[2]]$map, size=0.07, aspectratio = 1.3)
- } else {emptyPlot("You have selected fewer periods!")}
-
- })#, height = 650, width = 800)
-
- output$TMPlot3 <- renderPlotly({
- TEMAP()
- #input$applyTM
- if (length(values$nexus$TM)>=3){
- plot.ly(values$nexus$TM[[3]]$map, size=0.07, aspectratio = 1.3)
- } else {emptyPlot("You have selected fewer periods!")}
-
- })#, height = 650, width = 800)
-
- output$TMPlot4 <- renderPlotly({
- TEMAP()
- #input$applyTM
- if (length(values$nexus$TM)>=4){
- plot.ly(values$nexus$TM[[4]]$map, size=0.07, aspectratio = 1.3)
- } else (emptyPlot("You have selected fewer periods!"))
-
- })#, height = 650, width = 800)
-
- output$TMPlot5 <- renderPlotly({
- TEMAP()
- #input$applyTM
- if (length(values$nexus$TM)>=5){
- plot.ly(values$nexus$TM[[5]]$map, size=0.07, aspectratio = 1.3)
- } else (emptyPlot("You have selected fewer periods!"))
-
- })#, height = 650, width = 800)
-
- output$NetPlot1 <- renderVisNetwork({
- TEMAP()
- k=1
- values$network1<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$nexus$Net[[k]])
-
- values$network1$VIS
-
- })
-
- output$NetPlot2 <- renderVisNetwork({
- TEMAP()
- k=2
- values$network2<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$nexus$Net[[k]])
-
- values$network2$VIS
-
- })
-
- output$NetPlot3 <- renderVisNetwork({
- TEMAP()
- k=3
- values$network3<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$nexus$Net[[k]])
-
- values$network3$VIS
-
- })
-
- output$NetPlot4 <- renderVisNetwork({
- TEMAP()
- k=4
- values$network4<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$nexus$Net[[k]])
-
- values$network4$VIS
-
- })
-
- output$NetPlot5 <- renderVisNetwork({
- TEMAP()
- k=5
- values$network5<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
- labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
- shape=input$coc.shape, net=values$nexus$Net[[k]])
-
- values$network5$VIS
-
- })
-
- output$TMTable1 <- DT::renderDT({
- TEMAP()
-
- tmData=values$nexus$TM[[1]]$words[,-4]
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map_Period_1',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map_Period_1',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map_Period_1',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTable2 <- DT::renderDT({
- TEMAP()
-
- tmData=values$nexus$TM[[2]]$words[,-4]
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map_Period_2',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map_Period_2',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map_Period_2',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTable3 <- DT::renderDT({
- TEMAP()
-
- tmData=values$nexus$TM[[3]]$words[,-4]
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map_Period_3',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map_Period_3',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map_Period_3',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTable4 <- DT::renderDT({
- TEMAP()
-
- tmData=values$nexus$TM[[4]]$words[,-4]
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map_Period_4',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map_Period_4',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map_Period_4',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTable5 <- DT::renderDT({
- TEMAP()
-
- tmData=values$nexus$TM[[5]]$words[,-4]
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map_Period_5',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map_Period_5',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map_Period_5',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster1 <- DT::renderDT({
- TEMAP()
- tmData <- values$nexus$TM[[1]]$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster2 <- DT::renderDT({
- TEMAP()
- tmData <- values$nexus$TM[[2]]$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster3 <- DT::renderDT({
- TEMAP()
- tmData <- values$nexus$TM[[3]]$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster4 <- DT::renderDT({
- TEMAP()
- tmData <- values$nexus$TM[[4]]$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- output$TMTableCluster5 <- DT::renderDT({
- TEMAP()
- tmData <- values$nexus$TM[[5]]$clusters[,c(7,1:4,6)]
- names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
-
- DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Thematic_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
- formatStyle(names(tmData), backgroundColor = 'white')
- #return(Data)
- })
-
- ### INTELLECTUAL STRUCTURE ####
-
- ### Co-citation network ----
- COCITnetwork <- eventReactive(input$applyCocit,{
-
- values <- intellectualStructure(input,values)
- #dev.off();file.remove(t) ### end of trick
-
- values$network<-igraph2vis(g=values$cocitnet$graph,curved=(input$cocit.curved=="Yes"),
- labelsize=input$citlabelsize, opacity=0.7,type=input$citlayout,
- shape=input$cocit.shape, net=values$cocitnet, shadow=(input$cocit.shadow=="Yes"))
- })
-
- output$cocitPlot <- renderVisNetwork({
-
- COCITnetwork()
-
- isolate(values$network$VIS)
-
- })
-
- output$network.cocit <- downloadHandler(
- filename = "Co_citation_network.net",
- content <- function(file) {
- igraph::write.graph(values$cocitnet$graph_pajek,file=file, format="pajek")
- #rio::export(values$M, file=file)
- },
- contentType = "net"
- )
-
- output$cocitTable <- DT::renderDT({
- COCITnetwork()
- cocitData=values$cocitnet$cluster_res
- names(cocitData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
- DT::datatable(cocitData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'CoCitation_Network',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'CoCitation_Network',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'CoCitation_Network',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cocitData))-1))))) %>%
- formatStyle(names(cocitData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- ### save coc network image as html ####
- output$networkCocit.fig <- downloadHandler(
- filename = "network.html",
- content <- function(con) {
- savenetwork(con)
- },
- contentType = "html"
- )
-
- ### Degree Plot Co-citation analysis ####
- output$cocitDegree <- renderPlotly({
- COCITnetwork()
- p <- degreePlot(values$cocitnet)
- plot.ly(p)
- })
-
- ### Historiograph ----
- Hist <- eventReactive(input$applyHist,{
-
- withProgress(message = 'Calculation in progress',
- value = 0, {
- values <- historiograph(input,values)
- })
-
- fx <- list(
- family = "Old Standard TT, serif",
- size = 11,
- color = "black"
- )
-
- a <- list(
- ticks = "outside",
- autotick = FALSE,
- ticktext = values$histPlot$axis$label,
- tickvals = values$histPlot$axis$values,
- tickmode = "array",
- showticklabels = TRUE,
- tickangle = 270,
- tickfont = fx,
- ticklen = 2,
- tickwidth = 2,
- tickcolor = toRGB("black")
- )
-
- g <- plot.ly(values$histPlot$g, side="r", size=0.05, aspectratio = 1.5, height=-0.1) %>%
- layout(xaxis = a, autosize=TRUE ,showlegend = FALSE,
- hoverlabel = list(font=list(size=input$histlabelsize+9)))
- return(g)
- })
-
- output$HGplot.save <- downloadHandler(
- filename = function() {
-
- paste("Historiograph-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- ggsave(filename = file, plot = values$histPlot$g, dpi = as.numeric(input$HGdpi), height = input$HGh, width = input$HGh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$histPlot <- renderPlotly({
-
- Hist()
-
- })
- output$histTable <- DT::renderDT({
- LCS=values$histResults$LCS
- s=sort(LCS,decreasing = TRUE)[input$histNodes]
- ind=which(LCS>=s)
- Data=values$histResults$histData
- Data=Data[ind,]
- Data$DOI<- paste0('',Data$DOI,'')
- DT::datatable(Data, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Historiograph_Network',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Historiograph_Network',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Historiograph_Network',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(Data))-1))))) %>%
- formatStyle(names(Data), backgroundColor = 'white') %>%
- formatStyle(
- 'GCS',
- background = styleColorBar(Data$GCS, 'steelblue'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center'
- ) %>%
- formatStyle(
- 'LCS',
- background = styleColorBar(Data$LCS, 'steelblue'),
- backgroundSize = '100% 90%',
- backgroundRepeat = 'no-repeat',
- backgroundPosition = 'center'
- )
- #return(Data)
-
- })
-
- ### SOCIAL STRUCTURE ####
- ### Collaboration network ----
- COLnetwork <- eventReactive(input$applyCol,{
-
- values <- socialStructure(input,values)
-
- values$network<-igraph2vis(g=values$colnet$graph,curved=(input$soc.curved=="Yes"),
- labelsize=input$collabelsize, opacity=input$colAlpha,type=input$collayout,
- shape=input$col.shape, net=values$colnet, shadow=(input$col.shadow=="Yes"))
- })
- output$colPlot <- renderVisNetwork({
-
- COLnetwork()
-
- values$network$VIS
-
- })
-
- output$network.col <- downloadHandler(
- filename = "Collaboration_network.net",
- content <- function(file) {
- igraph::write.graph(values$colnet$graph_pajek,file=file, format="pajek")
- #rio::export(values$M, file=file)
- },
- contentType = "net"
- )
-
- output$colTable <- DT::renderDT({
- COLnetwork()
- colData=values$colnet$cluster_res
- names(colData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
-
- DT::datatable(colData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'Collaboration_Network',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'Collaboration_Network',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'Collaboration_Network',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(colData))-1))))) %>%
- formatStyle(names(colData), backgroundColor = 'white')
- #return(Data)
-
- })
- ### save coc network image as html ####
- output$networkCol.fig <- downloadHandler(
- filename = "network.html",
- content <- function(con) {
- savenetwork(con)
- },
- contentType = "html"
- )
-
-
- ### Degree Plot Collaboration analysis ####
- output$colDegree <- renderPlotly({
- COLnetwork()
- p <- degreePlot(values$colnet)
- plot.ly(p)
- })
-
- ### WPPlot ----
- WMnetwork<- eventReactive(input$applyWM,{
- values$WMmap=countrycollaboration(values$M,label=FALSE,edgesize=input$WMedgesize/2,min.edges=input$WMedges.min)
- })
-
- output$CCplot.save <- downloadHandler(
- filename = function() {
-
- paste("CountryCollaborationMap-", Sys.Date(), ".png", sep="")
- },
- content <- function(file) {
- g <- values$WMmap$g + labs(title = "Country Collaboration Map")
- ggsave(filename = file, plot = g, dpi = as.numeric(input$CCdpi), height = input$CCh, width = input$CCh*2, bg="white")
- },
- contentType = "png"
- )
-
- output$WMPlot<- renderPlot({
-
- WMnetwork()
- plot(values$WMmap$g)
-
- }, #width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)),
- width = exprToFunction(as.numeric(input$dimension[1])*0.6),
- height = exprToFunction(as.numeric(input$dimension[2])*0.85),
- res = 150)
-
- output$WMTable <- DT::renderDT({
- WMnetwork()
- colData=values$WMmap$tab
- colData=colData[,c(1,2,9)]
- names(colData)=c("From","To","Frequency")
-
- DT::datatable(colData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
- options = list(pageLength = 10, dom = 'Bfrtip',
- buttons = list('pageLength',
- list(extend = 'copy'),
- list(extend = 'csv',
- filename = 'World_Collaboration_Map',
- title = " ",
- header = TRUE),
- list(extend = 'excel',
- filename = 'World_Collaboration_Map',
- title = " ",
- header = TRUE),
- list(extend = 'pdf',
- filename = 'World_Collaboration_Map',
- title = " ",
- header = TRUE),
- list(extend = 'print')),
- lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
- columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(colData))-1))))) %>%
- formatStyle(names(colData), backgroundColor = 'white')
- #return(Data)
-
- })
-
- ### COMMON FUNCTIONS ####
-
-
- # displayResolution <- function() {
- # session$clientData$output_plot1_width
- # }
-
- getFileNameExtension <- function (fn) {
- # remove a path
- splitted <- strsplit(x=fn, split='/')[[1]]
- # or use .Platform$file.sep in stead of '/'
- fn <- splitted [length(splitted)]
- ext <- ''
- splitted <- strsplit(x=fn, split='\\.')[[1]]
- l <-length (splitted)
- if (l > 1 && sum(splitted[1:(l-1)] != '')) ext <-splitted [l]
- # the extention must be the suffix of a non-empty name
- ext
- }
-
- # string preview (stopwords)
- strPreview <- function(string, sep=","){
- str1 <- unlist(strsplit(string, sep))
- str1 <- str1[1:min(c(length(str1),5))]
- str1 <- paste(str1, collapse=sep)
- HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
- }
-
- # string preview (synonyms)
- strSynPreview <- function(string){
- string <- string[1]
- str1 <- unlist(strsplit(string, ";"))
- str1 <- str1[1:min(c(length(str1),5))]
- str1 <- paste(paste(str1[1], " <- ",collapse=""),paste(str1[-1], collapse=";"), collapse="")
- HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
- }
-
- # from ggplot to plotly
- plot.ly <- function(g, flip=FALSE, side="r", aspectratio=1, size=0.15,data.type=2, height=0){
-
- g <- g + labs(title=NULL)
- print("Fatto")
- a <- ggplot_build(g)$data
-
- ymin <- unlist(lapply(a, function(l){
- if ("y" %in% names(l)){
- min(l["y"])
- }
- })) %>% min(na.rm=TRUE)
-
- ymax <- unlist(lapply(a, function(l){
- if ("y" %in% names(l)){
- max(l["y"])
- }
- })) %>% max(na.rm=TRUE)
-
- xmin <- unlist(lapply(a, function(l){
- if ("x" %in% names(l)){
- min(l["x"])
- }
- })) %>% min(na.rm=TRUE)
-
- xmax <- unlist(lapply(a, function(l){
- if ("x" %in% names(l)){
- max(l["x"])
- }
- })) %>% max(na.rm=TRUE)
-
- if (isTRUE(flip)){
- xrange <- c(ymin,ymax)
- yrange <- c(xmin,xmax)
- }else{
- yrange <- c(ymin,ymax)
- xrange <- c(xmin,xmax)
- }
-
- # if (isTRUE(flip)){
- # yrange <- range(ggplot_build(g)$data[[data.type]]$x)
- # xrange <- range(ggplot_build(g)$data[[data.type]]$y)
- # }else{
- # xrange <- range(ggplot_build(g)$data[[data.type]]$x)
- # yrange <- range(ggplot_build(g)$data[[data.type]]$y)
- # }
-
- sizex = diff(xrange)*size
- sizey = diff(yrange)*size*aspectratio
-
- y <- min(yrange)+0.2
-
- if (side=="l"){
- x <- min(xrange)+0.2
- }else{
- x <- max(xrange)-0.2-sizex
- }
-
- ggplotly(g, tooltip = "text") %>%
- config(displaylogo = FALSE,
- modeBarButtonsToRemove = c(
- 'sendDataToCloud',
- 'pan2d',
- 'select2d',
- 'lasso2d',
- 'toggleSpikelines',
- 'hoverClosestCartesian',
- 'hoverCompareCartesian'
- )) %>%
- layout(
- images = list(
- source = raster2uri(as.raster(values$logo)),
- x = x, y = y+height,
- sizex = sizex, sizey = sizey,
- xref = "x", yref = "y",
- xanchor = "left", yanchor = "bottom",
- sizing = "stretch"
- )
- )
- }
-
- freqPlot <- function(xx,x,y, textLaby,textLabx, title){
-
-
- xl <- c(max(xx[,x])-0.02-diff(range(xx[,x]))*0.125, max(xx[,x])-0.02)+1
- yl <- c(1,1+length(unique(xx[,y]))*0.125)
-
- Text <- paste(textLaby,": ",xx[,y],"\n",textLabx, ": ",xx[,x])
-
- g <- ggplot(xx, aes(x =xx[,x], y = xx[,y], label = xx[,x], text=Text)) +
- geom_segment(aes(x = 0, y = xx[,y], xend = xx[,x], yend = xx[,y]), color = "grey50") +
- geom_point(aes(color=-xx[,x], size=xx[,x]), show.legend = FALSE) +
- scale_radius(range=c(5, 12))+
- geom_text(color = "white", size = 3) +
- scale_y_discrete(limits = rev(xx[,y])) +
- scale_fill_continuous(type = "gradient")+
- labs(title=title, y = textLaby)+
- labs(x = textLabx)+
- expand_limits(y= c(1, length(xx[,y]) + 1))+
- theme_minimal()+
- theme(axis.text.y = element_text(angle=0, hjust=0)) +
- annotation_custom(values$logoGrid, xmin = xl[1], xmax = xl[2], ymin = yl[1], ymax = yl[2])
-
- return(g)
- }
-
- emptyPlot<-function(errortext){
- g=ggplot()+
- theme_void() + theme(legend.position="none")+
- annotate("text", x = 4, y = 25, label = errortext, size=10)
- plot(g)
- }
-
- count.duplicates <- function(DF){
- x <- do.call('paste', c(DF, sep = '\r'))
- ox <- order(x)
- rl <- rle(x[ox])
- cbind(DF[ox[cumsum(rl$lengths)],,drop=FALSE],count = rl$lengths)
-
- }
-
- reduceRefs<- function(A){
-
- ind=unlist(regexec("*V[0-9]", A))
- A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
- ind=unlist(regexec("*DOI ", A))
- A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
- return(A)
- }
-
-
- initial <- function(values){
- values$results <- list("NA")
- values$log <- "working..."
- values$load <- "FALSE"
- values$field = values$cocngrams = "NA"
- values$citField = values$colField = values$citSep= "NA"
- values$NetWords = values$NetRefs = values$ColNetRefs=matrix(NA,1,1)
- values$Title <- "Network"
- values$Histfield <- "NA"
- values$histlog <- "working..."
- values$kk <- 0
- values$histsearch <- "NA"
- values$citShortlabel <- "NA"
- values$S <- list("NA")
- values$GR <- "NA"
-
- return(values)
- }
-
-
- ### ANALYSIS FUNCTIONS ####
- ### Descriptive functions ----
- Hindex_plot <- function(values, type){
-
- hindex<-function(values,type){
-
- switch(type,
- author={
- AU <- trim(gsub(",","",names(tableTag(values$M,"AU"))))
- values$H <- Hindex(values$M, field = "author", elements = AU, sep = ";", years=Inf)$H
- },
- source={
- SO <- names(sort(table(values$M$SO),decreasing = TRUE))
- values$H <- Hindex(values$M, field = "source", elements = SO, sep = ";", years=Inf)$H
- }
- )
-
- return(values)
- }
-
- values<-hindex(values, type = type)
-
- xx=values$H
- if (type=="author"){
- K=input$Hkauthor
- measure=input$HmeasureAuthors
- title="Author Local Impact"
- xn="Authors"
- } else {
- K=input$Hksource
- measure=input$HmeasureSources
- title="Source Local Impact"
- xn="Sources"
- }
- if (K>dim(xx)[1]){
- k=dim(xx)[1]
- } else {k=K}
-
- switch(measure,
- h={m=2},
- g={m=3},
- m={m=4
- xx[,m] <-round(xx[,m],2) },
- tc={m=5}
- )
- xx <- xx[order(-xx[,m]),]
- xx <- xx[1:k,c(1,m)]
-
-
- g <- freqPlot(xx,x=2,y=1, textLaby = xn, textLabx = paste("Impact Measure:",toupper(measure)), title = paste(title,"by",toupper(measure),"index"))
-
- res<-list(values=values,g=g)
- return(res)
- }
-
- descriptive <- function(values,type){
-
-
- switch(type,
- "tab1"={
- if (values$results[[1]]=="NA"){
- values$results=biblioAnalysis(values$M)
- }
- if (values$S[[1]][1]=="NA"){
- values$S=summary(values$results,k=Inf,verbose=FALSE)
- }
- #TAB=data.frame(Information=gsub("[[:digit:]]", "", S$MainInformation), Data=gsub("[^0-9]", "", S$MainInformation))
- TAB=data.frame(values$S$MainInformationDF)
- #cat(S$MainInformation)
- },
- "tab2"={
- TAB <- values$M %>% group_by(.data$PY) %>%
- count() %>%
- rename(Year = .data$PY,
- Articles = .data$n) %>%
- right_join(data.frame(Year=seq(min(values$M$PY,na.rm=TRUE),max(values$M$PY, na.rm=TRUE))), by="Year") %>%
- mutate(Articles = replace_na(.data$Articles,0)) %>%
- arrange(.data$Year) %>% as.data.frame()
-
- ny=diff(range(TAB$Year))
- values$GR=round(((TAB[nrow(TAB),2]/TAB[1,2])^(1/(ny))-1)*100, digits = 2)
- },
- "tab3"={
- listAU <- (strsplit(values$M$AU, ";"))
- nAU <- lengths(listAU)
- fracAU <- rep(1/nAU,nAU)
- TAB <- tibble(Author=unlist(listAU), fracAU=fracAU) %>%
- group_by(.data$Author) %>%
- summarize(
- Articles = n(),
- AuthorFrac = sum(.data$fracAU)
- ) %>%
- arrange(desc(.data$Articles)) %>% as.data.frame()
- names(TAB)=c("Authors","Articles","Articles Fractionalized")
- #print(S$MostProdAuthors)
- },
- "tab4"={
- y <- as.numeric(substr(Sys.Date(),1,4))
- TAB <- values$M %>%
- mutate(TCperYear = .data$TC/(y+1-.data$PY)) %>%
- select(.data$SR,.data$DI, .data$TC, .data$TCperYear, .data$PY) %>%
- group_by(.data$PY) %>%
- mutate(NTC = .data$TC/mean(.data$TC)) %>%
- ungroup() %>%
- select(-.data$PY) %>%
- arrange(desc(.data$TC)) %>%
- as.data.frame()
- names(TAB)=c("Paper", "DOI","Total Citations","TC per Year","Normalized TC")
- },
- "tab5"={
-
- TAB <- countryCollab(values$M)
- TAB <- TAB %>%
- mutate(Freq = .data$Articles/sum(.data$Articles)) %>%
- mutate(MCP_Ratio = .data$MCP/.data$Articles)
- },
- "tab6"={
- if (!"AU1_CO" %in% names(values$M)){
- values$M <- metaTagExtraction(values$M, "AU1_CO")
- }
- TAB <- values$M %>%
- select(.data$AU1_CO, .data$TC) %>%
- drop_na(.data$AU1_CO) %>%
- rename(Country = .data$AU1_CO,
- TotalCitation = .data$TC) %>%
- group_by(.data$Country) %>%
- summarise("TC"=sum(.data$TotalCitation),"Average Article Citations"=sum(.data$TotalCitation)/length(.data$TotalCitation)) %>%
- arrange(-.data$TC) %>% as.data.frame(.data,stringasfactor=FALSE)
- },
- "tab7"={
- TAB <- values$M %>%
- select(.data$SO) %>%
- group_by(.data$SO) %>%
- count() %>%
- arrange(desc(.data$n)) %>%
- rename(Sources = .data$SO,
- Articles = .data$n) %>%
- as.data.frame()
- },
-
- "tab10"={
- TAB<-mapworld(values$M)$tab
- },
- "tab11"={
- if(!("AU_UN" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_UN")}
- TAB <- data.frame(Affiliation=unlist(strsplit(values$M$AU_UN, ";"))) %>%
- group_by(.data$Affiliation) %>%
- count() %>%
- drop_na(.data$Affiliation) %>%
- arrange(desc(.data$n)) %>%
- rename(Articles = .data$n) %>%
- as.data.frame()
- },
- "tab12"={
- TAB=tableTag(values$M,"C1")
- TAB=data.frame(Affiliations=names(TAB), Articles=as.numeric(TAB),stringsAsFactors = FALSE)
- TAB=TAB[nchar(TAB[,1])>4,]
- #names(TAB)=c("Affiliations", "Articles")
-
- },
- "tab13"={
- CR<-localCitations(values$M,fast.search = FALSE, verbose = FALSE)
- TAB <- CR$Authors
- #TAB=data.frame(Authors=names(CR$Authors$Author), Citations=as.numeric(CR$Cited),stringsAsFactors = FALSE)
- }
- )
- values$TAB=TAB
- res=list(values=values,TAB=TAB)
- return(res)
- }
-
- wordlist <- function(M, Field, n, measure, ngrams, remove.terms=NULL, synonyms=NULL){
- switch(Field,
- ID={v=tableTag(values$M,"ID", remove.terms = remove.terms, synonyms = synonyms)},
- DE={v=tableTag(values$M,"DE", remove.terms = remove.terms, synonyms = synonyms)},
- TI={
- if (!("TI_TM" %in% names(M))){
- v=tableTag(M,"TI", ngrams=ngrams, remove.terms=remove.terms, synonyms = synonyms)
-
- }},
- AB={if (!("AB_TM" %in% names(M))){
- v=tableTag(M,"AB", ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)
- }}
- )
- names(v)=tolower(names(v))
- #v=tableTag(values$M,"ID")
- n=min(c(n,length(v)))
- Words=data.frame(Terms=names(v)[1:n], Frequency=(as.numeric(v)[1:n]), stringsAsFactors = FALSE)
- W=Words
- switch(measure,
- identity={},
- sqrt={W$Frequency=sqrt(W$Frequency)},
- log={W$Frequency=log(W$Frequency+1)},
- log10={W$Frequency=log10(W$Frequency+1)}
- )
-
- results=list(v=v,W=W, Words=Words)
- return(results)
- }
-
- readStopwordsFile <- function(file, sep=","){
- if (!is.null(file)){
- req(file$datapath)
- remove.terms <- unlist(strsplit(readr::read_lines(file$datapath), sep))
- }else{remove.terms <- NULL}
- return(remove.terms)
- }
-
- readSynWordsFile <- function(file, sep=","){
- if (!is.null(file)){
- req(file$datapath)
- syn.terms <- readr::read_lines(file$datapath)
- if (sep!=";") syn.terms <- gsub(sep,";",syn.terms)
- }else{syn.terms <- NULL}
- return(syn.terms)
- }
-
- mapworld <- function(M){
- if (!("AU_CO" %in% names(M))){M=metaTagExtraction(M,"AU_CO")}
- CO=as.data.frame(tableTag(M,"AU_CO"),stringsAsFactors = FALSE)
- CO$Tab=gsub("UNITED KINGDOM","UK",CO$Tab)
- CO$Tab=gsub("KOREA","SOUTH KOREA",CO$Tab)
-
- map.world <- map_data("world")
- map.world$region=toupper(map.world$region)
-
- dplyr::anti_join(CO, map.world, by = c('Tab' = 'region'))
-
- country.prod <- dplyr::left_join( map.world, CO, by = c('region' = 'Tab'))
-
- tab=data.frame(country.prod %>%
- dplyr::group_by(region) %>%
- dplyr::summarise(Freq=mean(Freq)))
-
- tab=tab[!is.na(tab$Freq),]
-
- tab=tab[order(-tab$Freq),]
-
- breaks=as.numeric(round(quantile(CO$Freq,c(0.2,0.4,0.6,0.8,1))))
- names(breaks)=breaks
- breaks=log(breaks)
-
- g <- ggplot(country.prod, aes( x = .data$long, y = .data$lat, group=.data$group, text=paste("Country: ",.data$region,"\nN.of Documents: ",.data$Freq))) +
- geom_polygon(aes(fill = log(Freq), group=group)) +
- scale_fill_continuous(low='dodgerblue', high='dodgerblue4',breaks=breaks)+
- guides(fill = guide_legend(reverse = T)) +
- #geom_text(data=centroids, aes(label = centroids$Tab, x = centroids$long, y = centroids$lat, group=centroids$Tab)) +
- labs(fill = 'N.Documents'
- ,title = 'Country Scientific Production'
- ,x = NULL
- ,y = NULL) +
- theme(text = element_text(color = '#333333')
- ,plot.title = element_text(size = 28)
- ,plot.subtitle = element_text(size = 14)
- ,axis.ticks = element_blank()
- ,axis.text = element_blank()
- ,panel.grid = element_blank()
- ,panel.background = element_rect(fill = '#FFFFFF') #'#333333'
- ,plot.background = element_rect(fill = '#FFFFFF')
- ,legend.position = c(.18,.36)
- ,legend.background = element_blank()
- ,legend.key = element_blank()
- ) + annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)
-
- results=list(g=g,tab=tab)
- return(results)
- }
-
- ### Structure fuctions ----
- CAmap <- function(input, values){
- if ((input$CSfield %in% names(values$M))){
-
- if (input$CSfield %in% c("TI","AB")){
- ngrams <- as.numeric(input$CSngrams)
- }else{
- ngrams <- 1
- }
-
- ### load file with terms to remove
- if (input$CSStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$CSStop, sep=input$CSSep))
- }else{remove.terms <- NULL}
- values$CSremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$FASynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$FASyn, sep=input$FASynSep))
- }else{synonyms <- NULL}
- values$FAsyn.terms <- synonyms
- ### end of block
-
- tab=tableTag(values$M,input$CSfield, ngrams=ngrams)
- if (length(tab>=2)){
-
- minDegree=as.numeric(tab[input$CSn])
-
- values$CS <- conceptualStructure(values$M, method=input$method , field=input$CSfield, minDegree=minDegree, clust=input$nClustersCS,
- k.max = 8, stemming=F, labelsize=input$CSlabelsize,documents=input$CSdoc,graph=FALSE, ngrams=ngrams,
- remove.terms=remove.terms, synonyms = synonyms)
-
-
- }else{emptyPlot("Selected field is not included in your data collection")
- values$CS=list("NA")}
-
- }else{
- emptyPlot("Selected field is not included in your data collection")
- values$CS=list("NA")
-
- }
- }
-
- historiograph <- function(input,values){
-
- min.cit <- 1
- # if (input$histsearch=="FAST"){
- # min.cit=quantile(values$M$TC,0.75, na.rm = TRUE)
- # }else{min.cit=1}
-
- if (values$Histfield=="NA"){
- values$histResults <- histNetwork(values$M, min.citations=min.cit, sep = ";")
- values$Histfield="done"
- }
- titlelabel <- input$titlelabel=="TRUE"
- values$histlog<- (values$histPlot <- histPlot(values$histResults, n=input$histNodes, size =input$histsize, labelsize = input$histlabelsize, title_as_label = titlelabel, verbose=FALSE))
- return(values)
- }
-
-
- ### Network functions ----
-
- degreePlot <- function(net){
- deg <- data.frame(node = names(net$nodeDegree), x= (1:length(net$nodeDegree)), y = net$nodeDegree)
- p <- ggplot(data = deg, aes(x=.data$x, y=.data$y,
- text=paste("Node ",.data$x," - Degree ",.data$y, sep="")))+
- geom_point()+
- geom_line(aes(group="NA"),color = '#002F80', alpha = .5) +
- theme(text = element_text(color = "#444444")
- ,panel.background = element_rect(fill = '#FFFFFF')
- ,panel.grid.minor = element_line(color = '#EFEFEF')
- ,panel.grid.major = element_line(color = '#EFEFEF')
- ,plot.title = element_text(size = 24)
- ,axis.title = element_text(size = 14, color = '#555555')
- ,axis.title.y = element_text(vjust = 1, angle = 0)
- ,axis.title.x = element_text(hjust = 0)
- ,axis.line.x = element_line(color="black",size=0.5)
- ,axis.line.y = element_line(color="black",size=0.5)
- ) +
- labs(x = "Node", y="Degree", title = "Node Degrees")
- return(p)
- }
-
- cocNetwork <- function(input,values){
-
- n = input$Nodes
- label.n = input$Labels
-
- ### load file with terms to remove
- if (input$COCStopFile=="Y"){
- remove.terms <- trimws(readStopwordsFile(file=input$COCStop, sep=input$COCSep))
- }else{remove.terms <- NULL}
- values$COCremove.terms <- remove.terms
- ### end of block
- ### load file with synonyms
- if (input$COCSynFile=="Y"){
- synonyms <- trimws(readSynWordsFile(file=input$COCSyn, sep=input$COCSynSep))
- }else{synonyms <- NULL}
- values$COCsyn.terms <- synonyms
- ### end of block
-
- if ((input$field %in% names(values$M))){
-
- if ((dim(values$NetWords)[1])==1 | !(input$field==values$field) | !(input$cocngrams==values$cocngrams) | ((dim(values$NetWords)[1])!=input$Nodes) ){
-
- values$field=input$field
- values$ngrams <- input$cocngrams
-
- switch(input$field,
- ID={
- values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "keywords", n = n, sep = ";", remove.terms=remove.terms, synonyms = synonyms)
- values$Title= "Keywords Plus Network"
- },
- DE={
- values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "author_keywords", n = n, sep = ";", remove.terms=remove.terms, synonyms = synonyms)
- values$Title= "Authors' Keywords network"
- },
- TI={
- #if(!("TI_TM" %in% names(values$M))){
- values$M=termExtraction(values$M,Field="TI",verbose=FALSE, ngrams=as.numeric(input$cocngrams), remove.terms=remove.terms, synonyms = synonyms)
- #}
- values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "titles", n = n, sep = ";")
- values$Title= "Title Words network"
- },
- AB={
- #if(!("AB_TM" %in% names(values$M))){
- values$M=termExtraction(values$M,Field="AB",verbose=FALSE, ngrams=as.numeric(input$cocngrams), remove.terms=remove.terms, synonyms = synonyms)
- #}
- values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "abstracts", n = n, sep = ";")
- values$Title= "Abstract Words network"
- })
-
- }
-
- if (label.n>n){label.n=n}
- if (input$normalize=="none"){normalize=NULL}else{normalize=input$normalize}
- if (input$label.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
- if (input$coc.curved=="Yes"){curved=TRUE}else{curved=FALSE}
-
- #par(bg="grey92", mar=c(0,0,0,0))
- values$cocnet=networkPlot(values$NetWords, normalize=normalize, Title = values$Title, type = input$layout,
- size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$edgesize*3, labelsize=input$labelsize,label.cex=label.cex,
- label.n=label.n,edges.min=input$edges.min,label.color = F, curved=curved,alpha=input$cocAlpha,
- cluster=input$cocCluster, remove.isolates = (input$coc.isolates=="yes"),
- community.repulsion = input$coc.repulsion/2, verbose = FALSE)
- if (input$cocyears=="Yes"){
- Y=fieldByYear(values$M, field = input$field, graph=FALSE)
- g=values$cocnet$graph
- label=igraph::V(g)$name
- ind=which(tolower(Y$df$item) %in% label)
- df=Y$df[ind,]
-
- #bluefunc <- colorRampPalette(c("lightblue", "darkblue"))
- #col=bluefunc((diff(range(df$year))+1)*10)
- col=heat.colors((diff(range(df$year))+1)*10)
- igraph::V(g)$color=col[(max(df$year)-df$year+1)*10]
- igraph::V(g)$year=df$year
- values$cocnet$graph=g
- }
-
- }else{
- emptyPlot("Selected field is not included in your data collection")
- }
- return(values)
- }
-
- intellectualStructure <- function(input,values){
- n = input$citNodes
- label.n = input$citLabels
-
- if ((dim(values$NetRefs)[1])==1 | !(input$citField==values$citField) | !(input$citSep==values$citSep) | !(input$citShortlabel==values$citShortlabel) | ((dim(values$NetRefs)[1])!=input$citNodes)){
-
- values$citField=input$citField
- values$citSep=input$citSep
- if (input$citShortlabel=="Yes"){shortlabel=TRUE}else{shortlabel=FALSE}
- values$citShortlabel=input$citShortlabel
- switch(input$citField,
- CR={
- values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "references", n = n, sep = input$citSep, shortlabel=shortlabel)
- values$Title= "Cited References network"
-
- },
- CR_AU={
- if(!("CR_AU" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="CR_AU", sep = input$citSep)}
- values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "authors", n = n, sep = input$citSep)
- values$Title= "Cited Authors network"
- },
- CR_SO={
- if(!("CR_SO" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="CR_SO", sep = input$citSep)}
- values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "sources", n = n, sep = input$citSep)
- values$Title= "Cited Sources network"
- })
-
- }
-
- if (label.n>n){label.n=n}
- if (input$citlabel.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
- if (input$cocit.curved=="Yes"){curved=TRUE}else{curved=FALSE}
-
- values$cocitnet=networkPlot(values$NetRefs, normalize=NULL, Title = values$Title, type = input$citlayout,
- size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$citedgesize*3,
- labelsize=input$citlabelsize,label.cex=label.cex, curved=curved,
- label.n=label.n,edges.min=input$citedges.min,label.color = F,remove.isolates = (input$cit.isolates=="yes"),
- alpha=0.7, cluster=input$cocitCluster,
- community.repulsion = input$cocit.repulsion/2, verbose = FALSE)
- return(values)
- }
-
- socialStructure<-function(input,values){
- n = input$colNodes
- label.n = input$colLabels
-
- if ((dim(values$ColNetRefs)[1])==1 | !(input$colField==values$colField) | ((dim(values$ColNetRefs)[1])!=input$colNodes)){
-
- values$colField=input$colField
-
-
- values$cluster="walktrap"
- switch(input$colField,
- COL_AU={
- values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "authors", n = n, sep = ";")
- values$Title= "Author Collaboration network"
-
- },
- COL_UN={
- if(!("AU_UN" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_UN", sep=";")}
- values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "universities", n = n, sep = ";")
- values$Title= "Edu Collaboration network"
- },
- COL_CO={
- if(!("AU_CO" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_CO", sep=";")}
- values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "countries", n = n, sep = ";")
- values$Title= "Country Collaboration network"
- #values$cluster="none"
- })
-
- }
-
- if (label.n>n){label.n=n}
- if (input$colnormalize=="none"){normalize=NULL}else{normalize=input$colnormalize}
- if (input$collabel.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
- if (input$soc.curved=="Yes"){curved=TRUE}else{curved=FALSE}
-
- type=input$collayout
- if (input$collayout=="worldmap"){type="auto"}
-
- values$colnet=networkPlot(values$ColNetRefs, normalize=normalize, Title = values$Title, type = type,
- size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$coledgesize*3,
- labelsize=input$collabelsize,label.cex=label.cex, curved=curved,
- label.n=label.n,edges.min=input$coledges.min,label.color = F,alpha=input$colAlpha,
- remove.isolates = (input$col.isolates=="yes"), cluster=input$colCluster,
- community.repulsion = input$col.repulsion/2, verbose = FALSE)
-
- return(values)
-
- }
-
- countrycollaboration <- function(M,label,edgesize,min.edges){
- M=metaTagExtraction(M,"AU_CO")
- net=biblioNetwork(M,analysis="collaboration",network="countries")
- CO=data.frame(Tab=rownames(net),Freq=diag(net),stringsAsFactors = FALSE)
- bsk.network=igraph::graph_from_adjacency_matrix(net,mode="undirected")
- COedges=as.data.frame(igraph::ends(bsk.network,igraph::E(bsk.network),names=TRUE),stringsAsFactors = FALSE)
-
- map.world <- map_data("world")
- map.world$region=toupper(map.world$region)
- map.world$region=gsub("UK","UNITED KINGDOM",map.world$region)
- map.world$region=gsub("SOUTH KOREA","KOREA",map.world$region)
-
- country.prod <- dplyr::left_join( map.world, CO, by = c('region' = 'Tab'))
-
- breaks=as.numeric(round(quantile(CO$Freq,c(0.2,0.4,0.6,0.8,1))))
- names(breaks)=breaks
- breaks=log(breaks)
- data("countries",envir=environment())
- names(countries)[1]="Tab"
-
- COedges=dplyr::inner_join(COedges,countries, by=c('V1'='Tab'))
- COedges=dplyr::inner_join(COedges,countries, by=c('V2'='Tab'))
- COedges=COedges[COedges$V1!=COedges$V2,]
- COedges=count.duplicates(COedges)
- tab=COedges
- COedges=COedges[COedges$count>=min.edges,]
-
- g=ggplot(country.prod, aes( x = .data$long, y = .data$lat, group = .data$group )) +
- geom_polygon(aes(fill = log(Freq))) +
- scale_fill_continuous(low='dodgerblue', high='dodgerblue4',breaks=breaks)+
- #guides(fill = guide_legend(reverse = T)) +
- guides(colour=FALSE, fill=FALSE)+
- geom_curve(data=COedges, aes(x = .data$Longitude.x , y = .data$Latitude.x, xend = .data$Longitude.y, yend = .data$Latitude.y, # draw edges as arcs
- color = "firebrick4", size = .data$count, group=.data$continent.x),
- curvature = 0.33,
- alpha = 0.5) +
- scale_size_continuous(guide = FALSE, range = c(0.25, edgesize))+
- labs(title = NULL, x = "Latitude", y = "Longitude") +
- theme(text = element_text(color = '#333333')
- ,plot.title = element_text(size = 28)
- ,plot.subtitle = element_text(size = 14)
- ,axis.ticks = element_blank()
- ,axis.text = element_blank()
- ,panel.grid = element_blank()
- ,panel.background = element_rect(fill = '#FFFFFF') #'#333333'
- ,plot.background = element_rect(fill = '#FFFFFF')
- ,legend.position = c(.18,.36)
- ,legend.background = element_blank()
- ,legend.key = element_blank()
- ) + annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)
- if (isTRUE(label)){
- CO=dplyr::inner_join(CO,countries, by=c('Tab'='Tab'))
- g=g+
- ggrepel::geom_text_repel(data=CO, aes(x = .data$Longitude, y = .data$Latitude, label = .data$Tab, group=.data$continent), # draw text labels
- hjust = 0, nudge_x = 1, nudge_y = 4,
- size = 3, color = "orange", fontface = "bold")
- }
-
- results=list(g=g,tab=tab)
- return(results)
- }
- ### visNetwork tools ----
- netLayout <- function(type){
- switch(type,
- auto={l <- "layout_nicely"},
- circle={l <- "layout_in_circle"},
- mds={l <- "layout_with_mds"},
- star={l <- "layout_as_star"},
-
- sphere={l <- "layout_on_sphere"},
- fruchterman={l <- "layout_with_fr"},
- kamada={l <- "layout_with_kk"}
- )
- return(l)
- }
-
- savenetwork <- function(con){
- vn=values$network$vn
- visNetwork(nodes = vn$nodes, edges = vn$edges, type="full", smooth=TRUE, physics=FALSE, height = "2000px",width = "2000px" ) %>%
- visNodes(shape="box", font=list(color="black"),scaling=list(label=list(enables=TRUE))) %>%
- visIgraphLayout(layout = values$network$l) %>%
- visEdges(smooth = values$network$curved) %>%
- visOptions(highlightNearest =list(enabled = T, hover = T, degree=1), nodesIdSelection = T) %>%
- visInteraction(dragNodes = TRUE, navigationButtons = TRUE, hideEdgesOnDrag = TRUE) %>% visExport() %>%
- visPhysics(enabled = FALSE) %>% visSave(con)
- }
-
- igraph2vis<-function(g,curved,labelsize,opacity,type,shape, net, shadow=TRUE){
-
- LABEL=igraph::V(g)$name
-
- LABEL[igraph::V(g)$labelsize==0]=""
-
- vn <- toVisNetworkData(g)
-
- vn$nodes$label=LABEL
- vn$edges$num=1
- vn$edges$dashes=FALSE
- vn$edges$dashes[vn$edges$lty==2]=TRUE
-
- ## opacity
- vn$nodes$color=adjustcolor(vn$nodes$color,alpha=min(c(opacity+0.2,1)))
- vn$edges$color=adjustcolor(vn$edges$color,alpha=opacity)
-
- ## removing multiple edges
- vn$edges=unique(vn$edges)
-
- ## labelsize
- scalemin=20
- scalemax=150
- Min=min(vn$nodes$font.size)
- Max=max(vn$nodes$font.size)
- if (Max>Min){
- size=(vn$nodes$font.size-Min)/(Max-Min)*15*labelsize+10
- } else {size=10*labelsize}
- size[sizescalemax]=scalemax
- vn$nodes$font.size=size
- l<-netLayout(type)
-
- ### TO ADD SHAPE AND FONT COLOR OPTIONS
- coords <- net$layout
-
- vn$nodes$size <- vn$nodes$font.size*0.8
-
- if (shape %in% c("text")){
- vn$nodes$font.color <- vn$nodes$color
- }else{
- vn$nodes$font.color <- "black"
- }
-
- if (shape %in% c("dot","square")){
- vn$nodes$font.vadjust <- -0.7*vn$nodes$font.size
- }else{
- vn$nodes$font.vadjust <-0
- }
-
- VIS<-
- visNetwork(nodes = vn$nodes, edges = vn$edges, type="full", smooth=TRUE, physics=FALSE) %>%
- #visNodes(shape=shape, font=list(color="black")) %>%
- visNodes(shadow=shadow, shape=shape, font=list(color="black", size=vn$nodes$font.size,vadjust=vn$nodes$font.vadjust)) %>%
- visIgraphLayout(layout = "layout.norm", layoutMatrix = coords) %>%
- visEdges(smooth = curved) %>%
- visOptions(highlightNearest =list(enabled = T, hover = T, degree=1), nodesIdSelection = T) %>%
- visInteraction(dragNodes = TRUE, navigationButtons = TRUE, hideEdgesOnDrag = TRUE) %>%
- visOptions(manipulation = TRUE) %>%
- visExport(type = "png", name = "network",
- label = paste0("Export graph as png"), background = "#fff",
- float = "right", style = NULL, loadDependencies = TRUE)
- values$COCVIS=VIS
- return(list(VIS=VIS,vn=vn, type=type, l=l, curved=curved))
- }
-
- #### Common functions ----
-
- notifications <- function(){
-
- ## check connection and download notifications
- online <- is_online()
- location <- "https://www.bibliometrix.org/bs_notifications/biblioshiny_notifications.csv"
- if (isTRUE(is_online())){
- suppressWarnings(notifOnline <- read.csv(location, header=TRUE, sep=","))
- #notifOnline <- notifOnline[nchar(notifOnline)>2]
- #n <- strsplit(notifOnline,",")
- #notsOnline <- unlist(lapply(n,function(l) l[1]))
- #linksOnline <- unlist(lapply(n,function(l) l[2]))
- notifOnline$href[nchar(notifOnline$href)<6] <- NA
- }
-
- ## check if a file exists on the local machine and load it
- switch(Sys.info()[['sysname']],
- Windows= {home <- Sys.getenv('R_USER')},
- Linux = {home <- Sys.getenv('HOME')},
- Darwin = {home <- Sys.getenv('HOME')})
-
- file <- paste(home,"/biblioshiny_notifications.csv", sep="")
- fileTrue <- file.exists(file)
- if (isTRUE(fileTrue)){
- suppressWarnings(notifLocal <- read.csv(file, header=TRUE, sep=","))
- #notifLocal <- readLines(file)
- #linksLocal[nchar(linksLocal)<6] <- NA
- }
-
-
- A <- c("noA","A")
- B <- c("noB","B")
- status <- paste(A[online+1],B[fileTrue+1],sep="")
-
- switch(status,
- # missing both files (online and local)
- noAnoB={
- notifTot <- data.frame(nots="No notifications", href=NA, status="info") %>% mutate(status = "info")
- },
- # missing online file. The local one exists.
- noAB={
- notifTot <- notifLocal %>% filter(.data$action == TRUE) %>% mutate(status = "info")
- },
- # missing the local file. The online one exists.
- AnoB={
- notifOnline <- notifOnline %>%
- dplyr::slice_head(n=5)
- notifTot <- notifOnline %>% filter(.data$action == TRUE) %>% mutate(status = "danger")
- notifOnline %>% filter(.data$action == TRUE) %>% write.csv(file=file, quote = FALSE, row.names = FALSE)
- },
- # both files exist.
- AB={
- notifTot <- left_join(notifOnline %>% mutate(status = "danger"),
- notifLocal%>% mutate(status = "info"), by="nots") %>%
- mutate(status = replace_na(.data$status.y,"danger")) %>%
- rename(href = .data$href.x,
- action = .data$action.x) %>%
- select(nots, href, action, status) %>%
- arrange(.data$status) %>%
- filter(.data$action == TRUE) %>%
- dplyr::slice_head(n=5)
- notifTot %>% select(-.data$status) %>% write.csv(file=file, quote = FALSE, row.names = FALSE)
-
- })
-
- #notifTot <- notifTot[1:(min(5,nrow(notifTot))),]
- return(notifTot)
- }
-
-
- is_online <- function(site="https://www.bibliometrix.org/") {
- tryCatch({
- readLines(site,n=1)
- TRUE
- },
- warning = function(w) invokeRestart("muffleWarning"),
- error = function(e) FALSE)
- }
-
- getFileNameExtension <- function (fn) {
- # remove a path
- splitted <- strsplit(x=fn, split='/')[[1]]
- # or use .Platform$file.sep in stead of '/'
- fn <- splitted [length(splitted)]
- ext <- ''
- splitted <- strsplit(x=fn, split='\\.')[[1]]
- l <-length (splitted)
- if (l > 1 && sum(splitted[1:(l-1)] != '')) ext <-splitted [l]
- # the extention must be the suffix of a non-empty name
- ext
- }
-
- # string preview (stopwords)
- strPreview <- function(string, sep=","){
- str1 <- unlist(strsplit(string, sep))
- str1 <- str1[1:min(c(length(str1),5))]
- str1 <- paste(str1, collapse=sep)
- HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
- }
-
- # string preview (synonyms)
- strSynPreview <- function(string){
- string <- string[1]
- str1 <- unlist(strsplit(string, ";"))
- str1 <- str1[1:min(c(length(str1),5))]
- str1 <- paste(paste(str1[1], " <- ",collapse=""),paste(str1[-1], collapse=";"), collapse="")
- HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
- }
-
- # from ggplot to plotly
- plot.ly <- function(g, flip=FALSE, side="r", aspectratio=1, size=0.15,data.type=2, height=0){
-
- g <- g + labs(title = NULL)
- # a <- ggplot_build(g)$data
- #
- # ymin <- unlist(lapply(a, function(l){
- # if ("y" %in% names(l)){
- # min(l["y"])
- # }
- # })) %>% min(na.rm=TRUE)
- #
- # ymax <- unlist(lapply(a, function(l){
- # if ("y" %in% names(l)){
- # max(l["y"])
- # }
- # })) %>% max(na.rm=TRUE)
- #
- # xmin <- unlist(lapply(a, function(l){
- # if ("x" %in% names(l)){
- # min(l["x"])
- # }
- # })) %>% min(na.rm=TRUE)
- #
- # xmax <- unlist(lapply(a, function(l){
- # if ("x" %in% names(l)){
- # max(l["x"])
- # }
- # })) %>% max(na.rm=TRUE)
- #
- # if (isTRUE(flip)){
- # xrange <- c(ymin,ymax)
- # yrange <- c(xmin,xmax)
- # }else{
- # yrange <- c(ymin,ymax)
- # xrange <- c(xmin,xmax)
- # }
- #
- #
- # sizex = diff(xrange)*size
- # sizey = diff(yrange)*size*aspectratio
- #
- # y <- min(yrange)+0.2
- #
- # if (side=="l"){
- # x <- min(xrange)+0.2
- # }else{
- # x <- max(xrange)-0.2-sizex
- # }
-
- ggplotly(g, tooltip = "text") %>%
- config(displaylogo = FALSE,
- modeBarButtonsToRemove = c(
- 'sendDataToCloud',
- 'pan2d',
- 'select2d',
- 'lasso2d',
- 'toggleSpikelines',
- 'hoverClosestCartesian',
- 'hoverCompareCartesian',
- 'toImage'
- )) #%>%
- # layout(
- # images = list(
- # source = raster2uri(as.raster(values$logo)),
- # x = x, y = y+height,
- # sizex = sizex, sizey = sizey,
- # xref = "x", yref = "y",
- # xanchor = "left", yanchor = "bottom",
- # sizing = "stretch"
- # )
- # )
- }
-
- freqPlot <- function(xx,x,y, textLaby,textLabx, title){
-
-
- xl <- c(max(xx[,x])-0.02-diff(range(xx[,x]))*0.125, max(xx[,x])-0.02)+0.5
- yl <- c(1,1+length(unique(xx[,y]))*0.125)
-
- Text <- paste(textLaby,": ",xx[,y],"\n",textLabx, ": ",xx[,x])
-
- g <- ggplot(xx, aes(x =xx[,x], y = xx[,y], label = xx[,x], text=Text)) +
- geom_segment(aes(x = 0, y = xx[,y], xend = xx[,x], yend = xx[,y]), color = "grey50") +
- geom_point(aes(color=-xx[,x], size=xx[,x]), show.legend = FALSE) +
- scale_radius(range=c(7, 15))+
- geom_text(color = "white", size = 3) +
- scale_y_discrete(limits = rev(xx[,y])) +
- scale_fill_continuous(type = "gradient")+
- labs(title=title, y = textLaby)+
- labs(x = textLabx)+
- expand_limits(y= c(1, length(xx[,y]) + 1))+
- theme_minimal()+
- theme(axis.text.y = element_text(angle=0, hjust=0)) +
- annotation_custom(values$logoGrid, xmin = xl[1], xmax = xl[2], ymin = yl[1], ymax = yl[2])
-
- return(g)
- }
-
- emptyPlot<-function(errortext){
- g=ggplot()+
- theme_void() + theme(legend.position="none")+
- annotate("text", x = 4, y = 25, label = errortext, size=10)
- plot(g)
- }
-
- count.duplicates <- function(DF){
- x <- do.call('paste', c(DF, sep = '\r'))
- ox <- order(x)
- rl <- rle(x[ox])
- cbind(DF[ox[cumsum(rl$lengths)],,drop=FALSE],count = rl$lengths)
-
- }
-
- reduceRefs<- function(A){
-
- ind=unlist(regexec("*V[0-9]", A))
- A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
- ind=unlist(regexec("*DOI ", A))
- A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
- return(A)
- }
-
-
- initial <- function(values){
- values$results <- list("NA")
- values$log <- "working..."
- values$load <- "FALSE"
- values$field = values$cocngrams = "NA"
- values$citField = values$colField = values$citSep= "NA"
- values$NetWords = values$NetRefs = values$ColNetRefs=matrix(NA,1,1)
- values$Title <- "Network"
- values$Histfield <- "NA"
- values$histlog <- "working..."
- values$kk <- 0
- values$histsearch <- "NA"
- values$citShortlabel <- "NA"
- values$S <- list("NA")
- values$GR <- "NA"
-
- return(values)
- }
-
-
-
-
- observe({
- if (!(input$sidebarmenu %in% c("biblioshinyy","mainInfo")) & !isTRUE(values$checkControlBar)){
- updateControlbar("controlbar2")
- values$checkControlBar <- TRUE
- #updateControlbarMenu("item_controlbar")
- }
- if ((input$sidebarmenu %in% c("biblioshinyy","mainInfo")) & isTRUE(values$checkControlBar)){
- updateControlbar("controlbar2")
- values$checkControlBar <- FALSE
- }
- })
-
- # observe({
- # if( input$sidebarmenu != "biblioshinyy"){
- # shinyjs::addCssClass(selector = "aside.control-sidebar", class = "control-sidebar-collapse")
- # } else{
- # shinyjs::removeCssClass(selector = "aside.control-sidebar", class = "control-sidebar-collapse")
- # }
- # })
-
- output$controlbar <- renderUI({
- controlbarMenu(
- controlbarItem(
- h2(strong("Options"),align="center"),
- fluidPage(
- fluidRow(
- column(width = 1),
- column(width=11,
- ## Load Data ----
- conditionalPanel(condition = 'input.sidebarmenu == "loadData"',
- h3(strong("Import or Load ")),
- #br(),
- selectInput(
- "load",
- label = "Please, choose what to do",
- choices = c(
- " " = "null",
- "Import raw file(s)" = "import",
- "Load bibliometrix file(s)" = "load",
- "Use a sample collection" = "demo"
- ),
- selected = "null"
- ),
- conditionalPanel(
- condition = "input.load == 'demo'",
- helpText(h4(strong("The use of bibliometric approaches in business and management disciplines.")),
- h5(strong("Dataset 'Management'")),
- em("A collection of scientific articles about the use of bibliometric approaches",
- "in business and management disciplines."),
- br(),
- em("Period: 1985 - 2020
- , Source WoS.")
- )
- ),
- #br(),
- conditionalPanel(
- condition = "input.load == 'import'",
- selectInput(
- "dbsource",
- label = "Database",
- choices = c(
- "Web of Science (WoS/WoK)" = "isi",
- "Scopus" = "scopus",
- "Dimensions" = "dimensions",
- "Lens.org" = "lens",
- "PubMed" = "pubmed",
- "Cochrane Library" = "cochrane"
- ),
- selected = "isi"
- )
- ),
- conditionalPanel(
- condition = "input.load != 'null' & input.load != 'demo'",
- conditionalPanel(
- condition = "input.load == 'load'",
- helpText(em("Load a collection in XLSX or R format previously exported from bibliometrix")
- )),
- fileInput(
- "file1",
- "Choose a file",
- multiple = FALSE,
- accept = c(
- ".csv",
- ".txt",
- ".ciw",
- ".bib",
- ".xlsx",
- ".zip",
- ".xls",
- ".rdata",
- ".rda",
- ".rds"
- )
- )
- ),
- #h6("Here accept single .txt/.bib/.csv/.xslx/.RData files, or multiple .txt/.bib/.csv files compressed in a single .zip archive."),
- conditionalPanel(condition = "input.load != 'null'",
- actionButton("applyLoad", strong("START"),
- style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%"),
- width = "100%"),
- tags$hr(),
-
- uiOutput("textLog"),
- #shinycssloaders::withSpinner(verbatimTextOutput("log")),
-
- tags$hr(),
-
- h3(strong(
- "Export collection"
- )),
- #br(),
-
- selectInput(
- 'save_file',
- 'Save as:',
- choices = c(
- ' ' = 'null',
- 'Excel' = 'xlsx',
- 'R Data Format' = 'RData'
- ),
- selected = 'null'
- ),
- conditionalPanel(condition = "input.save_file != 'null'",
- downloadButton("collection.save", strong("Export"),
- style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%")
- )
- ),
- ## Gathering Data ----
- conditionalPanel(condition = 'input.sidebarmenu == "gathData"',
- h3(strong(
- "Gather data using APIs "
- )),
- br(),
-
- selectInput(
- "dbapi",
- label = "Database",
- choices = c("DS Dimensions" = "ds",
- "PubMed" = "pubmed"),
- selected = "pubmed"
- ),
- ## Dimenions API
- conditionalPanel(
- condition = "input.dbapi == 'ds'",
- br(),
- actionButton("dsShow", h5(strong("1. Configure API request")),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- h5(tags$b("Your Query")),
- verbatimTextOutput("queryLog2", placeholder = FALSE),
- h5(tags$b("Documents returned using your query")),
- verbatimTextOutput("sampleLog2", placeholder = FALSE),
- #
- #
- # uiOutput("sliderLimit"),
-
-
- ),
- ### Pubmed API
- conditionalPanel(
- condition = "input.dbapi == 'pubmed'",
- br(),
- actionButton("pmShow", h5(strong("1. Configure API request")),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- h5(tags$b("Your Query")),
- verbatimTextOutput("pmQueryLog2", placeholder = FALSE),
- h5(tags$b("Documents returned using your query")),
- verbatimTextOutput("pmSampleLog2", placeholder = FALSE),
-
- ),
- tags$hr(),
- #h4(em(strong("Gather metadata"))),
- actionButton("apiApply", h5(strong("2. Download metadata")),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- tags$hr(),
-
- h3(strong(
- "Export a bibliometrix file "
- )),
- br(),
-
- selectInput(
- 'save_file_api',
- 'Save as:',
- choices = c(
- ' ' = 'null',
- 'Excel' = 'xlsx',
- 'R Data Format' = 'RData'
- ),
- selected = 'null'
- ),
- conditionalPanel(condition = "input.save_file_api != 'null'",
- downloadButton("collection.save_api", strong("Export"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Filters ----
- conditionalPanel(condition = 'input.sidebarmenu == "filters"',
- h3(strong("Filters")),
- br(),
- actionButton("applyFilter", strong("Run"),style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%",
- icon = fa_i(name ="play")),
- h5(" "),
- #br(),
- #span(h5((strong("Dataset Overview "))),style="color:CornflowerBlue"),
- box(h6(htmlOutput("textDim")),
- width = "100%"),
- # box(h5(htmlOutput("textDim")),
- # width = "100%"),
- #htmlOutput("textDim"),
- br(),
- #uiOutput("textDim"),
- uiOutput("selectLA"),
- uiOutput("sliderPY"),
- uiOutput("selectType"),
- uiOutput("sliderTCpY"),
- #uiOutput("selectSource"),
- selectInput("bradfordSources",
- label = "Source by Bradford Law Zones",
- choices = c("Core Sources"="core",
- "Core + Zone 2 Sources"="zone2",
- "All Sources"="all"),
- selected = "all")
- ),
- ## Annual Scientific Prod ----
- conditionalPanel(condition = 'input.sidebarmenu == "annualScPr"',
- br(),
- h4(strong("Annual Growth Rate")),
- br(),
- verbatimTextOutput("CAGR", placeholder = TRUE)
- ),
- br(),
- br(),
- conditionalPanel(condition = 'input.sidebarmenu == "annualScPr"',
- selectInput(
- 'ASPdpi',
- label = h4(strong("Export plot")),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- )
- ),
- br(),
- br(),
- conditionalPanel(condition = 'input.sidebarmenu == "annualScPr" & input.ASPdpi != "null"',
- #h4(em(strong("Height (in inches)")), align="center"),
- sliderInput(
- 'ASPh',
- label =h4(em(strong("Height (in inches)"))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("ASPplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px; vertical-align: 'middle';font-size: 20px;",
- width = "100%")
- ),
- ## Average Cit Per Year ----
- conditionalPanel(condition = 'input.sidebarmenu == "averageCitPerYear"',
- selectInput(
- 'ACpYdpi',
- h4(strong("Export plot"), align ="center"),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.ACpYdpi != 'null'",
- sliderInput(
- 'ACpYh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("ACpYplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%")
- )
- ),
- ## Three field Plot ----
- conditionalPanel(condition = 'input.sidebarmenu == "threeFieldPlot"',
- # actionButton("apply3F", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- #collapsed = TRUE,
- fluidRow(
- (column(6, selectInput("CentralField",
- label = "Middle Field",
- choices = c("Authors" = "AU",
- "Affiliations" = "AU_UN",
- "Countries"="AU_CO",
- "Keywords" = "DE",
- "Keywords Plus" = "ID",
- "Titles" = "TI_TM",
- "Abstract" = "AB_TM",
- "Sources" = "SO",
- "References" = "CR",
- "Cited Sources" = "CR_SO"),
- selected = "AU"))),
- (column(6,numericInput("CentralFieldn",
- label=("Number of items"),
- min = 1, max = 50, step = 1, value = 20)))),
- fluidRow(
- (column(6,selectInput("LeftField",
- label = "Left Field",
- choices = c("Authors" = "AU",
- "Affiliations" = "AU_UN",
- "Countries"="AU_CO",
- "Keywords" = "DE",
- "Keywords Plus" = "ID",
- "Titles" = "TI_TM",
- "Abstract" = "AB_TM",
- "Sources" = "SO",
- "References" = "CR",
- "Cited Sources" = "CR_SO"),
- selected = "CR"))),
- (column(6, numericInput("LeftFieldn",
- label=("Number of items"),
- min = 1, max = 50, step = 1, value = 20)))),
- fluidRow(
- (column(6,selectInput("RightField",
- label = "Right Field",
- choices = c("Authors" = "AU",
- "Affiliations" = "AU_UN",
- "Countries"="AU_CO",
- "Keywords" = "DE",
- "Keywords Plus" = "ID",
- "Titles" = "TI_TM",
- "Abstract" = "AB_TM",
- "Sources" = "SO",
- "References" = "CR",
- "Cited Sources" = "CR_SO"),
- selected = "DE"))),
- (column(6,numericInput("RightFieldn",
- label=("Number of items"),
- min = 1, max = 50, step = 1, value = 20))))
- )),
- ## Relevant Sources ----
- conditionalPanel(condition = 'input.sidebarmenu == "relevantSources"',
- # actionButton("applyMRSources", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- h4(strong("Parameters: ")),
- " ",
- numericInput("MostRelSourcesK",
- label=("Number of Sources"),
- value = 10),
- selectInput(
- 'MRSdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MRSdpi != 'null'",
- sliderInput(
- 'MRSh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MRSplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Local Cited Sources ----
- conditionalPanel(condition ='input.sidebarmenu == "localCitedSources"',
- # actionButton("applyMLCSources", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%")
- h4(strong("Parameters: ")),
- " ",
- numericInput("MostRelCitSourcesK",
- label=("Number of Sources"),
- value = 10),
- selectInput(
- 'MLCSdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MLCSdpi != 'null'",
- sliderInput(
- 'MLCSh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MLCSplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
- width = "100%")
- )
- ),
- ## Bradford Law ----
- conditionalPanel(condition ='input.sidebarmenu == "bradford"',
- selectInput(
- 'BLdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.BLdpi != 'null'",
- sliderInput(
- 'BLh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("BLplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )),
- ## Source Impact ----
- conditionalPanel(condition ='input.sidebarmenu == "sourceImpact"',
- # actionButton("applyHsource", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput("HmeasureSources",
- label = "Impact measure",
- choices = c("H-Index"="h",
- "G-Index"="g",
- "M-Index"="m",
- "Total Citation"="tc"),
- selected = "h"),
- " ",
- numericInput("Hksource",
- label=("Number of sources"),
- value = 10)),
- selectInput(
- 'SIdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.SIdpi != 'null'",
- sliderInput(
- 'SIh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("SIplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Source Dynamics ----
- conditionalPanel(condition ='input.sidebarmenu == "sourceDynamics"',
- # actionButton("applySOGrowth", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput("cumSO", "Occurrences",
- choices = c("Cumulate" = "Cum",
- "Per year" = "noCum"),
- selected = "Cum"),
- # selectInput("SOse", "Confidence Interval",
- # choices = c("Yes" = "Yes",
- # "No" = "No"),
- # selected = "No"),
- hr(),
- sliderInput("topSO", label = "Number of Sources", min = 1, max = 50, step = 1, value = c(1,5))),
- selectInput(
- 'SDdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.SDdpi != 'null'",
- sliderInput(
- 'SDh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("SDplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )),
- ## Most relevant Authors ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostRelAuthors"',
- # actionButton("applyMRAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- numericInput("MostRelAuthorsK",
- label=("Number of Authors"),
- value = 10),
- " ",
- selectInput("AuFreqMeasure",
- label = "Frequency measure",
- choices = c("N. of Documents "="t",
- "Percentage"="p",
- "Fractionalized Frequency"="f"),
- selected = "t")),
- selectInput(
- 'MRAdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MRAdpi != 'null'",
- sliderInput(
- 'MRAh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MRAplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Local Cited Authors ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitedAuthors"',
- # actionButton("applyMLCAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(strong("Parameters: ")),
- " ",
- numericInput("MostCitAuthorsK",
- label=("Number of Authors"),
- value = 10),
- selectInput(
- 'MLCAdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MLCAdpi != 'null'",
- sliderInput(
- 'MLCAh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MLCAplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Authors production over time ----
- conditionalPanel(condition = 'input.sidebarmenu == "authorsProdOverTime"',
- # actionButton("applyAUoverTime", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(strong("Parameters: ")),
- " ",
- numericInput("TopAuthorsProdK",
- label=("Number of Authors"),
- value = 10),
- selectInput(
- 'APOTdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.APOTdpi != 'null'",
- sliderInput(
- 'APOTh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("APOTplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Lotka law ----
- conditionalPanel(condition = 'input.sidebarmenu == "lotka"',
- selectInput(
- 'LLdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.LLdpi != 'null'",
- sliderInput(
- 'LLh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("LLplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Author Impact ----
- conditionalPanel(condition = 'input.sidebarmenu == "authorImpact"',
- # actionButton("applyHAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput("HmeasureAuthors",
- label = "Impact measure",
- choices = c("H-Index"="h",
- "G-Index"="g",
- "M-Index"="m",
- "Total Citation"="tc"),
- selected = "h"),
- " ",
- numericInput("Hkauthor",
- label=("Number of authors"),
- value = 10)),
- selectInput(
- 'AIdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.AIdpi != 'null'",
- sliderInput(
- 'AIh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("AIplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Relevant Affiliations ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostRelAffiliations"',
- # actionButton("applyMRAffiliations", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput("disAff",
- label = "Affiliation Name Disambiguation",
- choices = c("Yes"="Y",
- "No"="N"),
- selected = "Y"),
- " ",
- numericInput("MostRelAffiliationsK",
- label=("Number of Affiliations"),
- value = 10)),
- selectInput(
- 'AFFdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.AFFdpi != 'null'",
- sliderInput(
- 'AFFh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("AFFplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Corresponding Author country ----
- conditionalPanel(condition = 'input.sidebarmenu == "correspAuthorCountry"',
- # actionButton("applyCAUCountries", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(strong("Parameters: ")),
- numericInput("MostRelCountriesK",
- label=("Number of Countries"),
- value = 20),
- selectInput(
- 'MRCOdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MRCOdpi != 'null'",
- sliderInput(
- 'MRCOh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MRCOplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Country Scientific Production ----
- conditionalPanel(condition = 'input.sidebarmenu == "countryScientProd"',
- selectInput(
- 'CSPdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.CSPdpi != 'null'",
- sliderInput(
- 'CSPh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("CSPplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Cited Countries ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostCitedCountries"',
- # actionButton("applyMCCountries", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput("CitCountriesMeasure",
- label = "Measure",
- choices = c("Total Citations"="TC",
- "Average Citations per Year"="TCY"),
- selected = "TC"),
- " ",
- numericInput("MostCitCountriesK",
- label=("Number of Countries"),
- value = 10)),
- selectInput(
- 'MCCdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MCCdpi != 'null'",
- sliderInput(
- 'MCCh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MCCplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Global Cited Documents
- conditionalPanel(condition = 'input.sidebarmenu == "mostGlobalCitDoc"',
- # actionButton("applyMGCDocuments", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- br(),
- br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- numericInput("MostCitDocsK",
- label=("Number of Documents"),
- value = 10),
- " ",
- selectInput("CitDocsMeasure",
- label = "Measure",
- choices = c("Total Citations"="TC",
- "Total Citations per Year"="TCY"),
- selected = "TC")),
- selectInput(
- 'MGCDdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MGCDdpi != 'null'",
- sliderInput(
- 'MGCDh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MGCDplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- # Most Local Cited Document
- conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitDoc"',
- # actionButton("applyMLCDocuments", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- br(),
- br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- numericInput("MostLocCitDocsK",
- label=("Number of Documents"),
- value = 10),
- " ",
- selectInput(inputId = "LocCitSep",
- label = "Field separator character",
- choices = c(";" = ";",
- ". " = ". ",
- "," = ","),
- selected = ";")),
- selectInput(
- 'MLCDdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MLCDdpi != 'null'",
- sliderInput(
- 'MLCDh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MLCDplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Most Local Cited References ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitRef"',
- # actionButton("applyMLCReferences", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- numericInput("MostCitRefsK",
- label=("Number of Documents"),
- value = 10),
- " ",
- selectInput(inputId = "CitRefsSep",
- label = "Field separator character",
- choices = c(";" = ";",
- ". " = ". ",
- "," = ","),
- selected = ";")),
- selectInput(
- 'MLCRdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MLCRdpi != 'null'",
- sliderInput(
- 'MLCRh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MLCRplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Reference spectroscopy
- conditionalPanel(condition = 'input.sidebarmenu == "ReferenceSpect"',
- # actionButton("applyRPYS", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- br(),
- br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput(inputId = "rpysSep",
- label = "Field separator character",
- choices = c(";" = ";",
- ". " = ". ",
- "," = ","),
- selected = ";"),
- h4(em(strong("Time slice"))),
- fluidRow(column(6,
- numericInput(inputId = "rpysMinYear",
- label = "Starting Year",
- value = NA,
- step = 1)),
- column(6,
- numericInput(inputId = "rpysMaxYear",
- label = "End Year",
- value = NA,
- step = 1)
- ))),
- selectInput(
- 'RSdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.RSdpi != 'null'",
- sliderInput(
- 'RSh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("RSplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
-
- )
- ),
- ## Most Frequent Words ----
- conditionalPanel(condition = 'input.sidebarmenu == "mostFreqWords"',
- # actionButton("applyMFWords", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- selectInput("MostRelWords", "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.MostRelWords == 'AB' |input.MostRelWords == 'TI'",
- selectInput("MRWngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- numericInput("MostRelWordsN", label = "Number of words", min = 2, max = 100, step = 1, value = 10),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("MostRelWordsStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.MostRelWordsStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("MostRelWordsStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("MostRelWordsSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("MostRelWordsStopPreview"))
- ),
- selectInput("MRWSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.MRWSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("MRWSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("MRWSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("MRWSynPreview"))
- )),
- selectInput(
- 'MRWdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.MRWdpi != 'null'",
- sliderInput(
- 'MRWh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("MRWplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"))
- ),
- ## Word cloud ----
- conditionalPanel(condition = 'input.sidebarmenu == "wcloud"',
- # actionButton("applyWordCloud", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(em(strong(" "))),
- " ",
- selectInput("summaryTerms", "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.summaryTerms == 'AB' |input.summaryTerms == 'TI'",
- selectInput("summaryTermsngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- #hr(),
- numericInput("n_words", label = "Number of words", min = 10, max = 500, step = 1, value = 50),
- #hr(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("WCStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.WCStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("WCStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
- selectInput("WCSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ",")
- #,h5(htmlOutput("WCStopPreview"))
- ),
- selectInput("WCSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.WCSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("WCSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("WCSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ",")
- #,h5(htmlOutput("WCSynPreview"))
- )),
- hr(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- selectInput("measure", "Word occurrence by",
- choices = c("Frequency" = "freq",
- "Square root" = "sqrt",
- "Log" = "log",
- "Log10" = "log10"),
- selected = "freq")
- ),
- column(6,
- selectInput("wcShape", "Shape",
- choices = c("Circle" = "circle",
- "Cardiod" = "cardioid",
- "Diamond" = "diamond",
- "Pentagon" = "pentagon",
- "Star" = "star",
- "Triangle-forward" = "triangle-forward"
- ,"Triangle" = "triangle"),
- selected = "circle")
- )),
- fluidRow(column(6,
- selectInput("font", label = "Font type",
- choices = c("Impact", "Comic Sans MS (No plz!)" = "Comic Sans MS",
- "Arial", "Arial Black", "Tahoma", "Verdana", "Courier New",
- "Georgia", "Times New Roman", "Andale Mono"))
- ),
- column(6,
- selectInput("wcCol", "Text colors",
- choices = c("Random Dark" = "random-dark",
- "Random Light" = "random-light"),
- selected = "random-dark")
- )),
- fluidRow(column(6,
- numericInput("scale", label = "Font size", min=0.2,max=5,step=0.1,value=1)
- ),
- column(6,
- numericInput("ellipticity", label = "Ellipticity", min=0,max=1,step=0.05,value=0.65)
- )),
- fluidRow(column(6,
- numericInput("padding", label = "Padding", min = 0, max = 5, value = 1, step = 1)
- ),
- column(6,
- numericInput("rotate", label = "Rotate", min = 0, max = 20, value = 0, step = 1)
- ))
- )
- ),
- ## Tree Map ----
- conditionalPanel(condition = 'input.sidebarmenu == "treemap"',
- # actionButton("applyTreeMap", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- selectInput("treeTerms", "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.treeTerms == 'AB' |input.treeTerms == 'TI'",
- selectInput("treeTermsngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- numericInput("treen_words", label = "Number of words", min = 10, max = 200, step = 5, value = 50),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("TreeMapStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TreeMapStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("TreeMapStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TreeMapSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TreeMapStopPreview"))
- ),
- selectInput("TreeMapSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TreeMapSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("TreeMapSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TreeMapSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TreeMapSynPreview"))
- )
- )
- ),
- ## Word dynamics ----
- conditionalPanel(condition = 'input.sidebarmenu == "wordDynamics"',
- # actionButton("applyWD", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- selectInput("growthTerms", "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("cumTerms", "Occurrences",
- choices = c("Cumulate" = "Cum",
- "Per year" = "noCum"),
- selected = "Cum"),
- conditionalPanel(condition = "input.growthTerms == 'AB' |input.growthTerms == 'TI'",
- selectInput("growthTermsngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- sliderInput("topkw", label = "Number of words", min = 1, max = 100, step = 1, value = c(1,10))),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("WDStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.WDStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("WDStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("WDSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("WDStopPreview"))
- ),
- selectInput("WDSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.WDSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("WDSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("WDSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("WDSynPreview"))
- )),
- hr(),
- selectInput(
- 'WDdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.WDdpi != 'null'",
- sliderInput(
- 'WDh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("WDplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
-
- )
- ),
- ## Trend Topic ----
- conditionalPanel(condition = 'input.sidebarmenu == "trendTopic"',
- # actionButton("applyTrendTopics", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- #h4(em(strong("Method Parameters:"))),
- selectInput("trendTerms", "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.trendTerms == 'TI' | input.trendTerms == 'AB'",
- selectInput("trendTermsngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- conditionalPanel(
- condition = "input.trendTerms == 'TI' | input.trendTerms == 'AB'",
- selectInput("trendStemming", label="Word Stemming",
- choices = c("Yes" = TRUE,
- "No" = FALSE),
- selected = FALSE)),
- uiOutput("trendSliderPY"),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("TTStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TTStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("TTStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TTSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TTStopPreview"))
- ),
- selectInput("TTSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TTSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("TTSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TTSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TTSynPreview"))
- )),
- hr(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- #uiOutput("trendMinFreq"),
- fluidRow(column(6,
- numericInput("trendMinFreq", label = "Word Minimum Frequency", min = 0, max = 100, value = 5, step = 1),
- ),
- column(6,
- numericInput("trendNItems", label = "Number of Words per Year", min = 1, max = 20, step = 1, value = 5)
- ))),
- #sliderInput("trendSize", label = "Word label size", min = 0, max = 20, step = 1, value = 5),
- selectInput(
- 'TTdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "Please select a dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.TTdpi != 'null'",
- sliderInput(
- 'TTh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("TTplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Coupling ----
- conditionalPanel(condition = 'input.sidebarmenu == "coupling"',
- # actionButton("applyCM", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(em(strong(" "))),
- " ",
- selectInput("CManalysis",
- label = "Unit of Analysis",
- choices = c("Documents" = "documents",
- "Authors" = "authors",
- "Sources" = "sources"),
- selected = "documents"),
- " ",
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- #selectInput("cmNP",
- # label = h4(em(strong("Parameters: "))),
- # choices = c("Hide Parameters" = "hide",
- # "Show Parameters" = "show"),
- # selected = "hide"),
- #conditionalPanel(condition = "input.cmNP == 'show'",
- #" ",
- selectInput("CMfield",
- label = "Coupling measured by",
- choices = c("References" ="CR",
- "Keywords Plus" = "ID",
- "Author's Keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "CR"),
- conditionalPanel(condition = "input.CMfield == 'TI' | input.CMfield == 'AB'",
- selectInput("CMstemming", label="Word Stemming",
- choices = c("Yes" = TRUE,
- "No" = FALSE),
- selected = FALSE)),
- selectInput("CMimpact",
- label = "Impact measure",
- choices = c("Local Citation Score" = "local",
- "Global Citation Score" = "global"),
- selected = "local"),
- selectInput("CMlabeling",
- label = "Cluster labeling by",
- choices = c("None" = "none",
- "Keyword Plus" = "ID",
- "Authors' keywords" = "DE",
- "Title terms" = "TI",
- "Abstract terms" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.CMlabeling == 'TI' | input.CMlabeling == 'AB'",
- selectInput("CMngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- fluidRow(column(6,
- numericInput("CMn", label="Number of Units\n ",value=250,min=50,max=5000,step=1)),
- column(6,
- numericInput("CMfreq", label="Min Cluster Freq. ",value=5,min=1,max=100,step=1))),
- fluidRow(column(6,
- numericInput("CMn.labels", label="Labels per cluster",value=3,min=1,max=10,step=1)),
- column(6,
- numericInput("sizeCM", label="Label size",value=0.3,min=0.0,max=1,step=0.05)))
- ),
-
- selectInput(
- 'CMdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "Dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.CMdpi != 'null'",
- sliderInput(
- 'CMh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("CMplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Co-Occurence Network ----
- conditionalPanel(condition = 'input.sidebarmenu == "coOccurenceNetwork"',
- # actionButton("applyCoc", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- #" ",
- #h4(em(strong("Network Parameters: "))),
- selectInput("field",
- "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's Keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.field == 'TI' | input.field == 'AB'",
- selectInput("cocngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("COCStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.COCStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("COCStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("COCSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("COCStopPreview"))
- ),
- selectInput("COCSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.COCSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("COCSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("COCSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("COCSynPreview"))
- )),
- br(),
- box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- selectInput("layout",
- label = "Network Layout",
- choices = c("Automatic layout"="auto",
- "Circle"="circle",
- "Fruchterman & Reingold"="fruchterman",
- "Kamada & Kawai"="kamada",
- "MultiDimensional Scaling"="mds",
- "Sphere"="sphere",
- "Star"="star"),
- selected = "auto")
- ),
- column(6,
- selectInput("cocCluster",
- label = "Clustering Algorithm",
- choices = c("None" = "none",
- "Edge Betweenness" = "edge_betweenness",
- "InfoMap" = "infomap",
- "Leading Eigenvalues" = "leading_eigen",
- "Louvain" = "louvain",
- "Spinglass" = "spinglass",
- "Walktrap" = "walktrap"),
- selected = "louvain")
- )),
- fluidRow(column(6,
- selectInput("normalize",
- label = "Normalization",
- choices = c("none",
- "association",
- "jaccard",
- "salton",
- "inclusion",
- "equivalence"),
- selected = "association")
- ),
- column(6,
- selectInput("cocyears",
- label = "Node Color by Year",
- choices = c("No" = "No",
- "Yes"= "Yes"),
- selected = "No")
- )),
- fluidRow(column(6,
- numericInput(inputId = "Nodes",
- label = "Number of Nodes",
- min = 5,
- max = 1000,
- value = 50,
- step = 1)
- ),
- column(6,
- numericInput(inputId = "coc.repulsion",
- label = "Repulsion Force",
- min = 0,
- max = 1,
- value = 0.1,
- step = 0.1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="coc.isolates",
- label = "Remove Isolated Nodes",
- choices = c("Yes" = "yes",
- "No" = "no"),
- selected = "yes")
- ),
- column(6,
- numericInput("edges.min",
- label=("Minimum Number of Edges"),
- value = 2,
- step = 1,
- min = 0)
- )
- )),
- #uiOutput("Focus"),
- br(),
- #h4(em(strong("Graphical Parameters: "))),
- #br(),
- box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- numericInput(inputId = "cocAlpha",
- label = "Opacity",
- min = 0,
- max = 1,
- value = 0.7,
- step=0.05)
- ),
- column(6,
- numericInput(inputId = "Labels",
- label = "Number of labels",
- min = 0,
- max = 1000,
- value = 50,
- step = 1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="label.cex",
- label = "Label cex",
- choices = c("Yes",
- "No"),
- selected = "Yes")
- ),
- column(6,
- selectInput(inputId ="coc.shape",
- label = "Node Shape",
- choices = c(
- "Box"="box",
- "Circle"="circle",
- "Dot"="dot",
- "Ellipse"="ellipse",
- "Square"="square",
- "Text"="text"),
- selected = "dot")
- )),
- fluidRow(column(6,
- numericInput(inputId = "labelsize",
- label = "Label size",
- min = 0.0,
- max = 20,
- value = 6,
- step = 0.10)
- ),
- column(6,
- numericInput(
- inputId = "edgesize",
- label = "Edge size",
- min = 0.5,
- max = 20,
- value = 5,
- step=0.5)
- )),
- fluidRow(column(6,
- selectInput(inputId ="coc.shadow",
- label = "Node shadow",
- choices = c("Yes",
- "No"),
- selected = "No")
- ),
- column(6,
- selectInput(inputId ="coc.curved",
- label = "Curved edges",
- choices = c("Yes",
- "No"),
- selected = "No")
-
- )
- )
- ),
- br(),
- fluidRow(column(6,
- downloadButton("network.coc", strong("Save Pajek"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- ),
- column(6,
- downloadButton("networkCoc.fig", strong("Save HTML"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- )
- )
- ),
- ## Thematic Map ----
- conditionalPanel(condition = 'input.sidebarmenu == "thematicMap"',
- # actionButton("applyTM", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(em(strong(" "))),
- " ",
- selectInput("TMfield",
- label = "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's Keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.TMfield == 'TI' | input.TMfield == 'AB'",
- selectInput("TMngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- conditionalPanel(
- condition = "input.TMfield == 'TI' | input.TMfield == 'AB'",
- selectInput("TMstemming", label="Word Stemming",
- choices = c("Yes" = TRUE,
- "No" = FALSE),
- selected = FALSE)),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("TMStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TMStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("TMStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TMSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TMStopPreview"))
- ),
- selectInput("TMapSynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TMapSynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("TMapSyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TMapSynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TMapSynPreview"))
- )),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- numericInput("TMn", label="Number of Words",value=250,min=50,max=5000,step=1)
- ),
- column(6,
- numericInput("TMfreq", label="Min Cluster Frequency (per thousand docs)",value=5,min=1,max=100,step=1)
- )),
- fluidRow(column(6,
- numericInput("TMn.labels", label="Number of Labels",value=3,min=0,max=10,step=1)
- ),
- column(6,
- numericInput("sizeTM", label="Label size",value=0.3,min=0.0,max=1,step=0.05)
- ))
- ),
- selectInput(
- 'TMdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.TMdpi != 'null'",
- sliderInput(
- 'TMh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("TMplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Thematic Evolution ----
- conditionalPanel(condition = 'input.sidebarmenu == "thematicEvolution"',
- # actionButton("applyTE", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(em(strong(" "))),
- " ",
- selectInput("TEfield",
- label = "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's Keywords" = "DE",
- "Titles" = "TI",
- "Abstracts
- " = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.TEfield == 'TI' | input.TEfield == 'AB'",
- selectInput("TEngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("TEStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TEStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("TEStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TESep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TEStopPreview"))
- ),
- selectInput("TESynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.TESynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("TESyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("TESynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("TESynPreview"))
- )),
- br(),
- box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- numericInput("nTE", label="Number of Words",value=250,min=50,max=5000,step=1)
- ),
- column(6,
- numericInput("fTE", label="Min Cluster Frequency (per thousand docs)",value=5,min=1,max=100,step=1)
- )),
- fluidRow(column(6,
- selectInput("TEmeasure",
- label = "Weight index",
- choices = c("Inclusion Index" = "inclusion",
- "Inclusion Index weighted by Word-Occurrences" = "weighted",
- "Stability Index" = "stability"
- ),
- selected = "weighted")
- ),
- column(6,
- numericInput("minFlowTE", label="Min Weight Index",value=0.1,min=0.02,max=1,step=0.02)
- )),
- fluidRow(column(6,
- numericInput("sizeTE", label="Label size",value=0.3,min=0.0,max=1,step=0.05)
- ),
- column(6,
- numericInput("TEn.labels", label="Number of Labels (for each cluster)",value=1,min=1,max=5,step=1)
- ))
- ),
- br(),
- box(title = p(strong("Time Slices"),style='font-size:16px;color:black;'),
- collapsible = FALSE, width = 15,
- solidHeader = FALSE, collapsed = FALSE,
- numericInput("numSlices", label="Number of Cutting Points",min=1,max=4,value=1),
- "Please, write the cutting points (in year) for your collection",
- uiOutput("sliders")
- )
- ),
- ## Factorial Analysis
- conditionalPanel(condition = 'input.sidebarmenu == "factorialAnalysis"',
- # actionButton("applyCA", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- br(),
- br(),
- selectInput("method",
- label = "Method",
- choices = c("Correspondence Analysis" = "CA",
- "Multiple Correspondence Analysis" = "MCA",
- "Multidimensional Scaling"= "MDS"),
- selected = "MCA"),
- selectInput("CSfield",
- label = "Field",
- choices = c("Keywords Plus" = "ID",
- "Author's Keywords" = "DE",
- "Titles" = "TI",
- "Abstracts" = "AB"),
- selected = "ID"),
- conditionalPanel(condition = "input.CSfield == 'TI' | input.CSfield == 'AB'",
- selectInput("CSngrams",'N-Grams',
- choices = c("Unigrams" = "1",
- "Bigrams" = "2",
- "Trigrams" = "3"),
- selected = 1)),
- br(),
- box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- selectInput("CSStopFile", "Load a list of terms to remove",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.CSStopFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
- ),
- fileInput("CSStop", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("CSSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("CSStopPreview"))
- ),
- selectInput("FASynFile", "Load a list of synonyms",
- choices = c("Yes" = "Y",
- "No" = "N"),
- selected = "N"),
- conditionalPanel(condition = "input.FASynFile == 'Y'",
- helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
- h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
- Rows have to be separated by return separator (\\n)."))
- ),
- fileInput("FASyn", "",
- multiple = FALSE,
- accept = c("text/csv",
- "text/comma-separated-values,text/plain",
- ".csv",
- ".txt")),
-
- selectInput("FASynSep", "File Separator",
- choices = c('Comma ","' = ",",
- 'Semicolon ";"' = ";",
- 'Tab '= "\t"),
- selected = ","),
- h5(htmlOutput("FASynPreview"))
- )),
- #h4(em(strong("FA Parameters: "))),
- br(),
- box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- numericInput("CSn",
- label=("Number of terms"),
- value = 50, step = 1)),
- column(6,
- selectInput("nClustersCS",
- label = "N. of Clusters",
- choices = c("Auto" = "0",
- "2" = "2",
- "3" = "3",
- "4" = "4",
- "5" = "5",
- "6" = "6",
- "7" = "7",
- "8" = "8"),
- selected = "0")))
- ),
- br(),
- box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- #h4(em(strong("Graphical Parameters: "))),
- fluidRow(column(6,
- numericInput(
- inputId = "CSlabelsize",
- label = "Label size",
- min = 5,
- max = 30,
- value = 10)),
- column(6,
- numericInput("CSdoc",
- label=("Num. of documents"),
- value = 5)))
- ),
- selectInput(
- 'FAdpi',
- h4(strong(
- "Export plots as png"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.FAdpi != 'null'",
- sliderInput(
- 'FAh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("FA1plot.save", strong("Term Factorial Map "),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- h4(" "),
- downloadButton("FA2plot.save", strong("Topic Dendrogram "),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- h4(" "),
- downloadButton("FA3plot.save", strong("Most Contributing Map "),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%"),
- h4(" "),
- downloadButton("FA4plot.save", strong("Most Cited Map "),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Co-citation Network ----
- conditionalPanel(condition = 'input.sidebarmenu == "coCitationNetwork"',
- # actionButton("applyCocit", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- #" ",
- #h4(em(strong("Network Parameters: "))),
- selectInput("citField",
- label = "Field",
- choices = c("Papers" = "CR",
- "Authors" = "CR_AU",
- "Sources" = "CR_SO"),
- selected = "CR"),
- selectInput(inputId = "citSep",
- label = "Field separator character",
- choices = c('";" (Semicolon)' = ";",
- '". " (Dot and 3 or more spaces)' = ". ",
- '"," (Comma)' = ","),
- selected = "';'"),
- box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- selectInput("citlayout",
- label = "Network Layout",
- choices = c("Automatic layout"="auto",
- "Circle"="circle",
- "Fruchterman & Reingold"="fruchterman",
- "Kamada & Kawai"="kamada",
- "MultiDimensional Scaling"="mds",
- "Sphere"="sphere",
- "Star"="star"),
- selected = "auto")
- ),
- column(6,
- selectInput("cocitCluster",
- label = "Clustering Algorithm",
- choices = c("None" = "none",
- "Edge Betweenness" = "edge_betweenness",
- "InfoMap" = "infomap",
- "Leading Eigenvalues" = "leading_eigen",
- "Louvain" = "louvain",
- "Spinglass" = "spinglass",
- "Walktrap" = "walktrap"),
- selected = "louvain")
- )),
- fluidRow(column(6,
- numericInput(inputId = "citNodes",
- label = "Number of Nodes",
- min = 5,
- max = 1000,
- value = 50,
- step = 1)
- ),
- column(6,
- numericInput(inputId = "cocit.repulsion",
- label = "Repulsion Force",
- min = 0,
- max = 1,
- value = 0.1,
- step = 0.1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="cit.isolates",
- label = "Remove Isolated Nodes",
- choices = c("Yes" = "yes",
- "No" = "no"),
- selected = "yes")
- ),
- column(6,
- numericInput("citedges.min",
- label=("Minimum Number of Edges"),
- value = 2,
- step = 1,
- min = 0)
- )
- )),
- #uiOutput("Focus"),
- #br(),
- #h4(em(strong("Graphical Parameters: "))),
- #br(),
- box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- selectInput(inputId ="citShortlabel",
- label = "Short Label",
- choices = c("Yes",
- "No"),
- selected = "Yes"),
-
- ),
- column(6,
- numericInput(inputId = "citLabels",
- label = "Number of labels",
- min = 0,
- max = 1000,
- value = 50,
- step = 1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="citlabel.cex",
- label = "Label cex",
- choices = c("Yes",
- "No"),
- selected = "Yes")
- ),
- column(6,
- selectInput(inputId ="cocit.shape",
- label = "Node Shape",
- choices = c(
- "Box"="box",
- "Circle"="circle",
- "Dot"="dot",
- "Ellipse"="ellipse",
- "Square"="square",
- "Text"="text"),
- selected = "dot")
- )),
- fluidRow(column(6,
- numericInput(inputId = "citlabelsize",
- label = "Label size",
- min = 0.0,
- max = 20,
- value = 2,
- step = 0.10)
- ),
- column(6,
- numericInput(
- inputId = "citedgesize",
- label = "Edge size",
- min = 0.5,
- max = 20,
- value = 5,
- step=0.5)
- )),
- fluidRow(column(6,
- selectInput(inputId ="cocit.shadow",
- label = "Node shadow",
- choices = c("Yes",
- "No"),
- selected = "No")
- ),
- column(6,
- selectInput(inputId ="cocit.curved",
- label = "Curved edges",
- choices = c("Yes",
- "No"),
- selected = "No")
-
- )
- )
- ),
- br(),
- fluidRow(column(6,
- downloadButton("network.cocit", strong("Save Pajek"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- ),
- column(6,
- downloadButton("networkCocit.fig", strong("Save HTML"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- )
- )
- ),
- ## Historiograph ----
- conditionalPanel(condition = 'input.sidebarmenu == "historiograph"',
- # actionButton("applyHist", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- #selectInput('save_colnet', 'Save network as:', choices = c('No, thanks!' = 'no_thanks', 'Pajek format' = 'pajek')),
- #conditionalPanel(condition = "input.save_colnet == 'pajek'"
- # br(),
- # br(),
- numericInput(inputId = "histNodes",
- label = "Number of Nodes",
- min = 5,
- max = 100,
- value = 20,
- step = 1),
- " ",
- br(),
- box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE,
- collapsed = FALSE,
- selectInput(inputId = "titlelabel",
- label = "Node label",
- choices = c("Short id (1st Author, Year)" = "FALSE",
- "Document Title" = "TRUE"),
- selected = "FALSE"),
- fluidRow(column(6,
- numericInput(inputId = "histlabelsize",
- label = "Label size",
- min = 0.0,
- max = 20,
- value = 3, step = 1)),
- column(6,
- numericInput(inputId = "histsize",
- label = "Node size",
- min = 0,
- max = 20,
- value = 4, step = 1)))
- ),
- selectInput(
- 'HGdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.HGdpi != 'null'",
- sliderInput(
- 'HGh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("HGplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- ),
- ## Collaboration Network ----
- conditionalPanel(condition = 'input.sidebarmenu == "collabNetwork"',
- # actionButton("applyCol", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- #" ",
- #h4(em(strong("Network Parameters: "))),
- selectInput("colField",
- label = "Field",
- choices = c("Authors" = "COL_AU",
- "Institutions" = "COL_UN",
- "Countries" = "COL_CO"),
- selected = "COL_AU"),
- br(),
- box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- selectInput("collayout",
- label = "Network Layout",
- choices = c("Automatic layout"="auto",
- "Circle"="circle",
- "Fruchterman & Reingold"="fruchterman",
- "Kamada & Kawai"="kamada",
- "MultiDimensional Scaling"="mds",
- "Sphere"="sphere",
- "Star"="star"),
- selected = "auto")
- ),
- column(6,
- selectInput("colCluster",
- label = "Clustering Algorithm",
- choices = c("None" = "none",
- "Edge Betweenness" = "edge_betweenness",
- "InfoMap" = "infomap",
- "Leading Eigenvalues" = "leading_eigen",
- "Louvain" = "louvain",
- "Spinglass" = "spinglass",
- "Walktrap" = "walktrap"),
- selected = "louvain")
- )),
- fluidRow(column(6,
- selectInput("colnormalize",
- label = "Normalization",
- choices = c("none",
- "association",
- "jaccard",
- "salton",
- "inclusion",
- "equivalence"),
- selected = "association")
- )),
- fluidRow(column(6,
- numericInput(inputId = "colNodes",
- label = "Number of Nodes",
- min = 5,
- max = 1000,
- value = 50,
- step = 1)
- ),
- column(6,
- numericInput(inputId = "col.repulsion",
- label = "Repulsion Force",
- min = 0,
- max = 1,
- value = 0.1,
- step = 0.1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="col.isolates",
- label = "Remove Isolated Nodes",
- choices = c("Yes" = "yes",
- "No" = "no"),
- selected = "yes")
- ),
- column(6,
- numericInput("coledges.min",
- label=("Minimum Number of Edges"),
- value = 1,
- step = 1,
- min = 0)
- )
- )),
- #uiOutput("Focus"),
- #h4(em(strong("Graphical Parameters: "))),
- br(),
- box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
- collapsible = TRUE, width = 15,
- solidHeader = FALSE, collapsed = TRUE,
- fluidRow(column(6,
- numericInput(inputId = "colAlpha",
- label = "Opacity",
- min = 0,
- max = 1,
- value = 0.7,
- step=0.05)
- ),
- column(6,
- numericInput(inputId = "colLabels",
- label = "Number of labels",
- min = 0,
- max = 1000,
- value = 50,
- step = 1)
- )),
- fluidRow(column(6,
- selectInput(inputId ="collabel.cex",
- label = "Label cex",
- choices = c("Yes",
- "No"),
- selected = "Yes")
- ),
- column(6,
- selectInput(inputId ="col.shape",
- label = "Node Shape",
- choices = c(
- "Box"="box",
- "Circle"="circle",
- "Dot"="dot",
- "Ellipse"="ellipse",
- "Square"="square",
- "Text"="text"),
- selected = "dot")
- )),
- fluidRow(column(6,
- numericInput(inputId = "collabelsize",
- label = "Label size",
- min = 0.0,
- max = 20,
- value = 2,
- step = 0.10)
- ),
- column(6,
- numericInput(
- inputId = "coledgesize",
- label = "Edge size",
- min = 0.5,
- max = 20,
- value = 5,
- step=0.5)
- )),
- fluidRow(column(6,
- selectInput(inputId ="col.shadow",
- label = "Node shadow",
- choices = c("Yes",
- "No"),
- selected = "No")
- ),
- column(6,
- selectInput(inputId ="soc.curved",
- label = "Curved edges",
- choices = c("Yes",
- "No"),
- selected = "No")
-
- ))
- ),
- br(),
- fluidRow(column(6,
- downloadButton("network.col", strong("Save Pajek"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- ),
- column(6,
- downloadButton("networkCol.fig", strong("Save HTML"),
- style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
- width = "100%")
- )
- )
- ),
- ## Collaboration World Map ----
- conditionalPanel(condition = 'input.sidebarmenu == "collabWorldMap"',
- # actionButton("applyWM", strong("Run"),
- # style ="border-radius: 10px; border-width: 3px;",
- # width = "100%"),
- # br(),
- # br(),
- h4(strong("Method Parameters: ")),
- " ",
- numericInput("WMedges.min",
- label=("Min edges"),
- value = 2,
- step = 1),
- " ",
- br(),
- h4(strong("Graphical Parameters: ")),
- " ",
- sliderInput(inputId = "WMedgesize",
- label = "Edge size",
- min = 0.1,
- max = 20,
- value = 5),
- br(),
- selectInput(
- 'CCdpi',
- h4(strong(
- "Export plot"
- )),
- choices=c(
- "dpi value" = "null",
- "75 dpi" = "75",
- "150 dpi" = "150",
- "300 dpi" = "300",
- "600 dpi" = "600"
- ),
- selected = "null"
- ),
- conditionalPanel(condition = "input.CCdpi != 'null'",
- sliderInput(
- 'CCh',
- h4(em(strong(
- "Height (in inches)"
- ))),
- value = 7, min = 1, max = 20, step = 1),
- downloadButton("CCplot.save", strong("Export plot as png"),
- style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
- width = "100%")
- )
- )
- )
- )
- )
- )
- )
- })
-
-}
+#### SERVER ####
+
+server <- function(input, output,session){
+ session$onSessionEnded(stopApp)
+ ##
+
+ ## suppress warnings
+ options(warn = -1)
+ ##
+
+ ## file upload max size
+ maxUploadSize <- 200 # default value
+ maxUploadSize <- getShinyOption("maxUploadSize", maxUploadSize)
+ options(shiny.maxRequestSize=maxUploadSize*1024^2)
+
+ ## initial values
+ data("logo",package="bibliometrix",envir=environment())
+ values = reactiveValues()
+ values$logo <- logo
+ values$logoGrid <- grid::rasterGrob(logo,interpolate = TRUE)
+ values$h <- 7
+ values$w <- 14
+ values$results <- list("NA")
+ values$log <- "working..."
+ values$load="FALSE"
+ values$field = values$cocngrams = "NA"
+ values$citField=values$colField=values$citSep="NA"
+ values$NetWords=values$NetRefs=values$ColNetRefs=matrix(NA,1,1)
+ values$Title="Network"
+ values$Histfield="NA"
+ values$histlog="working..."
+ values$kk=0
+ #values$MRWremove.terms=NULL
+ values$M=data.frame(PY=0)
+ values$histsearch="NA"
+ values$citShortlabel="NA"
+ values$S=list("NA")
+ values$GR="NA"
+ values$dsToken <- "Wrong account or password"
+ values$dsSample <- 0
+ values$dsQuery <- ""
+ values$pmQuery <- " "
+ values$pmSample <- 0
+ values$ApiOk <- 0
+ values$checkControlBar <-FALSE
+
+ ## NOTIFICATION ITEM ----
+
+ output$notificationMenu <- renderMenu({
+
+ notifTot <- notifications()
+
+ values$nots <- apply(notifTot, 1, function(row) {
+
+ ## extract href from messages
+ if (is.na(row[["href"]])){href <- NULL
+ }else{
+ href <- paste("javascript:void(window.open('",row[["href"]],"', '_blank'))", sep="")
+ }
+
+ ## add bold to new messages and split the long ones in two rows
+ if (row[["status"]]=="danger"){ ### new messages
+ textRows <- paste("tags$strong('",row[["nots"]],"')", sep="")
+ textRows <- strsplit(substr(textRows,1,85), "(?<=.{48})", perl = TRUE)[[1]]
+ if (length(textRows)>1){
+ textRows <- paste("tags$div(",textRows[1],"',tags$br(),'",textRows[2],")", sep="")
+ }else{
+ textRows <- paste("tags$div(",textRows,")", sep="")
+ }
+ }else{ ## old messages
+ textRows <- strsplit(substr(row[["nots"]],1,70), "(?<=.{35})", perl = TRUE)[[1]]
+ if (length(textRows)>1){
+ textRows <- paste("tags$div('",textRows[1],"',tags$br(),'",textRows[2],"')", sep="")
+ }else{
+ textRows <- paste("tags$div('",textRows,"')", sep="")
+ }
+ }
+
+
+
+ notificationItem(
+ #text = row[["nots"]],
+ text = eval(parse(text=textRows)),
+ icon = if (row[["status"]]=="danger") {fa_i(name ="envelope")}else{fa_i(name ="envelope-open")},
+ status = row[["status"]],
+ href = href
+ )
+ })
+
+ if ("danger" %in% notifTot[["status"]]){
+ badge = "danger"
+ icon_name ="envelope"
+ } else {
+ badge = NULL
+ icon_name ="envelope-open"
+ }
+
+ dropdownMenu(type = "notifications",
+ .list = values$nots,
+ headerText ="",
+ badgeStatus = NULL,
+ icon = fa_i(name = icon_name)
+ #icon = icon_color
+ )
+ })
+
+ ###Menu sidebar ----
+
+ # Apply Data----
+ observe({
+ toggleElement(
+ id ="rest_of_sidebar",
+ condition = input[["applyLoad"]]
+ )
+ })
+
+ output$rest_of_sidebar <- renderMenu({
+ sidebarMenu(
+ menuItem("Filters",tabName = "filters",icon = fa_i(name ="filter")),
+ menuItem("Overview",tabName = "overview",icon=fa_i(name = "table"),startExpanded = FALSE,
+ menuSubItem("Main Information",tabName="mainInfo",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Annual Scientific Production",tabName = "annualScPr",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Average Citations per Year",tabName = "averageCitPerYear",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Three-Field Plot", tabName ="threeFieldPlot",icon = icon("chevron-right",lib = "glyphicon"))),
+ menuItem("Sources", tabName = "sources",icon = fa_i(name ="book"), startExpanded = FALSE,
+ menuSubItem("Most Relevant Sources", tabName = "relevantSources",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Most Local Cited Sources",tabName = "localCitedSources",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Bradford's Law",tabName = "bradford",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Source Impact",tabName = "sourceImpact",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Source Dynamics",tabName = "sourceDynamics",icon = icon("chevron-right",lib = "glyphicon"))),
+ menuItem("Authors", tabName = "authors",icon = fa_i(name="user"),startExpanded = FALSE,
+ "Authors",
+ menuSubItem("Most Relevant Authors", tabName = "mostRelAuthors",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Local Cited Authors",tabName = "mostLocalCitedAuthors",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Authors' Production over Time",tabName = "authorsProdOverTime",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Lotka's Law",tabName = "lotka",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Author Impact",tabName = "authorImpact",icon = icon("chevron-right", lib = "glyphicon")),
+ "Affiliations",
+ menuSubItem("Most Relevant Affiliations",tabName = "mostRelAffiliations",icon = icon("chevron-right", lib = "glyphicon")),
+ "Countries",
+ menuSubItem("Corresponding Author's Country",tabName = "correspAuthorCountry",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Country Scientific Production",tabName = "countryScientProd",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Cited Countries",tabName = "mostCitedCountries",icon = icon("chevron-right", lib = "glyphicon"))
+ ),
+ menuItem("Documents", tabName = "documents",icon = fa_i(name="layer-group"), startExpanded = FALSE,
+ "Documents",
+ menuSubItem("Most Global Cited Documents",tabName = "mostGlobalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Local Cited Documents",tabName = "mostLocalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
+ "Cited Refereces",
+ menuSubItem("Most Local Cited References",tabName = "mostLocalCitRef",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Reference Spectroscopy",tabName = "ReferenceSpect",icon = icon("chevron-right", lib = "glyphicon")),
+ "Words",
+ menuSubItem("Most Frequent Words",tabName = "mostFreqWords",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("WordCloud", tabName = "wcloud",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("TreeMap",tabName = "treemap",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Word Dynamics",tabName = "wordDynamics",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Trend Topics",tabName = "trendTopic",icon = icon("chevron-right", lib = "glyphicon"))
+ ),
+ menuItem("Clustering", tabName = "clustering",icon = fa_i(name ="spinner"),startExpanded = FALSE,
+ menuSubItem("Clustering by Coupling",tabName = "coupling",icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Conceptual Structure",tabName = "concepStructure",icon = fa_i(name="spell-check"),startExpanded = FALSE,
+ "Network Approach",
+ menuSubItem("Co-occurence Network",tabName = "coOccurenceNetwork",icon = icon("chevron-right", lib = "glyphicon") ),
+ menuSubItem("Thematic Map",tabName = "thematicMap", icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Thematic Evolution",tabName = "thematicEvolution", icon = icon("chevron-right", lib = "glyphicon")),
+ "Factorial Approach",
+ menuSubItem("Factorial Analysis", tabName = "factorialAnalysis", icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Intellectual Structure",tabName = "intStruct",icon = fa_i(name="gem"), startExpanded = FALSE,
+ menuSubItem("Co-citation Network",tabName = "coCitationNetwork", icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Historiograph",tabName = "historiograph", icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Social Structure",tabName = "socialStruct", icon = fa_i("users"),startExpanded = FALSE,
+ menuSubItem("Collaboration Network",tabName = "collabNetwork",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Collaboration WorldMap", tabName = "collabWorldMap",icon = icon("chevron-right", lib = "glyphicon")))
+ )
+ })
+
+ # Apply API ----
+ observe({
+ toggleElement(
+ id ="rest_of_sidebar",
+ condition = input[["apiApply"]]
+ )
+ })
+
+ output$rest_of_sidebar <- renderMenu({
+ sidebarMenu(
+ menuItem("Filters",tabName = "filters",icon = fa_i(name ="filter")),
+ menuItem("Overview",tabName = "overview",icon=fa_i(name = "table"),startExpanded = FALSE,
+ menuSubItem("Main Information",tabName="mainInfo",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Annual Scientific Production",tabName = "annualScPr",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Average Citations per Year",tabName = "averageCitPerYear",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Three-Field Plot", tabName ="threeFieldPlot",icon = icon("chevron-right",lib = "glyphicon"))),
+ menuItem("Sources", tabName = "sources",icon = fa_i(name ="book"), startExpanded = FALSE,
+ menuSubItem("Most Relevant Sources", tabName = "relevantSources",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Most Local Cited Sources",tabName = "localCitedSources",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Bradford's Law",tabName = "bradford",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Source Impact",tabName = "sourceImpact",icon = icon("chevron-right",lib = "glyphicon")),
+ menuSubItem("Source Dynamics",tabName = "sourceDynamics",icon = icon("chevron-right",lib = "glyphicon"))),
+ menuItem("Authors", tabName = "authors",icon = fa_i(name="user"),startExpanded = FALSE,
+ "Authors",
+ menuSubItem("Most Relevant Authors", tabName = "mostRelAuthors",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Local Cited Authors",tabName = "mostLocalCitedAuthors",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Authors' Production over Time",tabName = "authorsProdOverTime",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Lotka's Law",tabName = "lotka",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Author Impact",tabName = "authorImpact",icon = icon("chevron-right", lib = "glyphicon")),
+ "Affiliations",
+ menuSubItem("Most Relevant Affiliations",tabName = "mostRelAffiliations",icon = icon("chevron-right", lib = "glyphicon")),
+ "Countries",
+ menuSubItem("Corresponding Author's Country",tabName = "correspAuthorCountry",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Country Scientific Production",tabName = "countryScientProd",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Cited Countries",tabName = "mostCitedCountries",icon = icon("chevron-right", lib = "glyphicon"))
+ ),
+ menuItem("Documents", tabName = "documents",icon = fa_i(name="layer-group"), startExpanded = FALSE,
+ "Documents",
+ menuSubItem("Most Global Cited Documents",tabName = "mostGlobalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Most Local Cited Documents",tabName = "mostLocalCitDoc",icon = icon("chevron-right", lib = "glyphicon")),
+ "Cited Refereces",
+ menuSubItem("Most Local Cited References",tabName = "mostLocalCitRef",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Reference Spectroscopy",tabName = "ReferenceSpect",icon = icon("chevron-right", lib = "glyphicon")),
+ "Words",
+ menuSubItem("Most Frequent Words",tabName = "mostFreqWords",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("WordCloud", tabName = "wcloud",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("TreeMap",tabName = "treemap",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Word Dynamics",tabName = "wordDynamics",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Trend Topics",tabName = "trendTopic",icon = icon("chevron-right", lib = "glyphicon"))
+ ),
+ menuItem("Clustering", tabName = "clustering",icon = fa_i(name ="spinner"),startExpanded = FALSE,
+ menuSubItem("Clustering by Coupling",tabName = "coupling",icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Conceptual Structure",tabName = "concepStructure",icon = fa_i(name="spell-check"),startExpanded = FALSE,
+ "Network Approach",
+ menuSubItem("Co-occurence Network",tabName = "coOccurenceNetwork",icon = icon("chevron-right", lib = "glyphicon") ),
+ menuSubItem("Thematic Map",tabName = "thematicMap", icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Thematic Evolution",tabName = "thematicEvolution", icon = icon("chevron-right", lib = "glyphicon")),
+ "Factorial Approach",
+ menuSubItem("Factorial Analysis", tabName = "factorialAnalysis", icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Intellectual Structure",tabName = "intStruct",icon = fa_i(name="gem"), startExpanded = FALSE,
+ menuSubItem("Co-citation Network",tabName = "coCitationNetwork", icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Historiograph",tabName = "historiograph", icon = icon("chevron-right", lib = "glyphicon"))),
+ menuItem("Social Structure",tabName = "socialStruct", icon = fa_i("users"),startExpanded = FALSE,
+ menuSubItem("Collaboration Network",tabName = "collabNetwork",icon = icon("chevron-right", lib = "glyphicon")),
+ menuSubItem("Collaboration WorldMap", tabName = "collabWorldMap",icon = icon("chevron-right", lib = "glyphicon")))
+ )
+ })
+
+ # observe({
+ # toggleElement(
+ # id = "rest_of_sidebar",
+ # condition = input[["applyLoad"]]
+ # )
+ # })
+ #
+ # # menuItem("Quit", tabName = "quit",icon=icon("off",lib = "glyphicon")),
+ # # menuItem("K-Synth", icon = icon("globe",lib = "glyphicon"), badgeLabel = "Link", badgeColor = "blue",
+ # # href = "https://www.k-synth.unina.it")
+
+
+
+
+ ## LOAD MENU ----
+ format <- function(obj){
+ ext<- sub('.*\\.', '', obj[1])
+ switch(ext,
+ txt ={
+ format <- "plaintext"
+ },
+ csv ={
+ format <- "csv"
+ },
+ bib ={
+ format <- "bibtex"
+ },
+ ciw ={
+ format <- "endnote"
+ },
+ xlsx={
+ format <- "excel"
+ }
+ )
+ return(format)
+ }
+
+ ## smart_load function ----
+ smart_load <- function(file){
+ var <- load(file)
+ n <- length(var)
+ if (!"M" %in% var){
+ if (n == 1) {
+ eval(parse(text = paste0("M <- ", var)))
+ } else {
+ stop("I could not find bibliometrixDB object in your data file: ", file)
+ }
+ }
+ rm(list = var[var != "M"])
+ if ( ("M" %in% ls()) & inherits(M, "bibliometrixDB") ){
+ return(M)
+ } else {
+ stop("Please make sure your RData/Rda file contains a bibliometrixDB object (M).")
+ }
+ }
+
+ DATAloading<- eventReactive(input$applyLoad,{
+ # input$file1 will be NULL initially. After the user selects
+ # and uploads a file, it will be a data frame with 'name',
+ # 'size', 'type', and 'datapath' columns. The 'datapath'
+ # column will contain the local filenames where the data can
+ # be found.
+ if (input$load=="demo"){
+ data(management, package="bibliometrixData")
+ values = initial(values)
+ row.names(management) <- management$SR
+ values$M <- management
+ values$Morig = management
+ values$Histfield = "NA"
+ values$results = list("NA")
+ return()
+ }
+ inFile <- input$file1
+
+ if (!is.null(inFile) & input$load=="import") {
+ ext <- getFileNameExtension(inFile$datapath)
+ switch(
+ input$dbsource,
+ isi = {
+ switch(ext,
+ ### WoS ZIP Files
+ zip = {
+ D <- unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(D,
+ dbsource = input$dbsource,
+ format = format(D))
+ })
+ },
+ ### WoS Txt/Bib Files
+ {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = format(inFile$datapath))
+ })
+ })
+ },
+ scopus = {
+ switch(ext,
+ ### Scopus ZIP Files
+ zip = {
+ D <- unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(D,
+ dbsource = input$dbsource,
+ format = format(D))
+ })
+ },
+ ### Scopus CSV/Bib Files
+ csv = {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = "csv")
+ })
+ },
+ bib = {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = "bibtex")
+ })
+ })
+
+ },
+ lens = {
+ switch(ext,
+ ### Lens.org ZIP Files
+ zip = {
+ D <- unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(D,
+ dbsource = input$dbsource,
+ format = format(D))
+ })
+ },
+ ### Lens.org CSV Files
+ {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = format(inFile$datapath))
+ })
+ })
+ },
+ cochrane = {
+ switch(ext,
+ ### Cochrane ZIP Files
+ zip = {
+ D <- unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(D,
+ dbsource = input$dbsource,
+ format = format(D))
+ })
+ },
+ ### Cochrane txt files
+ {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = "plaintext")
+ })
+ })
+
+ },
+ pubmed = {
+ switch(ext,
+ ### Pubmed ZIP Files
+ zip = {
+ D <- unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(D,
+ dbsource = input$dbsource,
+ format = "pubmed")
+ })
+ },
+ ### Pubmed txt Files
+ txt = {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <- convert2df(inFile$datapath,
+ dbsource = input$dbsource,
+ format = "pubmed")
+ })
+ })
+ },
+ dimensions = {
+ switch(ext,
+ ### Dimensions ZIP Files
+ zip = {
+ D = unzip(inFile$datapath)
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <-
+ convert2df(D,
+ dbsource = input$dbsource,
+ format = format(D))
+ })
+ },
+ ### Dimensions Xlsx/csv Files
+ xlsx = {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <-
+ convert2df(
+ inFile$datapath,
+ dbsource = "dimensions",
+ format = "excel"
+ )
+ })
+ },
+ csv = {
+ withProgress(message = 'Conversion in progress',
+ value = 0, {
+ M <-
+ convert2df(
+ inFile$datapath,
+ dbsource = "dimensions",
+ format = "csv"
+ )
+ })
+ })
+
+ }
+ )
+
+ } else if (!is.null(inFile) & input$load=="load") {
+ ext <- tolower(getFileNameExtension(inFile$datapath))
+ #print(ext)
+ switch(ext,
+ ### excel format
+ xlsx={
+ #M <- rio::import(inFile$datapath)
+ M <- readxl::read_excel(inFile$datapath) %>% as.data.frame(stringsAsFactors=FALSE)
+ class(M) <- c("bibliometrixDB", "data.frame")
+ ### M row names
+ ### identify duplicated SRs
+ SR=M$SR
+ tab=table(SR)
+ tab2=table(tab)
+ ind=as.numeric(names(tab2))
+ ind=ind[which(ind>1)]
+ if (length(ind)>0){
+ for (i in ind){
+ indice=names(which(tab==i))
+ for (j in indice){
+ indice2=which(SR==j)
+ SR[indice2]=paste(SR[indice2],as.character(1:length(indice2)),sep=" ")
+ }
+ }
+ }
+
+ row.names(M) <- SR
+ },
+ ### RData format
+ rdata={
+ M <- smart_load(inFile$datapath)
+ },
+ rda={
+ M <- smart_load(inFile$datapath)
+ },
+ rds={
+ M <- readRDS(inFile$datapath)
+ })
+ } else if (is.null(inFile)) {return(NULL)}
+
+ values = initial(values)
+ values$M <- M
+ values$Morig = M
+ values$Histfield = "NA"
+ values$results = list("NA")
+
+
+ })
+ output$contents <- DT::renderDT({
+ DATAloading()
+ MData = as.data.frame(apply(values$M, 2, function(x) {
+ substring(x, 1, 150)
+ }), stringsAsFactors = FALSE)
+ MData$DOI <-
+ paste0(
+ '',
+ MData$DI,
+ ''
+ )
+ nome = c("DOI", names(MData)[-length(names(MData))])
+ MData = MData[nome]
+ DT::datatable(MData,escape = FALSE,rownames = FALSE, extensions = c("Buttons"),
+ options = list(
+ pageLength = 10,
+ dom = 'Bfrtip',
+ buttons = list(list(extend = 'pageLength'),
+ list(extend = 'print')),
+ lengthMenu = list(c(10, 25, 50, -1),
+ c('10 rows', '25 rows', '50 rows', 'Show all')),
+ columnDefs = list(list(
+ className = 'dt-center', targets = 0:(length(names(MData)) - 1)
+ ))
+ ),
+ class = 'cell-border compact stripe'
+ ) %>%
+ formatStyle(
+ names(MData),
+ backgroundColor = 'white',
+ textAlign = 'center',
+ fontSize = '70%'
+ )
+ })
+
+ ## export functions ----
+ output$collection.save <- downloadHandler(
+ filename = function() {
+
+ paste("Bibliometrix-Export-File-", Sys.Date(), ".",input$save_file, sep="")
+ },
+ content <- function(file) {
+ switch(input$save_file,
+ #xlsx={suppressWarnings(rio::export(values$M, file=file))},
+ xlsx={suppressWarnings(openxlsx::write.xlsx(values$M, file=file))},
+ RData={
+ M=values$M
+ save(M, file=file)
+ })
+
+ },
+ contentType = input$save_file
+ )
+
+ output$collection.save_api <- downloadHandler(
+ filename = function() {
+
+ paste("Bibliometrix-Export-File-", Sys.Date(), ".",input$save_file_api, sep="")
+ },
+ content <- function(file) {
+ switch(input$save_file_api,
+ #xlsx={suppressWarnings(rio::export(values$M, file=file))},
+ xlsx={suppressWarnings(openxlsx::write.xlsx(values$M, file=file))},
+ RData={
+ M=values$M
+ save(M, file=file)
+ })
+
+ },
+ contentType = input$save_file_api
+ )
+
+ output$textLog <- renderUI({
+ k=dim(values$M)[1]
+ if (k==1){k=0}
+ log=paste("Number of Documents ",k)
+ textInput("textLog", "Conversion results",
+ value=log)
+ })
+
+ dsModal <- function(failed = FALSE) {
+ modalDialog(
+ title = "Dimensions API",
+ size = "l",
+
+ h4(em(
+ strong("1) Get a token using your Dimensions credentials")
+ )),
+ textInput(
+ "dsAccount",
+ "Account",
+ "",
+ width = NULL,
+ placeholder = NULL
+ ),
+ passwordInput("dsPassword",
+ "Password",
+ "",
+ width = NULL,
+ placeholder = NULL),
+
+ actionButton("dsToken", "Get a token "),
+ h5(tags$b("Token")),
+ verbatimTextOutput("tokenLog", placeholder = FALSE),
+ tags$hr(),
+ h4(em(strong("2) Create a query"))),
+ textInput(
+ "dsWords",
+ "Words",
+ "",
+ width = NULL,
+ placeholder = NULL
+ ),
+ selectInput(
+ "dsFullsearch",
+ label = "search field",
+ choices = c("Title and Abstract only" = FALSE,
+ "Full text" = TRUE),
+ selected = FALSE
+ ),
+ textInput(
+ "dsCategories",
+ "Science Categories",
+ "",
+ width = NULL,
+ placeholder = NULL
+ ),
+ numericInput("dsStartYear", "Start Year", value = 1990),
+ numericInput("dsEndYear", "End Year", value = as.numeric(substr(Sys.time(), 1, 4))),
+
+
+ actionButton("dsQuery", "Create the query "),
+
+ h5(tags$b("Your query")),
+ verbatimTextOutput("queryLog", placeholder = FALSE),
+ h5(tags$b("Documents returned using your query")),
+ verbatimTextOutput("sampleLog", placeholder = FALSE),
+
+
+ uiOutput("sliderLimit"),
+
+ footer = tagList(
+ modalButton("Cancel"),
+ actionButton("dsok", "OK")
+ )
+ )
+ }
+
+ ### Show Dimensions modal when button is clicked.
+ observeEvent(input$dsShow, {
+ showModal(dsModal())
+ })
+
+ observeEvent(input$dsok, {
+ removeModal()
+ values$M <- data.frame(Message="Waiting for data")
+ })
+
+ output$tokenLog <- renderText({
+ input$dsToken
+ isolate({
+ capture.output(Token <- dsAuth(username = input$dsAccount, password = input$dsPassword))
+ #Token <- dsAuth(username = input$dsAccount, password = input$dsPassword)
+ if (Token==1){
+ values$dsToken <- "Wrong account or password"
+ }else{
+ values$dsToken <- Token
+ }
+ values$dsToken
+
+ })
+ })
+
+ DSQUERYload<- eventReactive(input$dsQuery,{
+ values$dsQuery <- dsQueryBuild(item = "publications",
+ words = input$dsWords,
+ full.search = input$dsFullsearch,
+ type = "article",
+ categories = input$dsCategories,
+ start_year = input$dsStartYear, end_year = input$dsEndYear)
+ dsSample <- 0
+ capture.output(dsSample <- dsApiRequest(token = values$dsToken, query = values$dsQuery, limit = 0))
+ if (class(dsSample)=="numeric"){
+ values$dsSample <- 0
+ }else{values$dsSample <- dsSample$total_count}
+ })
+
+ output$queryLog <- renderText({
+
+ DSQUERYload()
+ values$dsQuery
+
+ })
+
+ output$queryLog2 <- renderText({
+ DSQUERYload()
+ values$dsQuery
+ })
+
+ output$sampleLog <- renderText({
+ DSQUERYload()
+ mes <- paste("Dimensions returns ",values$dsSample, " documents", collapse="",sep="")
+ mes
+ })
+
+ output$sampleLog2 <- renderText({
+
+ if (nrow(values$M)<2) {n <- 0}else{n <- nrow(values$M)}
+ mes <- paste("Dimensions API returns ",n, " documents", collapse="",sep="")
+ values$ApiOk <- 0
+ return(mes)
+ })
+
+ output$sliderLimit <- renderUI({
+
+ sliderInput("sliderLimit", "Total document to download", min = 1,
+ max = values$dsSample, value = values$dsSample, step = 1)
+ })
+
+ ### API MENU: PubMed ----
+ ### PubMed modal
+ pmModal <- function(failed = FALSE) {
+ modalDialog(
+ title = "PubMed API",
+ size = "l",
+ h4(em(strong(
+ "1) Generate a valid query"
+ ))),
+ textInput(
+ "pmQueryText",
+ "Search terms",
+ " ",
+ width = NULL,
+ placeholder = NULL
+ ),
+ numericInput("pmStartYear", "Start Year", value = 1990),
+ numericInput("pmEndYear", "End Year", value = as.numeric(substr(Sys.time(
+ ), 1, 4))),
+ actionButton("pmQuery", "Try the query "),
+ h5(tags$b("Query Translation")),
+ verbatimTextOutput("pmQueryLog", placeholder = FALSE),
+ #h5(tags$b("Generated query")),
+ h5(tags$b("Documents returned using your query")),
+ verbatimTextOutput("pmSampleLog", placeholder = FALSE),
+ tags$hr(),
+ h4(em(
+ strong("2) Choose how many documents to download")
+ )),
+
+ uiOutput("pmSliderLimit"),
+
+ footer = tagList(
+ modalButton("Cancel"),
+ actionButton("pmok", "OK")
+ )
+ )
+ }
+
+ # Show modal when button is clicked.
+ observeEvent(input$pmShow, {
+ showModal(pmModal())
+ })
+
+ observeEvent(input$pmok, {
+ removeModal()
+ })
+
+ pmQUERYLOAD <- eventReactive(input$pmQuery,{
+
+ query = paste(input$pmQueryText,"[Title/Abstract] AND english[LA] AND Journal Article[PT] AND "
+ ,input$pmStartYear,":",input$pmEndYear,"[DP]", sep="")
+ res <- pmQueryTotalCount(query = query, api_key = NULL)
+ if (class(res)=="list"){
+ values$pmSample <- res$total_count
+ values$pmQuery <- res$query_translation}
+ values$pmQuery <- res$query_translation
+
+ })
+ output$pmQueryLog <- renderText({
+ pmQUERYLOAD()
+ values$pmQuery
+ })
+
+ output$pmQueryLog2 <- renderText({
+ pmQUERYLOAD()
+ values$pmQuery
+ })
+
+ output$pmSampleLog <- renderText({
+ pmQUERYLOAD()
+ mes <- paste("PubMed returns ",values$pmSample, " documents", collapse="",sep="")
+ mes
+
+ })
+ output$pmSampleLog2 <- renderText({
+ if (nrow(values$M)<2) {n <- 0}else{n <- nrow(values$M)}
+
+ mes <- paste("PubMed API returns ",n, " documents", collapse="",sep="")
+ values$ApiOk <- 0
+ return(mes)
+ })
+
+ output$pmSliderLimit <- renderUI({
+ sliderInput("pmSliderLimit", "Total document to download", min = 1,
+ max = values$pmSample, value = values$pmSample, step = 1)
+ })
+ ### API MENU: Content Download ----
+ APIDOWNLOAD <- eventReactive(input$apiApply,{
+ values = initial(values)
+ values$M <- data.frame(Message="Waiting for data")
+
+ switch(input$dbapi,
+ ds={
+ if (input$dsWords!="") {
+ #capture.output(
+ D <-
+ dsApiRequest(
+ token = values$dsToken,
+ query = values$dsQuery,
+ limit = input$sliderLimit
+ )
+ #)
+ M <- convert2df(D, "dimensions", "api")
+ values$ApiOk <- 1
+ values$M <- M
+ values$Morig = M
+
+ values$Histfield = "NA"
+ values$results = list("NA")
+
+ contentTable(values)
+ }
+ },
+ pubmed={
+ #if (exists("input$pmQueryText")){
+ if (input$pmQueryText !=" ") {
+ #capture.output(
+ D <-
+ pmApiRequest(
+ query = values$pmQuery,
+ limit = input$pmSliderLimit,
+ api_key = NULL
+ )
+ #)
+ M <- convert2df(D, "pubmed", "api")
+ values$ApiOk <- 1
+ values$M <- M
+ values$Morig = M
+
+ values$Histfield = "NA"
+ values$results = list("NA")
+
+ #contentTable(values)
+ }
+
+ })
+ })
+
+
+
+ output$apiContents <- DT::renderDT({
+ APIDOWNLOAD()
+ contentTable(values)
+ #}
+
+ })
+
+ ### function returns a formatted data.frame ----
+ contentTable <- function(values){
+ MData = as.data.frame(apply(values$M, 2, function(x) {
+ substring(x, 1, 150)
+ }), stringsAsFactors = FALSE)
+ MData$DOI <-
+ paste0(
+ '',
+ MData$DI,
+ ''
+ )
+ nome = c("DOI", names(MData)[-length(names(MData))])
+ MData = MData[nome]
+ DT::datatable(MData,escape = FALSE,rownames = FALSE, extensions = c("Buttons"),
+ options = list(
+ pageLength = 10,
+ dom = 'Bfrtip',
+ buttons = list(list(extend = 'pageLength'),
+ list(extend = 'print')),
+ lengthMenu = list(c(10, 25, 50, -1),
+ c('10 rows', '25 rows', '50 rows', 'Show all')),
+ columnDefs = list(list(
+ className = 'dt-center', targets = 0:(length(names(MData)) - 1)
+ ))
+ ),
+ class = 'cell-border compact stripe'
+ ) %>%
+ formatStyle(
+ names(MData),
+ backgroundColor = 'white',
+ textAlign = 'center',
+ fontSize = '70%'
+ )
+ }
+
+ output$textDim <- renderUI({
+ str1=paste("Documents ",dim(values$M)[1]," of ",dim(values$Morig)[1])
+ str2=paste("Sources ",length(unique(values$M$SO))," of ", length(unique(values$Morig$SO)))
+ str3=paste("Authors ",length(unique(unlist(strsplit(values$M$AU,";"))))," of ", length(unique(unlist(strsplit(values$Morig$AU,";")))))
+ HTML(paste("",str1, str2, str3, sep = '
'))
+ })
+
+ output$selectType <- renderUI({
+
+ artType=sort(unique(values$Morig$DT))
+ selectInput("selectType", "Document Type",
+ choices = artType,
+ selected = artType,
+ multiple =TRUE )
+ })
+ output$selectLA <- renderUI({
+
+ if ("LA" %in% names(values$Morig)){
+ LA <- sort(unique(values$Morig$LA))} else {
+ values$Morig$LA <- "N.A."
+ LA <- "N.A."
+ }
+ selectInput("selectLA", "Language",
+ choices = LA,
+ selected = LA,
+ multiple =TRUE )
+ })
+
+ output$sliderPY <- renderUI({
+
+ sliderInput("sliderPY", "Publication Year", min = min(values$Morig$PY,na.rm=T),sep="",
+ max = max(values$Morig$PY,na.rm=T), value = c(min(values$Morig$PY,na.rm=T),max(values$Morig$PY,na.rm=T)))
+ })
+
+ output$selectSource <- renderUI({
+ SO=sort(unique(values$Morig$SO))
+ selectInput("selectSource", "Source",
+ choices = SO,
+ selected = SO,
+ multiple = TRUE)
+
+ })
+
+ output$sliderTCpY <- renderUI({
+ Y <- as.numeric(substr(Sys.time(),1,4))
+ values$Morig <- values$Morig %>%
+ mutate(Age = Y - .data$PY+1,
+ TCpY = round(.data$TC/Age,2)) %>%
+ group_by(.data$PY) %>%
+ mutate(NTC = .data$TC/mean(.data$TC, na.rm=T)) %>%
+ as.data.frame()
+ sliderInput("sliderTCpY", "Average Citation per Year", min = floor(min(values$Morig$TCpY, na.rm=T)),
+ max = ceiling(max(values$Morig$TCpY,na.rm=T)), step=0.1,
+ value = c(floor(min(values$Morig$TCpY, na.rm=T)),ceiling(max(values$Morig$TCpY,na.rm=T))))
+ })
+
+ ## Update filtered data ----
+
+ DTfiltered <- eventReactive(input$applyFilter,{
+ M <- values$Morig
+ B <- bradford(M)$table
+ M <- subset(M, M$PY>=input$sliderPY[1] & M$PY<=input$sliderPY[2])
+ M <- subset(M, M$TCpY>=input$sliderTCpY[1] & M$TCpY<=input$sliderTCpY[2])
+ M <- subset(M, M$DT %in% input$selectType)
+ M <- subset(M, M$LA %in% input$selectLA)
+ switch(input$bradfordSources,
+ "core"={
+ SO=B$SO[B$Zone %in% "Zone 1"]
+ },
+ "zone2"={
+ SO=B$SO[B$Zone %in% c("Zone 1", "Zone 2")]
+ },
+ "all"={SO=B$SO})
+ M=M[M$SO %in% SO,]
+ values<-initial(values)
+ values$M=M
+ Mdisp=as.data.frame(apply(values$M,2,function(x){substring(x,1,150)}),stringsAsFactors = FALSE)
+ if (dim(Mdisp)[1]>0){
+ DT::datatable(Mdisp, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Filtered_DataTable',
+ title = "My Title",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Filtered_DataTable',
+ title = "My Title",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(Mdisp))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(Mdisp), backgroundColor = 'white',textAlign = 'center', fontSize = '70%')
+ }else{Mdisp=data.frame(Message="Empty collection",stringsAsFactors = FALSE, row.names = " ")}
+ })
+
+ output$dataFiltered <- DT::renderDT({
+
+ DTfiltered()
+
+ })
+
+ ## Main Info ----
+ output$MainInfo <- DT::renderDT({
+ DT::datatable(values$TABvb , rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 50, dom = 'Bfrtip',ordering=F,
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Main_Information',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Main_Information',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Main_Information',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ #lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ #columnDefs = list(list(className = 'dt-center', targets = "_all"),
+ # list(width = '50px', targets = 0)),
+ columnDefs = list(list(className = 'dt-center', targets = "_all"),
+ list(width = '350px', targets = 0))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$TABvb)[1], backgroundColor = 'white',textAlign = 'left', fontSize = '110%') %>%
+ formatStyle(names(values$TABvb)[2], backgroundColor = 'white',textAlign = 'right', fontSize = '110%')
+ })
+
+
+ #box1 ---------------
+ output$Timespan <- renderValueBox({
+
+ #TAB <- res$TAB
+ TAB <- ValueBoxes(values$M)
+ values$TABvb <- TAB
+ valueBox(value = p(TAB[TAB$Description=="Timespan", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong((TAB[TAB$Description=="Timespan", 2])), style = 'font-size:36px;color:white;', align="center"),
+ icon = fa_i(name="hourglass"), color = "blue",
+ width = NULL
+ )
+ })
+ #box2 ---------------
+ output$au <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Authors", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Authors", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="user"), color = "light-blue",
+ width = NULL)
+ })
+
+
+ #box3 ------------
+ output$kw <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Author's Keywords (DE)", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Author's Keywords (DE)", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="spell-check"), color = "aqua",
+ width = NULL)
+ })
+ #box4 ---------------
+ output$so <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p("Sources", style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Sources (Journals, Books, etc)", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name ="book"), color = "blue",
+ width = NULL)
+ })
+
+ #box5 --------------------
+ output$auS1 <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Authors of single-authored docs", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Authors of single-authored docs", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="pen-fancy"), color = "light-blue",
+ width = NULL)
+ })
+
+ #box6 -------------
+
+ output$cr <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="References", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="References", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="file"), color = "aqua",
+ width = NULL)
+ })
+
+ #box7 ----------------
+
+ output$doc <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Documents", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Documents", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="layer-group"), color = "blue",
+ width = NULL)
+ })
+ #box8 ---------------
+
+ output$col <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(strong("International Co-Authorship"), style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="International co-authorships %", 2]," %"), style = 'font-size:36px;color:white;',align="center"),
+ icon = icon("globe",lib = "glyphicon"), color = "light-blue",
+ width = NULL)
+ })
+
+
+ #box9 ---------------
+ output$agePerDoc <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Document Average Age", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Document Average Age", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="calendar"), color = "aqua",
+ width = NULL)
+ })
+ #box10 ------------------
+ output$cagr <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(strong("Annual Growth Rate"), style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Annual Growth Rate %", 2]," %"), style = 'font-size:36px;color:white;',align="center"),
+ icon = icon("arrow-up", lib="glyphicon"), color = "blue",
+ width = NULL)
+ })
+
+ #box11 ------
+ output$coAuPerDoc <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Co-Authors per Doc", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Co-Authors per Doc", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = fa_i(name="users"), color = "light-blue",
+ width = NULL)
+ })
+
+ #box12 -------
+ output$tc <- renderValueBox({
+ TAB <- values$TABvb
+ valueBox(value = p(TAB[TAB$Description=="Average citations per doc", 1], style = 'font-size:16px;color:white;'),
+ subtitle = p(strong(TAB[TAB$Description=="Average citations per doc", 2]), style = 'font-size:36px;color:white;',align="center"),
+ icon = icon("volume-up", lib = "glyphicon"), color = "aqua",
+ width = NULL)
+ })
+
+
+ ## Annual Production ----
+ output$CAGR <- renderText({
+ # Y=table(values$M$PY)
+ # ny=dim(Y)[1]
+ # values$GR<-round(((Y[ny]/Y[1])^(1/(ny-1))-1)*100,2)
+ paste0(values$GR," %")
+ })
+
+ output$AnnualProdPlot <- renderPlotly({
+ res <- descriptive(values,type="tab2")
+ values <-res$values
+ Y <- values$TAB
+
+ names(Y)=c("Year","Freq")
+ x <- c(max(Y$Year)-0.02-diff(range(Y$Year))*0.125, max(Y$Year)-0.02)+1
+ y <- c(min(Y$Freq),min(Y$Freq)+diff(range(Y$Freq))*0.125)
+
+
+ g=ggplot2::ggplot(Y, aes(x = .data$Year, y = .data$Freq, text=paste("Year: ",.data$Year,"\nN .of Documents: ",.data$Freq))) +
+ geom_line(aes(group="NA")) +
+ geom_area(aes(group="NA"),fill = 'grey90', alpha = .5) +
+ labs(x = 'Year'
+ , y = 'Articles'
+ , title = "Annual Scientific Production") +
+ scale_x_continuous(breaks= (Y$Year[seq(1,length(Y$Year),by=2)])) +
+ theme(text = element_text(color = "#444444")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 0)
+ ,axis.title.x = element_text(hjust = 0)
+ ,axis.text.x = element_text(vjust = 1, angle = 90)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) +
+ annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+ values$ASPplot <- g
+
+ #'#EFEFEF'
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.7, size=0.10)
+ })#, height = 500, width =900)
+
+ output$ASPplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("AnnualScientificProduction-", Sys.Date(), ".png", sep="")
+ },
+
+ content <- function(file) {
+ ggsave(filename = file, plot = values$ASPplot, dpi = as.numeric(input$ASPdpi), height = input$ASPh, width = input$ASPh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$AnnualProdTable <- DT::renderDT({
+ TAB <- values$TAB
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Annual_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Annual_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Annual_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+
+ ## Annual Citation per Year ----
+ output$AnnualTotCitperYearPlot <- renderPlotly({
+
+ if (values$results[[1]]=="NA"){
+ values$results=biblioAnalysis(values$M)}
+ x=values$results
+
+ # Total Citation Plot
+ Table2=aggregate(x$TotalCitation,by=list(x$Years),length)
+ Table2$xx=aggregate(x$TotalCitation,by=list(x$Years),mean)$x
+ Table2$Annual=NA
+ d=date()
+ d=as.numeric(substring(d,nchar(d)-3,nchar(d)))
+ Table2$Years=d-Table2$Group.1
+ Table2$Annual=Table2$xx/Table2$Years
+ names(Table2)=c("Year","N","MeanTCperArt","MeanTCperYear","CitableYears")
+
+ ## inserting missing years
+ YY=setdiff(seq(min(x$Years,na.rm=TRUE),max(x$Years,na.rm=TRUE)),Table2$Year)
+ if (length(YY>0)){
+ YY=data.frame(YY,0,0,0,0)
+ names(YY)=c("Year","N","MeanTCperArt","MeanTCperYear","CitableYears")
+ Table2=rbind(Table2,YY)
+ Table2=Table2[order(Table2$Year),]
+ row.names(Table2)=Table2$Year}
+
+ values$AnnualTotCitperYear=Table2
+ Table2$group="A"
+
+ x <- c(max(Table2$Year)-0.02-diff(range(Table2$Year))*0.125, max(Table2$Year)-0.02)+1
+ y <- c(min(Table2$MeanTCperYear),min(Table2$MeanTCperYear)+diff(range(Table2$MeanTCperYear))*0.125)
+
+ g <- ggplot(Table2, aes(x = .data$Year, y =.data$MeanTCperYear,text=paste("Year: ",.data$Year,"\nAverage Citations per Year: ",round(.data$MeanTCperYear,1)))) +
+ geom_line(aes(x = .data$Year, y = .data$MeanTCperYear, group=.data$group)) +
+ geom_area(aes(x = .data$Year, y = .data$MeanTCperYear, group=.data$group),fill = 'grey90', alpha = .5) +
+ labs(x = 'Year'
+ , y = 'Citations'
+ , title = "Average Article Citations per Year")+
+ scale_x_continuous(breaks= (Table2$Year[seq(1,length(Table2$Year),by=2)])) +
+ theme(text = element_text(color = "#444444")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 0)
+ ,axis.title.x = element_text(hjust = 0)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) +
+ annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+ values$ACpYplot <- g
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.7, size=0.10)
+ })
+
+ output$ACpYplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("AverageArticleCitationPerYear-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$ACpYplot, dpi = as.numeric(input$ACpYdpi), height = input$ACpYh, width = input$ACpYh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$AnnualTotCitperYearTable <- DT::renderDT({
+
+ TAB <- values$AnnualTotCitperYear
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Annual_Total_Citation_per_Year',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Annual_Total_Citation_per_Year',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Annual_Total_Citation_per_Year',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[c(3:4)], digits=2)
+
+ })
+
+ ## Three Fields Plot ----
+ TFP <- eventReactive(input$apply3F,{
+ fields=c(input$LeftField, input$CentralField, input$RightField)
+ threeFieldsPlot(values$M, fields=fields,n=c(input$LeftFieldn, input$CentralFieldn,input$RightFieldn))
+ })
+
+ output$ThreeFieldsPlot <- renderPlotly({
+ TFP()
+ })
+
+ # SOURCES MENU ----
+ ## Most Relevant Sources ----
+ MRSources <- eventReactive(input$applyMRSources,{
+ res <- descriptive(values,type="tab7")
+ values <-res$values
+ values$TABSo<-values$TAB
+ #xx=as.data.frame(values$results$Sources)
+ xx<- values$TAB
+ if (input$MostRelSourcesK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelSourcesK}
+ xx <- xx %>%
+ slice_head(n=k)
+ #xx=xx[1:k,]
+ #xx=subset(xx, row.names(xx) %in% row.names(xx)[1:k])
+ #xx$Articles=as.numeric(xx$Articles)
+ xx$Sources=substr(xx$Sources,1,50)
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Sources", textLabx = "N. of Documents", title = "Most Relevant Sources")
+
+ values$MRSplot <- g
+ return(g)
+ })
+
+ output$MRSplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostRelevantSources-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MRSplot, dpi = as.numeric(input$MRSdpi), height = input$MRSh, width = input$MRSh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+
+ output$MostRelSourcesPlot <- renderPlotly({
+ g <- MRSources()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.1, size=0.10)
+ })#, height = 500, width =900)
+
+
+ output$MostRelSourcesTable <- DT::renderDT({
+
+ g <- MRSources()
+
+ TAB <- values$TABSo
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Relevant_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Relevant_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Relevant_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+
+ ## Most Local Cited Sources ----
+ MLCSources <- eventReactive(input$applyMLCSources,{
+ values$M=metaTagExtraction(values$M,"CR_SO")
+ TAB=tableTag(values$M,"CR_SO")
+ TAB=data.frame(Sources=names(TAB),Articles=as.numeric(TAB),stringsAsFactors = FALSE)
+ values$TABSoCit<-TAB
+ #xx=as.data.frame(values$results$Sources)
+ xx<- TAB
+ if (input$MostRelCitSourcesK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelCitSourcesK}
+ #xx=xx[1:k,]
+ xx=subset(xx, row.names(xx) %in% row.names(xx)[1:k])
+ xx$Articles=as.numeric(xx$Articles)
+ xx$Sources=substr(xx$Sources,1,50)
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Cited Sources", textLabx = "N. of Local Citations", title = "Most Local Cited Sources")
+
+ values$MLCSplot <- g
+ return(g)
+ })
+
+ output$MLCSplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostLocalCitedSources-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MLCSplot, dpi = as.numeric(input$MLCSdpi), height = input$MLCSh, width = input$MLCSh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostRelCitSourcesPlot <- renderPlotly({
+
+ g <- MLCSources()
+
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostRelCitSourcesTable <- DT::renderDT({
+
+ g <- MLCSources()
+ TAB <- values$TABSoCit
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Cited_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Cited_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Cited_Sources',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+ ## Bradford's Law ----
+ output$bradfordPlot <- renderPlotly({
+
+ values$bradford=bradford(values$M)
+ plot.ly(values$bradford$graph,flip=FALSE, side="r", aspectratio=1.6, size=0.15)
+
+ })#,height = 600)
+
+ output$BLplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("BradfordLaws-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$bradford$graph, dpi = as.numeric(input$BLdpi), height = input$BLh, width = input$BLh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$bradfordTable <- DT::renderDT({
+
+ DT::datatable(values$bradford$table, rownames = FALSE,
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Bradford_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Bradford_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Bradford_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$bradford$table))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$bradford$table), backgroundColor = 'white',textAlign = 'center')
+ })
+ ## Sources' Impact ----
+ Hsource <- eventReactive(input$applyHsource,{
+ withProgress(message = 'Calculation in progress',
+ value = 0, {
+ res <- Hindex_plot(values,type="source")
+ })
+ values$SIplot <- res$g
+ plot.ly(res$g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+ })
+
+ output$SIplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("SourceImpact-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$SIplot, dpi = as.numeric(input$SIdpi), height = input$SIh, width = input$SIh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$SourceHindexPlot <- renderPlotly({
+ Hsource()
+ })#, height = 500, width =900)
+
+ output$SourceHindexTable <- DT::renderDT({
+
+ DT::datatable(values$H, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Source_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Source_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Source_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$H))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$H), backgroundColor = 'white',textAlign = 'center') %>%
+ formatRound(names(values$H)[4], digits=3)
+
+ })
+ ## Source Growth ----
+ SOGrowth <- eventReactive(input$applySOGrowth,{
+ #if (input$SOse=="Yes"){se=TRUE}else{se=FALSE}
+
+ if (input$cumSO=="Cum"){
+ cdf=TRUE
+ laby="Cumulate occurrences"
+ }else{
+ cdf=FALSE
+ laby="Annual occurrences"}
+
+ values$PYSO=sourceGrowth(values$M,input$topSO[2], cdf=cdf)
+ if (input$topSO[1]>1){
+ values$PYSO <- values$PYSO[-c(2:(input$topSO[1]))]
+ }
+
+ term=names(values$PYSO)[-1]
+
+ term=rep(term,each=dim(values$PYSO)[1])
+ n=dim(values$PYSO)[1]*(dim(values$PYSO)[2]-1)
+ freq=matrix(as.matrix(values$PYSO[,-1]),n,1)
+ values$SODF=data.frame(Year=rep(values$PYSO$Year,(dim(values$PYSO)[2]-1)),Source=term, Freq=freq, stringsAsFactors = TRUE)
+
+ Text <- paste(values$SODF$Source," (",values$SODF$Year,") ",values$SODF$Freq, sep="")
+
+ width_scale <- 1.7 * 26 / length(unique(values$SODF$Source))
+
+ x <- c(max(values$SODF$Year)-0.02-diff(range(values$SODF$Year))*0.15, max(values$SODF$Year)-0.02)+1
+ y <- c(min(values$SODF$Freq),min(values$SODF$Freq)+diff(range(values$SODF$Freq))*0.15)
+
+ g=ggplot(values$SODF, aes(x=values$SODF$Year,y=values$SODF$Freq, group=values$SODF$Source, color=values$SODF$Source, text=Text))+
+ geom_line()+
+ labs(x = 'Year'
+ , y = laby
+ , title = "Source Growth") +
+ scale_x_continuous(breaks= (values$PYSO$Year[seq(1,length(values$PYSO$Year),by=ceiling(length(values$PYSO$Year)/20))])) +
+ geom_hline(aes(yintercept=0), alpha=0.1)+
+ labs(color = "Source")+
+ #guides(fill = guide_legend(nrow = 5))+
+ theme(text = element_text(color = "#444444"),
+ legend.text=ggplot2::element_text(size=width_scale),
+ legend.box.margin = margin(6, 6, 6, 6),
+ legend.title=ggplot2::element_text(size=1.5*width_scale,face="bold"),
+ legend.position="bottom",
+ legend.direction = "vertical",
+ legend.key.size = grid::unit(width_scale/50, "inch"),
+ legend.key.width = grid::unit(width_scale/50, "inch")
+ ,plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 90)
+ ,axis.title.x = element_text(hjust = 0.95, angle = 0)
+ ,axis.text.x = element_text(size=10, angle = 90)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) + annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+
+ values$SDplot <- g
+ return(g)
+ #suppressWarnings(plot(g))
+ })
+
+ output$SDplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("SourceDynamics-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$SDplot, dpi = as.numeric(input$SDdpi), height = input$SDh, width = input$SDh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$soGrowthPlot <- renderPlotly({
+
+ g <- SOGrowth()
+
+ leg <- list(
+ orientation = 'h',
+ y = -0.15,
+ font = list(
+ family = "sans-serif",
+ size = 10,
+ color = "#000"),
+ bgcolor = "#FFFFFF",
+ bordercolor = "#FFFFFF",
+ borderwidth = 2)
+
+ plot.ly(g, flip=FALSE, side="r", aspectratio=1.8, size=0.10) %>%
+ layout(legend = leg) %>%
+ config(displaylogo = FALSE,
+ modeBarButtonsToRemove = c(
+ 'sendDataToCloud',
+ 'pan2d',
+ 'select2d',
+ 'lasso2d',
+ 'toggleSpikelines'
+ )) %>%
+ layout(hovermode = 'compare')
+ #suppressWarnings(plot(g))
+
+
+ #}, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 600, width = 900)
+ })
+
+ output$soGrowthtable <- DT::renderDT({
+
+ g <- SOGrowth()
+
+ soData=values$PYSO
+
+ DT::datatable(soData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Source_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Source_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Source_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(soData))-1))))) %>%
+ formatStyle(names(soData), backgroundColor = 'white')
+ #return(Data)
+ })
+
+ # AUTHORS MENU ----
+ ## Most Relevant Authors ----
+ MRAuthors <- eventReactive(input$applyMRAuthors,{
+ res <- descriptive(values,type="tab3")
+ values <-res$values
+ values$TABAu<-values$TAB
+
+ #xx=as.data.frame(values$results$Authors, stringsAsFactors = FALSE)
+ xx=values$TABAu
+ switch(input$AuFreqMeasure,
+ t={
+ lab="N. of Documents"
+ xx=xx[,1:2]
+ },
+ p={xx=xx[,1:2]
+ xx[,2]=as.numeric(xx[,2])/dim(values$M)[1]*100
+ lab="N. of Documents (in %)"
+ },
+ f={
+ xx=xx[,c(1,3)]
+ lab="N. of Documents (Fractionalized)"
+ })
+
+ xx[,2]=as.numeric(xx[,2])
+
+ if (input$MostRelAuthorsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelAuthorsK}
+
+ xx=xx[1:k,]
+ xx[,2]=round(xx[,2],1)
+
+ xx <- xx[order(-xx[,2]),]
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Authors", textLabx = lab, title = "Most Relevant Authors")
+
+ values$MRAplot <- g
+ return(g)
+ })
+
+ output$MRAplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostRelevantAuthors-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MRAplot, dpi = as.numeric(input$MRAdpi), height = input$MRAh, width = input$MRAh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostRelAuthorsPlot <- renderPlotly({
+
+ g <- MRAuthors()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostRelAuthorsTable <- DT::renderDT({
+
+ TAB <- values$TABAu
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Local_Cited_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Local_Cited_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Relevant_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[3], digits=2)
+
+ })
+ ## Most Cited Authors ----
+ MLCAuthors <- eventReactive(input$applyMLCAuthors,{
+ res <- descriptive(values,type="tab13")
+ values <-res$values
+ values$TABAuCit<-values$TAB
+
+ #xx=as.data.frame(values$results$Authors, stringsAsFactors = FALSE)
+ xx <- values$TABAuCit
+ lab <- "Local Citations"
+ xx[,2]=as.numeric(xx[,2])
+
+ if (input$MostCitAuthorsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostCitAuthorsK}
+
+ xx=xx[1:k,]
+ xx[,2]=round(xx[,2],1)
+
+ xx <- xx[order(-xx[,2]),]
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Authors", textLabx = lab, title = "Most Local Cited Authors")
+
+ values$MLCAplot <- g
+ return(g)
+ })
+
+ output$MLCAplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostLocalCitedAuthors-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MLCAplot, dpi = as.numeric(input$MLCAdpi), height = input$MLCAh, width = input$MLCAh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostCitAuthorsPlot <- renderPlotly({
+
+ g <- MLCAuthors()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostCitAuthorsTable <- DT::renderDT({
+
+ TAB <- values$TABAuCit
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Local_Cited_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Local_Cited_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Relevant_Authors',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+ ## Authors' Impact ----
+ HAuthors <- eventReactive(input$applyHAuthors,{
+ withProgress(message = 'Calculation in progress',
+ value = 0, {
+ res <- Hindex_plot(values,type="author")
+ })
+ values$AIplot <- res$g
+ return(res)
+ })
+
+ output$AIplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("AuthorImpact-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$AIplot, dpi = as.numeric(input$AIdpi), height = input$AIh, width = input$AIh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$AuthorHindexPlot <- renderPlotly({
+
+ res <- HAuthors()
+ plot.ly(res$g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+
+ })#, height = 500, width =900)
+
+ output$AuthorHindexTable <- DT::renderDT({
+
+ DT::datatable(values$H, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Author_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Author_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Author_Impact',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$H))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$H), backgroundColor = 'white',textAlign = 'center') %>%
+ formatRound(names(values$H)[4], 3)
+
+ })
+ ## Authors Production Over Time ----
+ AUoverTime <- eventReactive(input$applyAUoverTime,{
+ values$AUProdOverTime <- authorProdOverTime(values$M, k=input$TopAuthorsProdK, graph=FALSE)
+ })
+
+ output$APOTplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("AuthorsProductionOverTime-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$AUProdOverTime$graph, dpi = as.numeric(input$APOTdpi), height = input$APOTh, width = input$APOTh*2.5, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$TopAuthorsProdPlot <- renderPlotly({
+ AUoverTime()
+
+ plot.ly(values$AUProdOverTime$graph, flip=TRUE, side="l", aspectratio=1)
+
+
+ })#, height = 550, width =1100)
+
+ output$TopAuthorsProdTable <- DT::renderDT({
+ AUoverTime()
+
+ TAB <- values$AUProdOverTime$dfAU
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Author_Production_Over_Time',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Author_Production_Over_Time',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Author_Production_Over_Time',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[dim(TAB)[2]], 3)
+
+ })
+
+ output$TopAuthorsProdTablePapers <- DT::renderDT({
+ AUoverTime()
+ TAB <- values$AUProdOverTime$dfPapersAU
+ TAB$DOI=paste0('',TAB$DOI,'')
+ DT::datatable(TAB, rownames = FALSE, escape = FALSE,extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Author_Production_Over_Time_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Author_Production_Over_Time_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Author_Production_Over_Time_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[dim(TAB)[2]], 3)
+
+ })
+ ## Lotka Law ----
+ output$lotkaPlot <- renderPlotly({
+
+ values$lotka=lotka(biblioAnalysis(values$M))
+ AuProd=values$lotka$AuthorProd
+ AuProd$Theoretical=10^(log10(values$lotka$C)-2*log10(AuProd[,1]))
+ AuProd$Theoretical=AuProd$Theoretical/sum(AuProd$Theoretical)
+
+ x <- c(max(AuProd$N.Articles)-0.02-diff(range(AuProd$N.Articles))*0.125, max(AuProd$N.Articles)-0.02)+1
+ y <- c(min(AuProd$Freq*100),min(AuProd$Freq*100)+diff(range(AuProd$Freq*100))*0.125)
+
+ g=ggplot2::ggplot(AuProd, aes(x = .data$N.Articles, y = .data$Freq*100, text=paste("N.Articles: ",.data$N.Articles,"\n% of production: ",round(.data$Freq*100,1)))) +
+ geom_line(aes(group="NA")) +
+ geom_area(aes(group="NA"),fill = 'grey90', alpha = .5) +
+ geom_line(data=AuProd, aes(y=.data$Theoretical*100, group="NA"),linetype = "dashed",color="black",alpha=0.8)+
+ xlim(0,max(AuProd$N.Articles)+1)+
+ labs(x = 'Documents written'
+ , y = '% of Authors'
+ , title = "The Frequency Distribution of Scientific Productivity") +
+ #scale_x_continuous(breaks= (Y$Year[seq(1,length(Y$Year),by=2)])) +
+ theme(text = element_text(color = "#444444")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 0)
+ ,axis.title.x = element_text(hjust = 0)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) +
+ annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+ values$LLplot <- g
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.4, size=0.10)
+
+ })#,height = 600)
+
+ output$LLplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("LotkaLaw-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$LLplot, dpi = as.numeric(input$LLdpi), height = input$LLh, width = input$LLh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$lotkaTable <- DT::renderDT({
+ names(values$lotka$AuthorProd)=c("Documents written","N. of Authors","Proportion of Authors")
+ DT::datatable(values$lotka$AuthorProd, rownames = FALSE,
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Lotka_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Lotka_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Lotka_Law',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$lotka$AuthorProd))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$lotka$AuthorProd), backgroundColor = 'white',textAlign = 'center') %>%
+ formatRound(names(values$lotka$AuthorProd)[3], 3)
+ })
+
+
+ # Affiliations ----
+ ## Most Relevant Affliations ----
+ MRAffiliations <- eventReactive(input$applyMRAffiliations,{
+ if (input$disAff=="Y"){
+ res <- descriptive(values,type="tab11")
+ }else{
+ res <- descriptive(values,type="tab12")
+ }
+ xx=values$TAB
+ names(xx)=c("AFF","Freq")
+ values <-res$values
+ values$TABAff <- values$TAB
+
+
+ if (input$MostRelAffiliationsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelAffiliationsK}
+
+ xx=xx[1:k,]
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Affiliations", textLabx = "Articles", title = "Most Relevant Affiliations")
+
+ values$AFFplot <- g
+ return(g)
+ })
+
+ output$AFFplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostRelevantAffiliations-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$AFFplot, dpi = as.numeric(input$AFFdpi), height = input$AFFh, width = input$AFFh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostRelAffiliationsPlot <- renderPlotly({
+
+ g <- MRAffiliations()
+
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.15)
+ })#, height = 500, width =900)
+
+ output$MostRelAffiliationsTable <- DT::renderDT({
+ g <- MRAffiliations()
+
+ TAB <- values$TABAff
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Relevant_Affiliations',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Relevant_Affiliations',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Relevant_Affiliations',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+
+
+ # Countries ----
+ ## Country by Corresponding Authors ----
+ CAUCountries <- eventReactive(input$applyCAUCountries,{
+ res <- descriptive(values,type="tab5")
+ values <-res$values
+ values$TABCo <- values$TAB
+
+ k=input$MostRelCountriesK
+ xx <- values$TABCo %>% slice_head(n=k) %>%
+ select(.data$Country,.data$SCP,.data$MCP)
+ xx=xx[order(-(xx$SCP+xx$MCP)),]
+ xx1=cbind(xx[,1:2],rep("SCP",k))
+ names(xx1)=c("Country","Freq","Collaboration")
+ xx2=cbind(xx[,c(1,3)],rep("MCP",k))
+ names(xx2)=c("Country","Freq","Collaboration")
+ xx=rbind(xx2,xx1)
+ xx$Country=factor(xx$Country,levels=xx$Country[1:dim(xx2)[1]])
+
+ xx2 <- xx %>% dplyr::group_by(.data$Country) %>%
+ dplyr::summarize(Freq = sum(.data$Freq))
+
+ #x <- c(length(levels(xx2$Country))*(1-0.125)-0.02, length(levels(xx2$Country))-0.02)
+ x <- c(0.5,0.5+length(levels(xx2$Country))*0.125)+1
+ y <- c(max(xx2$Freq)-0.02-diff(range(xx2$Freq))*0.125,max(xx2$Freq)-0.02)
+
+ g=suppressWarnings(ggplot2::ggplot(data=xx, aes(x=.data$Country, y=.data$Freq,fill=.data$Collaboration, text=paste("Country: ",.data$Country,"\nN.of Documents: ",.data$Freq))) +
+ geom_bar(aes(group="NA"),stat="identity")+
+ scale_x_discrete(limits = rev(levels(xx$Country)))+
+ scale_fill_discrete(name="Collaboration",
+ breaks=c("SCP","MCP"))+
+ labs(title = "Corresponding Author's Country", x = "Countries", y = "N. of Documents",
+ caption = "SCP: Single Country Publications, MCP: Multiple Country Publications")+
+ #theme_minimal()
+ theme(plot.caption = element_text(size = 9, hjust = 0.5,
+ color = "blue", face = "italic")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ #,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major.y = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 0)
+ ,axis.title.x = element_text(hjust = 0)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ #,axis.line.y = element_line(color="black",size=0.5)
+ )+
+ coord_flip()) +
+ annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+
+ values$MRCOplot <- g
+ return(g)
+ })
+
+ output$MRCOplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostRelevantCountries-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MRCOplot, dpi = as.numeric(input$MRCOdpi), height = input$MRCOh, width = input$MRCOh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostRelCountriesPlot <- renderPlotly({
+
+ g <- CAUCountries()
+
+ plot.ly(g,flip=T, side="r", aspectratio=1.4, size=0.10, data.type=1)
+
+ })#, height = 500, width =900)
+
+ output$MostRelCountriesTable <- DT::renderDT({
+ g <- CAUCountries()
+
+ TAB <- values$TABCo
+ # TAB=format(TAB,justify="left",digits=3)
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Relevant_Countries_By_Corresponding_Author',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Relevant_Countries_By_Corresponding_Author',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Relevant_Countries_By_Corresponding_Author',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[5], digits=3) %>%
+ formatRound(names(TAB)[6], digits=3)
+
+ })
+
+ ## Country Production ----
+ output$countryProdPlot <- renderPlotly({
+ values$mapworld<-mapworld(values$M)
+ plot.ly(values$mapworld$g,flip=FALSE, side="r", aspectratio=1.7, size=0.07, data.type=1,height=15)
+ })#, height = 500, width =900)
+
+ output$CSPplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("CountryScientificProduction-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$mapworld$g, dpi = as.numeric(input$CSPdpi), height = input$CSPh, width = input$CSPh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$countryProdTable <- DT::renderDT({
+
+ TAB <- values$mapworld$tab
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Country_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Country_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Country_Production',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+ ## Most Cited Country ----
+ MCCountries <- eventReactive(input$applyMCCountries,{
+ res <- descriptive(values,type="tab6")
+ values <-res$values
+ values$TABCitCo <- values$TAB
+
+ xx=values$TAB
+ xx[,2]=as.numeric(xx[,2])
+ xx[,3]=as.numeric(xx[,3])
+ if (input$MostCitCountriesK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelAffiliationsK}
+ if (input$CitCountriesMeasure=="TC"){
+ xx=xx[1:k,c(1,2)]
+ laby="N. of Citations"
+ } else {
+ xx=xx[order(-xx[,3]),]
+ xx=xx[1:k,c(1,3)]
+ laby="N. of Citations per Year"
+ }
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Countries", textLabx = laby, title = "Most Cited Countries")
+
+ values$MCCplot <- g
+ return(g)
+ })
+
+ output$MCCplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostCitedCountries-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MCCplot, dpi = as.numeric(input$MCCdpi), height = input$MCCh, width = input$MCCh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostCitCountriesPlot <- renderPlotly({
+ g <- MCCountries()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1.3, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostCitCountriesTable <- DT::renderDT({
+ g <- MCCountries()
+ TAB <- values$TABCitCo
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Cited_Countries',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Cited_Countries',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Cited_Countries',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[3], 2)
+
+ })
+
+
+ # DOCUMENTS MENU ----
+ ## Most Global Cited Documents ----
+
+ MGCDocuments <- eventReactive(input$applyMGCDocuments,{
+ res <- descriptive(values,type="tab4")
+ values <-res$values
+ values$TABGlobDoc <- values$TAB
+
+ if (input$CitDocsMeasure=="TC"){
+ xx <- values$TABGlobDoc %>% select(1,3)
+ lab="Global Citations"} else {
+ xx <- values$TABGlobDoc %>% select(1,4)
+ lab="Global Citations per Year"
+ }
+
+ if (input$MostCitDocsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostCitDocsK}
+
+ xx=xx[1:k,]
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "Documents", textLabx = lab, title = "Most Global Cited Documents")
+
+ values$MGCDplot <- g
+ return(g)
+ })
+
+ output$MGCDplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostGlobalCitedDocuments-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MGCDplot, dpi = as.numeric(input$MGCDdpi), height = input$MGCDh, width = input$MGCDh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostCitDocsPlot <- renderPlotly({
+
+ g <- MGCDocuments()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostCitDocsTable <- DT::renderDT({
+ g <- MGCDocuments()
+ TAB <- values$TABGlobDoc
+ TAB$DOI<- paste0('',TAB$DOI,'')
+ DT::datatable(TAB, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Global_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Global_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Global_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[4], 2) %>%
+ formatRound(names(TAB)[5], 2)
+
+ })
+ ## Most Local Cited Documents ----
+ MLCDocuments <- eventReactive(input$applyMLCDocuments,{
+ withProgress(message = 'Calculation in progress',
+ value = 0, {
+ TAB <-localCitations(values$M, fast.search=FALSE, sep = input$LocCitSep)$Paper
+ TAB <- TAB %>%
+ group_by(.data$Year) %>%
+ mutate(Ratio = .data$LCS/.data$GCS*100,
+ NLCS = .data$LCS/mean(.data$LCS),
+ NGCS = .data$GCS/mean(.data$GCS)) %>%
+ ungroup() %>%
+ as.data.frame()
+
+ })
+
+ xx=data.frame(Document=as.character(TAB[,1]), DOI=as.character(TAB[,2]), Year=TAB[,3],
+ "Local Citations"=TAB[,4], "Global Citations"=TAB[,5],"LC/GC Ratio"=TAB[6],
+ "Normalized Local Citations"=TAB[,7],"Normalized Global Citations"=TAB[,8], stringsAsFactors = FALSE)
+ values$TABLocDoc=xx
+
+ if (input$MostLocCitDocsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostLocCitDocsK}
+
+ xx=xx[1:k,]
+
+ g <- freqPlot(xx,x=4,y=1, textLaby = "Documents", textLabx = "Local Citations", title = "Most Local Cited Documents")
+
+ values$MLCDplot <- g
+ return(g)
+ })
+
+ output$MLCDplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostLocalCitedDocuments-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MLCDplot, dpi = as.numeric(input$MLCDdpi), height = input$MLCDh, width = input$MLCDh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostLocCitDocsPlot <- renderPlotly({
+
+ g <- MLCDocuments()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=1, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostLocCitDocsTable <- DT::renderDT({
+
+ TAB <- values$TABLocDoc
+ TAB$DOI <- paste0('',TAB$DOI,'')
+
+ names(TAB)[4:8] <- c("Local Citations", "Global Citations","LC/GC Ratio (%)", "Normalized Local Citations","Normalized Global Citations")
+ DT::datatable(TAB, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Local_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Local_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Local_Cited_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%') %>%
+ formatRound(names(TAB)[c(6:8)], digits=2)
+
+ })
+
+ ## Most Local Cited References ----
+ MLCReferences <- eventReactive(input$applyMLCReferences,{
+ CR=citations(values$M,sep=input$CitRefsSep)$Cited
+ TAB=data.frame(names(CR),as.numeric(CR),stringsAsFactors = FALSE)
+ names(TAB)=c("Cited References", "Citations")
+ values$TABCitRef=TAB
+
+ xx=values$TABCitRef
+ if (input$MostCitRefsK>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostCitRefsK}
+
+ xx=xx[1:k,]
+ #xx[,1]=substr(xx[,1],1,50)
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = "References", textLabx = "Local Citations", title = "Most Local Cited References")
+
+ values$MLCRplot <- g
+ return(g)
+ })
+
+ output$MLCRplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostLocalCitedReferences-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MLCRplot, dpi = as.numeric(input$MLCRdpi), height = input$MLCRh, width = input$MLCRh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostCitRefsPlot <- renderPlotly({
+
+ g <- MLCReferences()
+ plot.ly(g,flip=FALSE, side="r", aspectratio=0.6, size=0.20)
+ })#, height = 500, width =900)
+
+ output$MostCitRefsTable <- DT::renderDT({
+ g <- MLCReferences()
+ TAB <- values$TABCitRef
+
+ TAB$link <- trimES(gsub("[[:punct:]]" , " ",reduceRefs(TAB[,1])))
+
+
+ TAB$link <- paste0('','link','')
+
+ TAB=TAB[,c(3,1,2)]
+ names(TAB)[1]="Google Scholar"
+ DT::datatable(TAB, rownames = FALSE, escape=FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Local_Cited_References',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Local_Cited_References',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Local_Cited_References',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+ ## Reference Spectroscopy ----
+ RPYS <- eventReactive(input$applyRPYS,{
+
+ timespan <- c(-Inf,Inf)
+ if (!is.na(input$rpysMinYear)){
+ timespan[1] <- input$rpysMinYear
+ }
+ if (!is.na(input$rpysMaxYear)){
+ timespan[2] <- input$rpysMaxYear
+ }
+ values$res <- rpys(values$M, sep=input$rpysSep, timespan=timespan, graph=FALSE)
+ })
+
+ output$RSplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("ReferenceSpectroscopy-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$res$spectroscopy, dpi = as.numeric(input$RSdpi), height = input$RSh, width = input$RSh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$rpysPlot <- renderPlotly({
+
+ RPYS()
+ plot.ly(values$res$spectroscopy, side="l", aspectratio = 1.3, size=0.10)
+
+ })#,height = 600, width = 900)
+
+ output$rpysTable <- DT::renderDT({
+ RPYS()
+ rpysData=values$res$rpysTable
+
+ DT::datatable(rpysData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'RPYS',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'RPYS',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'RPYS',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(rpysData))-1))))) %>%
+ formatStyle(names(rpysData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$crTable <- DT::renderDT({
+ RPYS()
+ crData=values$res$CR
+ crData$link <- paste0('','link','')
+
+ crData=crData[order(-as.numeric(crData$Year),-crData$Freq),]
+ names(crData)=c("Year", "Reference", "Local Citations", "Google link")
+ crData <- crData[,c(1,4,2,3)]
+ DT::datatable(crData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'RPYS_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'RPYS_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'RPYS_Documents',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(crData))-1))))) %>%
+ formatStyle(names(crData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+
+ # Words ----
+ ## Most Frequent Words ----
+ MFWords <- eventReactive(input$applyMFWords,{
+ if (input$MostRelWords %in% c("TI","AB")){
+ ngrams <- as.numeric(input$MRWngrams)
+ }else{
+ ngrams <- 1
+ }
+
+ ### load file with terms to remove
+ if (input$MostRelWordsStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$MostRelWordsStop, sep=input$MostRelWordsSep))
+ }else{remove.terms <- NULL}
+ values$MRWremove.terms <- remove.terms
+ ### end of block
+
+ ### load file with synonyms
+ if (input$MRWSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$MRWSyn, sep=input$MRWSynSep))
+ }else{synonyms <- NULL}
+ values$MRWsyn.terms <- synonyms
+ ### end of block
+
+ WR=wordlist(values$M,Field=input$MostRelWords,n=Inf,measure="identity", ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)$v
+
+ TAB=data.frame(names(WR),as.numeric(WR),stringsAsFactors = FALSE)
+ names(TAB)=c("Words", "Occurrences")
+ values$TABWord=TAB
+
+ xx=values$TABWord
+ if (input$MostRelWordsN>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=input$MostRelWordsN}
+
+ xx=xx[1:k,]
+ switch(input$MostRelWords,
+ ID={lab="Keywords Plus"},
+ DE={lab="Author's Keywords"},
+ TI={lab="Title's Words"},
+ AB={lab="Abstract's Words"})
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = lab, textLabx = "Occurrences", title = "Most Relevant Words")
+
+ values$MRWplot <- g
+ return(g)
+
+ })
+
+ output$MostRelWordsStopPreview <- renderUI({
+
+ if (!is.null(values$MRWremove.terms) | exists("values$MRWremove.terms")){
+ strPreview(values$MRWremove.terms, input$MostRelWordsSep)
+ }else{
+ strPreview(" ", input$MostRelWordsSep)
+ }
+ })
+
+ output$MRWSynPreview <- renderUI({
+
+ if (!is.null(values$MRWsyn.terms) | exists("values$MRWsyn.terms")){
+ strSynPreview(values$MRWsyn.terms)
+ }else{
+ strSynPreview(" ; ")
+ }
+ })
+
+ output$MRWplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostRelevantWords-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$MRWplot, dpi = as.numeric(input$MRWdpi), height = input$MRWh, width = input$MRWh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$MostRelWordsPlot <- renderPlotly({
+ g <- MFWords()
+ plot.ly(g, side="r", aspectratio = 1.3, size=0.10)
+ })#, height = 500, width =900)
+
+ output$MostRelWordsTable <- DT::renderDT({
+ g <- MFWords()
+
+ TAB <- values$TABWord
+
+ DT::datatable(TAB, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TAB))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(TAB), backgroundColor = 'white',textAlign = 'center', fontSize = '110%')
+
+ })
+ ## WordCloud ----
+ WordCloud <- eventReactive(input$applyWordCloud,{
+
+ if (input$summaryTerms %in% c("TI","AB")){
+ ngrams <- as.numeric(input$summaryTermsngrams)
+ }else{
+ ngrams <- 1
+ }
+
+ ### load file with terms to remove
+ if (input$WCStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$WCStop, sep=input$WCSep))
+ }else{remove.terms <- NULL}
+ values$WCremove.terms <- remove.terms
+ ### end of block
+
+ ### load file with synonyms
+ if (input$WCSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$WCSyn, sep=input$WCSynSep))
+ }else{synonyms <- NULL}
+ values$WCsyn.terms <- synonyms
+ ### end of block
+ print(values$WCsyn.terms )
+
+ resW=wordlist(M=values$M, Field=input$summaryTerms, n=input$n_words, measure=input$measure, ngrams=ngrams, remove.terms = remove.terms, synonyms = values$WCsyn.terms)
+
+ W=resW$W
+ values$Words=resW$Words
+
+ wordcloud2::wordcloud2(W, size = input$scale, minSize = 0, gridSize = input$padding,
+ fontFamily = input$font, fontWeight = 'normal',
+ color = input$wcCol, backgroundColor = "white", #input$wcBGCol,
+ minRotation = 0, maxRotation = input$rotate/10, shuffle = TRUE,
+ rotateRatio = 0.7, shape = input$wcShape, ellipticity = input$ellipticity,
+ widgetsize = NULL, figPath = NULL, hoverFunction = NULL)
+ })
+ output$wordcloud <- wordcloud2::renderWordcloud2({
+
+ WordCloud()
+ })
+
+ ## TreeMap ----
+ TreeMap <- eventReactive(input$applyTreeMap,{
+ if (input$treeTerms %in% c("TI","AB")){
+ ngrams <- as.numeric(input$treeTermsngrams)
+ }else{
+ ngrams <- 1
+ }
+ ### load file with terms to remove
+ if (input$TreeMapStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$TreeMapStop, sep=input$TreeMapSep))
+ }else{remove.terms <- NULL}
+ values$TreeMapremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$TreeMapSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$TreeMapSyn, sep=input$TreeMapSynSep))
+ }else{synonyms <- NULL}
+ values$TreeMapsyn.terms <- synonyms
+ ### end of block
+
+ resW=wordlist(M=values$M, Field=input$treeTerms, n=input$treen_words, measure="identity", ngrams=ngrams, remove.terms=remove.terms, synonyms = synonyms)
+
+ W=resW$W
+ values$TreeMap <- plot_ly(
+ type='treemap',
+ labels=W[,1],
+ parents="Tree",
+ values= W[,2],
+ textinfo="label+value+percent entry",
+ domain=list(column=0))
+
+ values$WordsT=resW$Words
+ return(resW$Words)
+
+ })
+
+ output$treemap <- renderPlotly({
+ TreeMap()
+ values$TreeMap
+ })
+
+ output$TreeMapStopPreview <- renderUI({
+
+ if (!is.null(values$TreeMapremove.terms) | exists("values$TreeMapremove.terms")){
+ strPreview(values$TreeMapremove.terms, input$TreeMapSep)
+ }else{
+ strPreview(" ", input$TreeMapSep)
+ }
+ })
+
+ output$TreeMapSynPreview <- renderUI({
+
+ if (!is.null(values$TreeMapsyn.terms) | exists("values$TreeMapsyn.terms")){
+ strSynPreview(values$TreeMapsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+
+ output$wordTable <- DT::renderDT({
+ WordCloud()
+
+ DT::datatable(values$Words, rownames = FALSE,
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$Words))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$Words), backgroundColor = 'white',textAlign = 'center')
+ })
+
+ output$treeTable <- DT::renderDT({
+ WordsT <- TreeMap()
+
+ DT::datatable(values$WordsT, rownames = FALSE,
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Most_Frequent_Words',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(values$WordsT))-1)))),
+ class = 'cell-border compact stripe') %>%
+ formatStyle(names(values$WordsT), backgroundColor = 'white',textAlign = 'center')
+
+ },height = 600, width = 900)
+ ## Word Dynamics ----
+ WDynamics <- eventReactive(input$applyWD,{
+ if (input$cumTerms=="Cum"){
+ cdf=TRUE
+ laby="Cumulate occurrences"
+ }else{
+ cdf=FALSE
+ laby="Annual occurrences"}
+ #if (input$se=="Yes"){se=TRUE}else{se=FALSE}
+
+ ### load file with terms to remove
+ if (input$WDStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$WDStop, sep=input$WDSep))
+ }else{remove.terms <- NULL}
+ values$WDremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$WDSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$WDSyn, sep=input$WDSynSep))
+ }else{synonyms <- NULL}
+ values$WDsyn.terms <- synonyms
+ ### end of block
+
+ switch(input$growthTerms,
+ ID={
+ KW=KeywordGrowth(values$M, Tag = "ID", sep = ";", top = input$topkw[2], cdf = cdf, remove.terms=remove.terms, synonyms = synonyms)
+
+ },
+ DE={
+ KW=KeywordGrowth(values$M, Tag = "DE", sep = ";", top = input$topkw[2], cdf = cdf, remove.terms=remove.terms, synonyms = synonyms)
+ },
+ TI={
+ #if (!("TI_TM" %in% names(values$M))){
+ values$M=termExtraction(values$M,Field = "TI", verbose=FALSE, ngrams=as.numeric(input$growthTermsngrams), remove.terms=remove.terms, synonyms = synonyms)
+ #}
+ KW=KeywordGrowth(values$M, Tag = "TI_TM", sep = ";", top = input$topkw[2], cdf = cdf)
+ },
+ AB={
+ #if (!("AB_TM" %in% names(values$M))){
+ values$M=termExtraction(values$M,Field = "AB", verbose=FALSE, ngrams=as.numeric(input$growthTermsngrams), remove.terms=remove.terms, synonyms = synonyms)
+ #}
+ KW=KeywordGrowth(values$M, Tag = "AB_TM", sep = ";", top = input$topkw[2], cdf = cdf)
+ }
+ )
+
+ values$KW=KW[,c(1,seq(input$topkw[1],input$topkw[2])+1)]
+
+ term=names(values$KW)[-1]
+ term=rep(term,each=dim(values$KW)[1])
+ n=dim(values$KW)[1]*(dim(values$KW)[2]-1)
+ freq=matrix(as.matrix(values$KW[,-1]),n,1)
+ values$DF=data.frame(Year=rep(values$KW$Year,(dim(values$KW)[2]-1)),Term=term, Freq=freq, stringsAsFactors = TRUE)
+
+ width_scale <- 2.5 * 26 / length(unique(values$DF$Term))
+
+ Text <- paste(values$DF$Term," (",values$DF$Year,") ",values$DF$Freq, sep="")
+
+ x <- c(max(values$DF$Year)-0.02-diff(range(values$SO$Year))*0.20, max(values$DF$Year)-0.02)-1
+ y <- c(min(values$DF$Freq),min(values$DF$Freq)+diff(range(values$DF$Freq))*0.20)
+
+ g <- ggplot(values$DF, aes(x=.data$Year,y=.data$Freq, group=.data$Term, color=.data$Term, text = Text))+
+ geom_line()+
+ labs(x = 'Year'
+ , y = laby
+ , title = "Word Growth") +
+ #ylim(0, NA) +
+ scale_x_continuous(breaks= (values$KW$Year[seq(1,length(values$KW$Year),by=ceiling(length(values$KW$Year)/20))])) +
+ geom_hline(aes(yintercept=0), alpha=0.1)+
+ labs(color = "Term")+
+ #guides(fill = guide_legend(nrow = 5))+
+ theme(text = element_text(color = "#444444"),
+ legend.text=ggplot2::element_text(size=width_scale),
+ legend.box.margin = margin(6, 6, 6, 6),
+ legend.title=ggplot2::element_text(size=1.5*width_scale,face="bold"),
+ legend.position="bottom",
+ legend.direction = "vertical",
+ legend.key.size = grid::unit(width_scale/50, "inch"),
+ legend.key.width = grid::unit(width_scale/50, "inch")
+ ,plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 90)
+ ,axis.title.x = element_text(hjust = 0.95, angle = 0)
+ ,axis.text.x = element_text(size=10, angle = 90)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) +
+ annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
+
+ values$WDplot <- g
+ return(g)
+ })
+
+ output$WDStopPreview <- renderUI({
+
+ if (!is.null(values$WDremove.terms) | exists("values$WDremove.terms")){
+ strPreview(values$WDremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$WDSynPreview <- renderUI({
+
+ if (!is.null(values$WDsyn.terms) | exists("values$WDsyn.terms")){
+ strSynPreview(values$WDsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ output$WDplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("WordDynamics-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$WDplot, dpi = as.numeric(input$WDdpi), height = input$WDh, width = input$WDh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$kwGrowthPlot <- renderPlotly({
+
+ g <- WDynamics()
+
+ leg <- list(
+ orientation = 'h',
+ y = -0.15,
+ font = list(
+ family = "sans-serif",
+ size = 10,
+ color = "#000"),
+ bgcolor = "#FFFFFF",
+ bordercolor = "#FFFFFF",
+ borderwidth = 2)
+
+ plot.ly(g, flip=FALSE, side="r", aspectratio=1.6, size=0.10) %>%
+ layout(legend = leg) %>%
+ config(displaylogo = FALSE,
+ modeBarButtonsToRemove = c(
+ 'sendDataToCloud',
+ 'pan2d',
+ 'select2d',
+ 'lasso2d',
+ 'toggleSpikelines'
+ )) %>%
+ layout(hovermode = 'compare')
+
+ #}, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 600, width = 900)
+ })
+
+ output$kwGrowthtable <- DT::renderDT({
+ g <- WDynamics()
+ kwData=values$KW
+
+ DT::datatable(kwData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Word_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Word_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Word_Dynamics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(kwData))-1))))) %>%
+ formatStyle(names(kwData), backgroundColor = 'white')
+ #return(Data)
+ })
+
+ ## Trend Topics ----
+ output$trendSliderPY <- renderUI({
+
+ sliderInput("trendSliderPY", "Timespan", min = min(values$M$PY,na.rm=T),sep="",
+ max = max(values$M$PY,na.rm=T), value = c(min(values$M$PY,na.rm=T),max(values$M$PY,na.rm=T)))
+ })
+
+ TrendTopics <- eventReactive(input$applyTrendTopics,{
+
+ ### load file with terms to remove
+ if (input$TTStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$TTStop, sep=input$TTSep))
+ }else{remove.terms <- NULL}
+ values$TTremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$TTSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$TTSyn, sep=input$TTSynSep))
+ }else{synonyms <- NULL}
+ values$TTsyn.terms <- synonyms
+ ### end of block
+
+ if (input$trendTerms %in% c("TI","AB")){
+ values$M=termExtraction(values$M, Field = input$trendTerms, stemming = input$trendStemming, verbose = FALSE, ngrams=as.numeric(input$trendTermsngrams))
+ field=paste(input$trendTerms,"_TM",sep="")
+ } else {field=input$trendTerms}
+ values$trendTopics <- fieldByYear(values$M, field = field, timespan = input$trendSliderPY, min.freq = input$trendMinFreq,
+ n.items = input$trendNItems, remove.terms = remove.terms, synonyms = synonyms,
+ dynamic.plot=TRUE, graph = FALSE)
+ return(values$trendTopics$graph)
+
+ })
+
+ output$TTStopPreview <- renderUI({
+
+ if (!is.null(values$TTremove.terms) | exists("values$TTremove.terms")){
+ strPreview(values$TTremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$TTSynPreview <- renderUI({
+
+ if (!is.null(values$TTsyn.terms) | exists("values$TTsyn.terms")){
+ strSynPreview(values$TTsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ output$TTplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("TrendTopics-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$trendTopics$graph, dpi = as.numeric(input$TTdpi), height = input$TTh, width = input$TTh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$trendTopicsPlot <- renderPlotly({
+ g <- TrendTopics()
+ plot.ly(g, flip=TRUE, side="r", size=0.1, aspectratio=1.3)
+ })#, height = 500, width =900)
+
+ # output$trendTopicsPlot <- renderPlot({
+ #
+ # TrendTopics()
+ # plot(values$trendTopics$graph)
+ #
+ # }, width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 700)
+
+
+ output$trendTopicsTable <- DT::renderDT({
+ TrendTopics()
+ tpData=values$trendTopics$df_graph
+
+ DT::datatable(tpData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Trend_Topics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Trend_Topics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Trend_Topics',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tpData))-1))))) %>%
+ formatStyle(names(tpData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ # Coupling ----
+
+ CMMAP <- eventReactive(input$applyCM,{
+
+ values$CM <- couplingMap(values$M, analysis=input$CManalysis, field=input$CMfield,
+ n=input$CMn, minfreq=input$CMfreq,
+ ngrams=as.numeric(input$CMngrams),
+ impact.measure=input$CMimpact,
+ stemming=input$CMstemming, size=input$sizeCM,
+ label.term = input$CMlabeling,
+ n.labels=input$CMn.labels, repel=FALSE)
+
+ validate(
+ need(values$CM$nclust > 0, "\n\nNo clusters in one or more periods. Please select a different set of parameters.")
+ )
+ })
+ output$CMPlot <- renderPlotly({
+
+ CMMAP()
+ plot.ly(values$CM$map, size=0.15, aspectratio = 1.3)
+
+ })#, height = 650, width = 800)
+
+ output$CMNetPlot <- renderVisNetwork({
+ CMMAP()
+ values$networkCM<-igraph2vis(g=values$CM$net$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$CM$net,shadow=FALSE)
+
+ values$networkCM$VIS
+
+ })
+
+ output$CMplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("CouplingMap-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$CM$map, dpi = as.numeric(input$CMdpi), height = input$CMh, width = input$CMh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$CMTable <- DT::renderDT({
+ CMMAP()
+ cmData=values$CM$data[,c(2,1,3,5)]
+
+ DT::datatable(cmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CouplingMap',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CouplingMap',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CouplingMap',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cmData))-1))))) %>%
+ formatStyle(names(cmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$CMTableCluster <- DT::renderDT({
+ CMMAP()
+ cmData=values$CM$clusters[,c(7,1:4,6)]
+
+ DT::datatable(cmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CouplingMap_Clusters',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CouplingMap_Clusters',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CouplingMap_Clusters',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cmData))-1))))) %>%
+ formatStyle(names(cmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+ ### Conceptual Structure #####
+
+ ### Co-occurrences network ----
+ COCnetwork <- eventReactive(input$applyCoc,{
+
+ values <- cocNetwork(input,values)
+
+
+ values$network<-igraph2vis(g=values$cocnet$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$cocnet, shadow=(input$coc.shadow=="Yes"))
+
+
+ })
+
+ output$cocPlot <- renderVisNetwork({
+
+ COCnetwork()
+
+ values$network$VIS
+
+ })
+
+ output$COCStopPreview <- renderUI({
+
+ if (!is.null(values$COCremove.terms) | exists("values$COCremove.terms")){
+ strPreview(values$COCremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$COCSynPreview <- renderUI({
+
+ if (!is.null(values$COCsyn.terms) | exists("values$COCsyn.terms")){
+ strSynPreview(values$COCsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ # output$cocPlotComm <- renderVisNetwork({
+ #
+ # g <- splitCommunities(values$cocnet$graph, n=NULL)
+ # igraph2vis(g=g,curved=(input$coc.curved=="Yes"),
+ # labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ # shape=input$coc.shape, net=values$cocnet)$VIS
+ #
+ # })
+
+ output$network.coc <- downloadHandler(
+ filename = "Co_occurrence_network.net",
+ content <- function(file) {
+ igraph::write.graph(values$cocnet$graph_pajek,file=file, format="pajek")
+
+ },
+ contentType = "net"
+ )
+
+ ### save coc network image as html ####
+ output$networkCoc.fig <- downloadHandler(
+ filename = "network.html",
+ content <- function(con) {
+ savenetwork(con)
+ },
+ contentType = "html"
+ )
+
+ output$cocTable <- DT::renderDT({
+ COCnetwork()
+ cocData=values$cocnet$cluster_res
+ names(cocData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
+ DT::datatable(cocData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CoWord_Network_Analysis',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CoWord_Network_Analysis',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CoWord_Network_Analysis',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cocData))-1))))) %>%
+ formatStyle(names(cocData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ ### Degree Plot Co-word analysis ####
+ output$cocDegree <- renderPlotly({
+ COCnetwork()
+ p <- degreePlot(values$cocnet)
+ plot.ly(p)
+ })
+
+
+ ### Correspondence Analysis ----
+
+ CSfactorial <- eventReactive(input$applyCA,{
+ values <- CAmap(input,values)
+ })
+
+ output$CSStopPreview <- renderUI({
+
+ if (!is.null(values$CSremove.terms) | exists("values$CSremove.terms")){
+ strPreview(values$CSremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$FASynPreview <- renderUI({
+
+ if (!is.null(values$FAsyn.terms) | exists("values$FAsyn.terms")){
+ strSynPreview(values$FAsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ output$FA1plot.save <- downloadHandler(
+ filename = function() {
+
+ paste("FactorialMap-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$CS$graph_terms, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
+ },
+ contentType = "png"
+ )
+ output$FA2plot.save <- downloadHandler(
+ filename = function() {
+
+ paste("Dendrogram-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$CS$graph_dendogram, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$FA3plot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostContribDocuments-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$CS$graph_documents_Contrib, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$FA4plot.save <- downloadHandler(
+ filename = function() {
+
+ paste("MostCitedDocuments-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$CS$graph_documents_TC, dpi = as.numeric(input$FAdpi), height = input$FAh, width = input$FAh*1.5, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$CSPlot1 <- renderPlot({
+ CSfactorial()
+ plot(values$CS$graph_terms)
+
+ }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
+ height = exprToFunction(as.numeric(input$dimension[2])*0.85),
+ res = 150)
+ #width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)), res = 150) #height = 650, width = 800)
+
+ output$CSPlot2 <- renderPlot({
+ CSfactorial()
+ if (input$method!="MDS"){
+
+ if (values$CS[[1]][1]!="NA"){
+
+ plot(values$CS$graph_documents_Contrib)
+ }else{
+ emptyPlot("Selected field is not included in your data collection")
+ }
+ }else{
+ emptyPlot("This plot is available only for CA or MCA analyses")
+ }
+
+ }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
+ height = exprToFunction(as.numeric(input$dimension[2])*0.85),
+ res = 150)
+
+ output$CSPlot3 <- renderPlot({
+ CSfactorial()
+ if (input$method!="MDS"){
+ if (values$CS[[1]][1]!="NA"){
+ plot(values$CS$graph_documents_TC)
+ }else{
+ emptyPlot("Selected field is not included in your data collection")
+ }
+ }else{
+ emptyPlot("This plot is available only for CA or MCA analyses")
+ }
+
+
+ }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
+ height = exprToFunction(as.numeric(input$dimension[2])*0.85),
+ res = 150)
+
+ output$CSPlot4 <- renderPlot({
+
+ CSfactorial()
+ if (values$CS[[1]][1]!="NA"){
+ plot(values$CS$graph_dendogram)
+ }else{
+ emptyPlot("Selected field is not included in your data collection")
+ }
+
+ }, width = exprToFunction(as.numeric(input$dimension[1])*0.6),
+ height = exprToFunction(as.numeric(input$dimension[2])*0.85),
+ res = 150)
+
+ output$CSTableW <- DT::renderDT({
+ CSfactorial()
+ switch(input$method,
+ CA={
+ WData=data.frame(word=row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
+ stringsAsFactors = FALSE)
+ names(WData)[4]="cluster"
+ },
+ MCA={
+ WData=data.frame(word=row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
+ stringsAsFactors = FALSE)
+ names(WData)[4]="cluster"
+ },
+ MDS={
+ WData=data.frame(word=row.names(values$CS$res), values$CS$res,
+ cluster=values$CS$km.res$cluster,stringsAsFactors = FALSE)
+ })
+
+ WData$Dim.1=round(WData$Dim.1,2)
+ WData$Dim.2=round(WData$Dim.2,2)
+
+ DT::datatable(WData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CoWord_Factorial_Analysis_Words_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(WData))-1))))) %>%
+ formatStyle(names(WData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$CSTableD <- DT::renderDT({
+ CSfactorial()
+ CSData=values$CS$docCoord
+ CSData=data.frame(Documents=row.names(CSData),CSData,stringsAsFactors = FALSE)
+ CSData$dim1=round(CSData$dim1,2)
+ CSData$dim2=round(CSData$dim2,2)
+ CSData$contrib=round(CSData$contrib,2)
+ DT::datatable(CSData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CoWord_Factorial_Analysis_Articles_By_Cluster',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(CSData))-1))))) %>%
+ formatStyle(names(CSData), backgroundColor = 'white')
+
+ })
+
+ ### Thematic Map ----
+ TMAP <- eventReactive(input$applyTM,{
+
+ if (input$TMfield %in% c("TI","AB")){
+ ngrams <- as.numeric(input$TMngrams)
+ }else{
+ ngrams <- 1
+ }
+
+ ### load file with terms to remove
+ if (input$TMStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$TMStop, sep=input$TMSep))
+ }else{remove.terms <- NULL}
+ values$TMremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$TMapSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$TMapSyn, sep=input$TMapSynSep))
+ }else{synonyms <- NULL}
+ values$TMapsyn.terms <- synonyms
+ ### end of block
+
+ values$TM <- thematicMap(values$M, field=input$TMfield,
+ n=input$TMn, minfreq=input$TMfreq, ngrams=ngrams,
+ stemming=input$TMstemming, size=input$sizeTM,
+ n.labels=input$TMn.labels, repel=FALSE, remove.terms=remove.terms, synonyms=synonyms)
+
+ validate(
+ need(values$TM$nclust > 0, "\n\nNo topics in one or more periods. Please select a different set of parameters.")
+ )
+ })
+ output$TMPlot <- renderPlotly({
+
+ TMAP()
+ plot.ly(values$TM$map, size=0.07, aspectratio = 1.3)
+
+ })#, height = 650, width = 800)
+
+ output$NetPlot <- renderVisNetwork({
+ TMAP()
+ values$networkTM<-igraph2vis(g=values$TM$net$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$TM$net)
+
+ values$networkTM$VIS
+
+ })
+
+ output$TMStopPreview <- renderUI({
+
+ if (!is.null(values$TMremove.terms) | exists("values$TMremove.terms")){
+ strPreview(values$TMremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$TMapSynPreview <- renderUI({
+
+ if (!is.null(values$TMapsyn.terms) | exists("values$TMapsyn.terms")){
+ strSynPreview(values$TMapsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ output$TMplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("ThematicMap-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$TM$map, dpi = as.numeric(input$TMdpi), height = input$TMh, width = input$TMh*1.5, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$TMTable <- DT::renderDT({
+ TMAP()
+ tmData=values$TM$words[,-4]
+
+
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster <- DT::renderDT({
+ TMAP()
+ tmData <- values$TM$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ ### Thematic Evolution ----
+ output$sliders <- renderUI({
+ numSlices <- as.integer(input$numSlices)
+ v=quantile(values$M$PY, seq(0,1,by=(1/(numSlices+1))), na.rm=TRUE)
+ v=round(v[-c(1,length(v))],0)
+ lapply(1:numSlices, function(i) {
+ # sliderInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),
+ # min=1990,max=2018,value=1990)
+
+ numericInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),value=v[i],min=min(values$M$PY, na.rm = TRUE)+1,max=max(values$M$PY, na.rm = TRUE)-1, step=1)
+ #numericInput(inputId = paste0("Slice", i), label = paste("Cutting Year", i),value=median(values$M$PY),min=min(values$M$PY)+1,max=max(values$M$PY)-1, step=1)
+ })
+ })
+
+ TEMAP <- eventReactive(input$applyTE,{
+ if (input$TEfield %in% c("TI","AB")){
+ ngrams <- as.numeric(input$TEngrams)
+ }else{
+ ngrams <- 1
+ }
+
+ ### load file with terms to remove
+ if (input$TEStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$TEStop, sep=input$TESep))
+ }else{remove.terms <- NULL}
+ values$TEremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$TESynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$TESyn, sep=input$TESynSep))
+ }else{synonyms <- NULL}
+ values$TEsyn.terms <- synonyms
+ ### end of block
+
+ values$yearSlices <- as.numeric()
+ for (i in 1:as.integer(input$numSlices)){
+ if (length(input[[paste0("Slice", i)]])>0){values$yearSlices=c(values$yearSlices,input[[paste0("Slice", i)]])}
+ }
+
+ if (length(values$yearSlices)>0){
+ values$nexus <- thematicEvolution(values$M, field=input$TEfield, values$yearSlices, n = input$nTE, minFreq = input$fTE, size = input$sizeTE,
+ n.labels=input$TEn.labels, repel=FALSE, ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)
+
+ validate(
+ need(values$nexus$check != FALSE, "\n\nNo topics in one or more periods. Please select a different set of parameters.")
+ )
+
+ plotThematicEvolution(Nodes = values$nexus$Nodes,Edges = values$nexus$Edges, measure = input$TEmeasure, min.flow = input$minFlowTE)
+ }
+ })
+
+ output$TEPlot <- plotly::renderPlotly({
+
+ TEMAP()
+
+ })
+
+ output$TEStopPreview <- renderUI({
+
+ if (!is.null(values$TEremove.terms) | exists("values$TEremove.terms")){
+ strPreview(values$TEremove.terms)
+ }else{
+ strPreview(" ")
+ }
+ })
+
+ output$TESynPreview <- renderUI({
+
+ if (!is.null(values$TEsyn.terms) | exists("values$TEsyn.terms")){
+ strSynPreview(values$TEsyn.terms)
+ }else{
+ strSynPreview(" ")
+ }
+ })
+
+ output$TETable <- DT::renderDT({
+ TEMAP()
+ TEData=values$nexus$Data
+ TEData=TEData[TEData$Inc_index>0,-c(4,8)]
+ names(TEData)=c("From", "To", "Words", "Weighted Inclusion Index", "Inclusion Index", "Occurrences", "Stability Index")
+ DT::datatable(TEData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Evolution',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Evolution',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Evolution',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(TEData))-1))))) %>%
+ formatStyle(names(TEData), backgroundColor = 'white') %>%
+ formatRound(names(TEData)[4], 2) %>%
+ formatRound(names(TEData)[5], 2) %>%
+ formatRound(names(TEData)[7], 2)
+ #return(Data)
+
+ })
+
+ output$TMPlot1 <- renderPlotly({
+ TEMAP()
+ #input$applyTM
+ if (length(values$nexus$TM)>=1){
+ plot.ly(values$nexus$TM[[1]]$map, size=0.07, aspectratio = 1.3)
+ } else {emptyPlot("You have selected fewer periods!")}
+
+ })#, height = 650, width = 800)
+
+ output$TMPlot2 <- renderPlotly({
+ TEMAP()
+ #input$applyTM
+ if (length(values$nexus$TM)>=2){
+ plot.ly(values$nexus$TM[[2]]$map, size=0.07, aspectratio = 1.3)
+ } else {emptyPlot("You have selected fewer periods!")}
+
+ })#, height = 650, width = 800)
+
+ output$TMPlot3 <- renderPlotly({
+ TEMAP()
+ #input$applyTM
+ if (length(values$nexus$TM)>=3){
+ plot.ly(values$nexus$TM[[3]]$map, size=0.07, aspectratio = 1.3)
+ } else {emptyPlot("You have selected fewer periods!")}
+
+ })#, height = 650, width = 800)
+
+ output$TMPlot4 <- renderPlotly({
+ TEMAP()
+ #input$applyTM
+ if (length(values$nexus$TM)>=4){
+ plot.ly(values$nexus$TM[[4]]$map, size=0.07, aspectratio = 1.3)
+ } else (emptyPlot("You have selected fewer periods!"))
+
+ })#, height = 650, width = 800)
+
+ output$TMPlot5 <- renderPlotly({
+ TEMAP()
+ #input$applyTM
+ if (length(values$nexus$TM)>=5){
+ plot.ly(values$nexus$TM[[5]]$map, size=0.07, aspectratio = 1.3)
+ } else (emptyPlot("You have selected fewer periods!"))
+
+ })#, height = 650, width = 800)
+
+ output$NetPlot1 <- renderVisNetwork({
+ TEMAP()
+ k=1
+ values$network1<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$nexus$Net[[k]])
+
+ values$network1$VIS
+
+ })
+
+ output$NetPlot2 <- renderVisNetwork({
+ TEMAP()
+ k=2
+ values$network2<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$nexus$Net[[k]])
+
+ values$network2$VIS
+
+ })
+
+ output$NetPlot3 <- renderVisNetwork({
+ TEMAP()
+ k=3
+ values$network3<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$nexus$Net[[k]])
+
+ values$network3$VIS
+
+ })
+
+ output$NetPlot4 <- renderVisNetwork({
+ TEMAP()
+ k=4
+ values$network4<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$nexus$Net[[k]])
+
+ values$network4$VIS
+
+ })
+
+ output$NetPlot5 <- renderVisNetwork({
+ TEMAP()
+ k=5
+ values$network5<-igraph2vis(g=values$nexus$Net[[k]]$graph,curved=(input$coc.curved=="Yes"),
+ labelsize=input$labelsize, opacity=input$cocAlpha,type=input$layout,
+ shape=input$coc.shape, net=values$nexus$Net[[k]])
+
+ values$network5$VIS
+
+ })
+
+ output$TMTable1 <- DT::renderDT({
+ TEMAP()
+
+ tmData=values$nexus$TM[[1]]$words[,-4]
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map_Period_1',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map_Period_1',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map_Period_1',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTable2 <- DT::renderDT({
+ TEMAP()
+
+ tmData=values$nexus$TM[[2]]$words[,-4]
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map_Period_2',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map_Period_2',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map_Period_2',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTable3 <- DT::renderDT({
+ TEMAP()
+
+ tmData=values$nexus$TM[[3]]$words[,-4]
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map_Period_3',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map_Period_3',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map_Period_3',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTable4 <- DT::renderDT({
+ TEMAP()
+
+ tmData=values$nexus$TM[[4]]$words[,-4]
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map_Period_4',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map_Period_4',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map_Period_4',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTable5 <- DT::renderDT({
+ TEMAP()
+
+ tmData=values$nexus$TM[[5]]$words[,-4]
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map_Period_5',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map_Period_5',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map_Period_5',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster1 <- DT::renderDT({
+ TEMAP()
+ tmData <- values$nexus$TM[[1]]$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster2 <- DT::renderDT({
+ TEMAP()
+ tmData <- values$nexus$TM[[2]]$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster3 <- DT::renderDT({
+ TEMAP()
+ tmData <- values$nexus$TM[[3]]$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster4 <- DT::renderDT({
+ TEMAP()
+ tmData <- values$nexus$TM[[4]]$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ output$TMTableCluster5 <- DT::renderDT({
+ TEMAP()
+ tmData <- values$nexus$TM[[5]]$clusters[,c(7,1:4,6)]
+ names(tmData) <- c("Cluster", "CallonCentrality","CallonDensity","RankCentrality","RankDensity","ClusterColor")
+
+ DT::datatable(tmData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Thematic_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(tmData))-1))))) %>%
+ formatStyle(names(tmData), backgroundColor = 'white')
+ #return(Data)
+ })
+
+ ### INTELLECTUAL STRUCTURE ####
+
+ ### Co-citation network ----
+ COCITnetwork <- eventReactive(input$applyCocit,{
+
+ values <- intellectualStructure(input,values)
+ #dev.off();file.remove(t) ### end of trick
+
+ values$network<-igraph2vis(g=values$cocitnet$graph,curved=(input$cocit.curved=="Yes"),
+ labelsize=input$citlabelsize, opacity=0.7,type=input$citlayout,
+ shape=input$cocit.shape, net=values$cocitnet, shadow=(input$cocit.shadow=="Yes"))
+ })
+
+ output$cocitPlot <- renderVisNetwork({
+
+ COCITnetwork()
+
+ isolate(values$network$VIS)
+
+ })
+
+ output$network.cocit <- downloadHandler(
+ filename = "Co_citation_network.net",
+ content <- function(file) {
+ igraph::write.graph(values$cocitnet$graph_pajek,file=file, format="pajek")
+ #rio::export(values$M, file=file)
+ },
+ contentType = "net"
+ )
+
+ output$cocitTable <- DT::renderDT({
+ COCITnetwork()
+ cocitData=values$cocitnet$cluster_res
+ names(cocitData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
+ DT::datatable(cocitData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'CoCitation_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'CoCitation_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'CoCitation_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(cocitData))-1))))) %>%
+ formatStyle(names(cocitData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ ### save coc network image as html ####
+ output$networkCocit.fig <- downloadHandler(
+ filename = "network.html",
+ content <- function(con) {
+ savenetwork(con)
+ },
+ contentType = "html"
+ )
+
+ ### Degree Plot Co-citation analysis ####
+ output$cocitDegree <- renderPlotly({
+ COCITnetwork()
+ p <- degreePlot(values$cocitnet)
+ plot.ly(p)
+ })
+
+ ### Historiograph ----
+ Hist <- eventReactive(input$applyHist,{
+
+ withProgress(message = 'Calculation in progress',
+ value = 0, {
+ values <- historiograph(input,values)
+ })
+
+ fx <- list(
+ family = "Old Standard TT, serif",
+ size = 11,
+ color = "black"
+ )
+
+ a <- list(
+ ticks = "outside",
+ autotick = FALSE,
+ ticktext = values$histPlot$axis$label,
+ tickvals = values$histPlot$axis$values,
+ tickmode = "array",
+ showticklabels = TRUE,
+ tickangle = 270,
+ tickfont = fx,
+ ticklen = 2,
+ tickwidth = 2,
+ tickcolor = toRGB("black")
+ )
+
+ g <- plot.ly(values$histPlot$g, side="r", size=0.05, aspectratio = 1.5, height=-0.1) %>%
+ layout(xaxis = a, autosize=TRUE ,showlegend = FALSE,
+ hoverlabel = list(font=list(size=input$histlabelsize+9)))
+ return(g)
+ })
+
+ output$HGplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("Historiograph-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ ggsave(filename = file, plot = values$histPlot$g, dpi = as.numeric(input$HGdpi), height = input$HGh, width = input$HGh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$histPlot <- renderPlotly({
+
+ Hist()
+
+ })
+ output$histTable <- DT::renderDT({
+ LCS=values$histResults$LCS
+ s=sort(LCS,decreasing = TRUE)[input$histNodes]
+ ind=which(LCS>=s)
+ Data=values$histResults$histData
+ Data=Data[ind,]
+ Data$DOI<- paste0('',Data$DOI,'')
+ DT::datatable(Data, escape = FALSE, rownames = FALSE, extensions = c("Buttons"),
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Historiograph_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Historiograph_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Historiograph_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(Data))-1))))) %>%
+ formatStyle(names(Data), backgroundColor = 'white') %>%
+ formatStyle(
+ 'GCS',
+ background = styleColorBar(Data$GCS, 'steelblue'),
+ backgroundSize = '100% 90%',
+ backgroundRepeat = 'no-repeat',
+ backgroundPosition = 'center'
+ ) %>%
+ formatStyle(
+ 'LCS',
+ background = styleColorBar(Data$LCS, 'steelblue'),
+ backgroundSize = '100% 90%',
+ backgroundRepeat = 'no-repeat',
+ backgroundPosition = 'center'
+ )
+ #return(Data)
+
+ })
+
+ ### SOCIAL STRUCTURE ####
+ ### Collaboration network ----
+ COLnetwork <- eventReactive(input$applyCol,{
+
+ values <- socialStructure(input,values)
+
+ values$network<-igraph2vis(g=values$colnet$graph,curved=(input$soc.curved=="Yes"),
+ labelsize=input$collabelsize, opacity=input$colAlpha,type=input$collayout,
+ shape=input$col.shape, net=values$colnet, shadow=(input$col.shadow=="Yes"))
+ })
+ output$colPlot <- renderVisNetwork({
+
+ COLnetwork()
+
+ values$network$VIS
+
+ })
+
+ output$network.col <- downloadHandler(
+ filename = "Collaboration_network.net",
+ content <- function(file) {
+ igraph::write.graph(values$colnet$graph_pajek,file=file, format="pajek")
+ #rio::export(values$M, file=file)
+ },
+ contentType = "net"
+ )
+
+ output$colTable <- DT::renderDT({
+ COLnetwork()
+ colData=values$colnet$cluster_res
+ names(colData)=c("Node", "Cluster", "Betweenness", "Closeness", "PageRank")
+
+ DT::datatable(colData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'Collaboration_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'Collaboration_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'Collaboration_Network',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(colData))-1))))) %>%
+ formatStyle(names(colData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+ ### save coc network image as html ####
+ output$networkCol.fig <- downloadHandler(
+ filename = "network.html",
+ content <- function(con) {
+ savenetwork(con)
+ },
+ contentType = "html"
+ )
+
+
+ ### Degree Plot Collaboration analysis ####
+ output$colDegree <- renderPlotly({
+ COLnetwork()
+ p <- degreePlot(values$colnet)
+ plot.ly(p)
+ })
+
+ ### WPPlot ----
+ WMnetwork<- eventReactive(input$applyWM,{
+ values$WMmap=countrycollaboration(values$M,label=FALSE,edgesize=input$WMedgesize/2,min.edges=input$WMedges.min)
+ })
+
+ output$CCplot.save <- downloadHandler(
+ filename = function() {
+
+ paste("CountryCollaborationMap-", Sys.Date(), ".png", sep="")
+ },
+ content <- function(file) {
+ g <- values$WMmap$g + labs(title = "Country Collaboration Map")
+ ggsave(filename = file, plot = g, dpi = as.numeric(input$CCdpi), height = input$CCh, width = input$CCh*2, bg="white")
+ },
+ contentType = "png"
+ )
+
+ output$WMPlot<- renderPlot({
+
+ WMnetwork()
+ plot(values$WMmap$g)
+
+ }, #width = "auto", height = reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*2/5,0)),
+ width = exprToFunction(as.numeric(input$dimension[1])*0.6),
+ height = exprToFunction(as.numeric(input$dimension[2])*0.85),
+ res = 150)
+
+ output$WMTable <- DT::renderDT({
+ WMnetwork()
+ colData=values$WMmap$tab
+ colData=colData[,c(1,2,9)]
+ names(colData)=c("From","To","Frequency")
+
+ DT::datatable(colData, escape = FALSE, rownames = FALSE, extensions = c("Buttons"), filter = 'top',
+ options = list(pageLength = 10, dom = 'Bfrtip',
+ buttons = list('pageLength',
+ list(extend = 'copy'),
+ list(extend = 'csv',
+ filename = 'World_Collaboration_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'excel',
+ filename = 'World_Collaboration_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'pdf',
+ filename = 'World_Collaboration_Map',
+ title = " ",
+ header = TRUE),
+ list(extend = 'print')),
+ lengthMenu = list(c(10,25,50,-1),c('10 rows', '25 rows', '50 rows','Show all')),
+ columnDefs = list(list(className = 'dt-center', targets = 0:(length(names(colData))-1))))) %>%
+ formatStyle(names(colData), backgroundColor = 'white')
+ #return(Data)
+
+ })
+
+ ### COMMON FUNCTIONS ####
+
+
+ # displayResolution <- function() {
+ # session$clientData$output_plot1_width
+ # }
+
+ getFileNameExtension <- function (fn) {
+ # remove a path
+ splitted <- strsplit(x=fn, split='/')[[1]]
+ # or use .Platform$file.sep in stead of '/'
+ fn <- splitted [length(splitted)]
+ ext <- ''
+ splitted <- strsplit(x=fn, split='\\.')[[1]]
+ l <-length (splitted)
+ if (l > 1 && sum(splitted[1:(l-1)] != '')) ext <-splitted [l]
+ # the extention must be the suffix of a non-empty name
+ ext
+ }
+
+ # string preview (stopwords)
+ strPreview <- function(string, sep=","){
+ str1 <- unlist(strsplit(string, sep))
+ str1 <- str1[1:min(c(length(str1),5))]
+ str1 <- paste(str1, collapse=sep)
+ HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
+ }
+
+ # string preview (synonyms)
+ strSynPreview <- function(string){
+ string <- string[1]
+ str1 <- unlist(strsplit(string, ";"))
+ str1 <- str1[1:min(c(length(str1),5))]
+ str1 <- paste(paste(str1[1], " <- ",collapse=""),paste(str1[-1], collapse=";"), collapse="")
+ HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
+ }
+
+ # from ggplot to plotly
+ plot.ly <- function(g, flip=FALSE, side="r", aspectratio=1, size=0.15,data.type=2, height=0){
+
+ g <- g + labs(title=NULL)
+ print("Fatto")
+ a <- ggplot_build(g)$data
+
+ ymin <- unlist(lapply(a, function(l){
+ if ("y" %in% names(l)){
+ min(l["y"])
+ }
+ })) %>% min(na.rm=TRUE)
+
+ ymax <- unlist(lapply(a, function(l){
+ if ("y" %in% names(l)){
+ max(l["y"])
+ }
+ })) %>% max(na.rm=TRUE)
+
+ xmin <- unlist(lapply(a, function(l){
+ if ("x" %in% names(l)){
+ min(l["x"])
+ }
+ })) %>% min(na.rm=TRUE)
+
+ xmax <- unlist(lapply(a, function(l){
+ if ("x" %in% names(l)){
+ max(l["x"])
+ }
+ })) %>% max(na.rm=TRUE)
+
+ if (isTRUE(flip)){
+ xrange <- c(ymin,ymax)
+ yrange <- c(xmin,xmax)
+ }else{
+ yrange <- c(ymin,ymax)
+ xrange <- c(xmin,xmax)
+ }
+
+ # if (isTRUE(flip)){
+ # yrange <- range(ggplot_build(g)$data[[data.type]]$x)
+ # xrange <- range(ggplot_build(g)$data[[data.type]]$y)
+ # }else{
+ # xrange <- range(ggplot_build(g)$data[[data.type]]$x)
+ # yrange <- range(ggplot_build(g)$data[[data.type]]$y)
+ # }
+
+ sizex = diff(xrange)*size
+ sizey = diff(yrange)*size*aspectratio
+
+ y <- min(yrange)+0.2
+
+ if (side=="l"){
+ x <- min(xrange)+0.2
+ }else{
+ x <- max(xrange)-0.2-sizex
+ }
+
+ ggplotly(g, tooltip = "text") %>%
+ config(displaylogo = FALSE,
+ modeBarButtonsToRemove = c(
+ 'sendDataToCloud',
+ 'pan2d',
+ 'select2d',
+ 'lasso2d',
+ 'toggleSpikelines',
+ 'hoverClosestCartesian',
+ 'hoverCompareCartesian'
+ )) %>%
+ layout(
+ images = list(
+ source = raster2uri(as.raster(values$logo)),
+ x = x, y = y+height,
+ sizex = sizex, sizey = sizey,
+ xref = "x", yref = "y",
+ xanchor = "left", yanchor = "bottom",
+ sizing = "stretch"
+ )
+ )
+ }
+
+ freqPlot <- function(xx,x,y, textLaby,textLabx, title){
+
+
+ xl <- c(max(xx[,x])-0.02-diff(range(xx[,x]))*0.125, max(xx[,x])-0.02)+1
+ yl <- c(1,1+length(unique(xx[,y]))*0.125)
+
+ Text <- paste(textLaby,": ",xx[,y],"\n",textLabx, ": ",xx[,x])
+
+ g <- ggplot(xx, aes(x =xx[,x], y = xx[,y], label = xx[,x], text=Text)) +
+ geom_segment(aes(x = 0, y = xx[,y], xend = xx[,x], yend = xx[,y]), color = "grey50") +
+ geom_point(aes(color=-xx[,x], size=xx[,x]), show.legend = FALSE) +
+ scale_radius(range=c(5, 12))+
+ geom_text(color = "white", size = 3) +
+ scale_y_discrete(limits = rev(xx[,y])) +
+ scale_fill_continuous(type = "gradient")+
+ labs(title=title, y = textLaby)+
+ labs(x = textLabx)+
+ expand_limits(y= c(1, length(xx[,y]) + 1))+
+ theme_minimal()+
+ theme(axis.text.y = element_text(angle=0, hjust=0)) +
+ annotation_custom(values$logoGrid, xmin = xl[1], xmax = xl[2], ymin = yl[1], ymax = yl[2])
+
+ return(g)
+ }
+
+ emptyPlot<-function(errortext){
+ g=ggplot()+
+ theme_void() + theme(legend.position="none")+
+ annotate("text", x = 4, y = 25, label = errortext, size=10)
+ plot(g)
+ }
+
+ count.duplicates <- function(DF){
+ x <- do.call('paste', c(DF, sep = '\r'))
+ ox <- order(x)
+ rl <- rle(x[ox])
+ cbind(DF[ox[cumsum(rl$lengths)],,drop=FALSE],count = rl$lengths)
+
+ }
+
+ reduceRefs<- function(A){
+
+ ind=unlist(regexec("*V[0-9]", A))
+ A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
+ ind=unlist(regexec("*DOI ", A))
+ A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
+ return(A)
+ }
+
+
+ initial <- function(values){
+ values$results <- list("NA")
+ values$log <- "working..."
+ values$load <- "FALSE"
+ values$field = values$cocngrams = "NA"
+ values$citField = values$colField = values$citSep= "NA"
+ values$NetWords = values$NetRefs = values$ColNetRefs=matrix(NA,1,1)
+ values$Title <- "Network"
+ values$Histfield <- "NA"
+ values$histlog <- "working..."
+ values$kk <- 0
+ values$histsearch <- "NA"
+ values$citShortlabel <- "NA"
+ values$S <- list("NA")
+ values$GR <- "NA"
+
+ return(values)
+ }
+
+
+ ### ANALYSIS FUNCTIONS ####
+ ### Descriptive functions ----
+ Hindex_plot <- function(values, type){
+
+ hindex<-function(values,type){
+
+ switch(type,
+ author={
+ AU <- trim(gsub(",","",names(tableTag(values$M,"AU"))))
+ values$H <- Hindex(values$M, field = "author", elements = AU, sep = ";", years=Inf)$H
+ },
+ source={
+ SO <- names(sort(table(values$M$SO),decreasing = TRUE))
+ values$H <- Hindex(values$M, field = "source", elements = SO, sep = ";", years=Inf)$H
+ }
+ )
+
+ return(values)
+ }
+
+ values<-hindex(values, type = type)
+
+ xx=values$H
+ if (type=="author"){
+ K=input$Hkauthor
+ measure=input$HmeasureAuthors
+ title="Author Local Impact"
+ xn="Authors"
+ } else {
+ K=input$Hksource
+ measure=input$HmeasureSources
+ title="Source Local Impact"
+ xn="Sources"
+ }
+ if (K>dim(xx)[1]){
+ k=dim(xx)[1]
+ } else {k=K}
+
+ switch(measure,
+ h={m=2},
+ g={m=3},
+ m={m=4
+ xx[,m] <-round(xx[,m],2) },
+ tc={m=5}
+ )
+ xx <- xx[order(-xx[,m]),]
+ xx <- xx[1:k,c(1,m)]
+
+
+ g <- freqPlot(xx,x=2,y=1, textLaby = xn, textLabx = paste("Impact Measure:",toupper(measure)), title = paste(title,"by",toupper(measure),"index"))
+
+ res<-list(values=values,g=g)
+ return(res)
+ }
+
+ descriptive <- function(values,type){
+
+
+ switch(type,
+ "tab2"={
+ TAB <- values$M %>% group_by(.data$PY) %>%
+ count() %>%
+ rename(Year = .data$PY,
+ Articles = .data$n) %>%
+ right_join(data.frame(Year=seq(min(values$M$PY,na.rm=TRUE),max(values$M$PY, na.rm=TRUE))), by="Year") %>%
+ mutate(Articles = replace_na(.data$Articles,0)) %>%
+ arrange(.data$Year) %>% as.data.frame()
+
+ ny=diff(range(TAB$Year))
+ values$GR=round(((TAB[nrow(TAB),2]/TAB[1,2])^(1/(ny))-1)*100, digits = 2)
+ },
+ "tab3"={
+ listAU <- (strsplit(values$M$AU, ";"))
+ nAU <- lengths(listAU)
+ fracAU <- rep(1/nAU,nAU)
+ TAB <- tibble(Author=unlist(listAU), fracAU=fracAU) %>%
+ group_by(.data$Author) %>%
+ summarize(
+ Articles = n(),
+ AuthorFrac = sum(.data$fracAU)
+ ) %>%
+ arrange(desc(.data$Articles)) %>% as.data.frame()
+ names(TAB)=c("Authors","Articles","Articles Fractionalized")
+ #print(S$MostProdAuthors)
+ },
+ "tab4"={
+ y <- as.numeric(substr(Sys.Date(),1,4))
+ TAB <- values$M %>%
+ mutate(TCperYear = .data$TC/(y+1-.data$PY)) %>%
+ select(.data$SR,.data$DI, .data$TC, .data$TCperYear, .data$PY) %>%
+ group_by(.data$PY) %>%
+ mutate(NTC = .data$TC/mean(.data$TC)) %>%
+ ungroup() %>%
+ select(-.data$PY) %>%
+ arrange(desc(.data$TC)) %>%
+ as.data.frame()
+ names(TAB)=c("Paper", "DOI","Total Citations","TC per Year","Normalized TC")
+ },
+ "tab5"={
+
+ TAB <- countryCollab(values$M)
+ TAB <- TAB %>%
+ mutate(Freq = .data$Articles/sum(.data$Articles)) %>%
+ mutate(MCP_Ratio = .data$MCP/.data$Articles)
+ },
+ "tab6"={
+ if (!"AU1_CO" %in% names(values$M)){
+ values$M <- metaTagExtraction(values$M, "AU1_CO")
+ }
+ TAB <- values$M %>%
+ select(.data$AU1_CO, .data$TC) %>%
+ drop_na(.data$AU1_CO) %>%
+ rename(Country = .data$AU1_CO,
+ TotalCitation = .data$TC) %>%
+ group_by(.data$Country) %>%
+ summarise("TC"=sum(.data$TotalCitation),"Average Article Citations"=sum(.data$TotalCitation)/length(.data$TotalCitation)) %>%
+ arrange(-.data$TC) %>% as.data.frame(.data,stringasfactor=FALSE)
+ },
+ "tab7"={
+ TAB <- values$M %>%
+ select(.data$SO) %>%
+ group_by(.data$SO) %>%
+ count() %>%
+ arrange(desc(.data$n)) %>%
+ rename(Sources = .data$SO,
+ Articles = .data$n) %>%
+ as.data.frame()
+ },
+
+ "tab10"={
+ TAB<-mapworld(values$M)$tab
+ },
+ "tab11"={
+ if(!("AU_UN" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_UN")}
+ TAB <- data.frame(Affiliation=unlist(strsplit(values$M$AU_UN, ";"))) %>%
+ group_by(.data$Affiliation) %>%
+ count() %>%
+ drop_na(.data$Affiliation) %>%
+ arrange(desc(.data$n)) %>%
+ rename(Articles = .data$n) %>%
+ as.data.frame()
+ },
+ "tab12"={
+ TAB=tableTag(values$M,"C1")
+ TAB=data.frame(Affiliations=names(TAB), Articles=as.numeric(TAB),stringsAsFactors = FALSE)
+ TAB=TAB[nchar(TAB[,1])>4,]
+ #names(TAB)=c("Affiliations", "Articles")
+
+ },
+ "tab13"={
+ CR<-localCitations(values$M,fast.search = FALSE, verbose = FALSE)
+ TAB <- CR$Authors
+ #TAB=data.frame(Authors=names(CR$Authors$Author), Citations=as.numeric(CR$Cited),stringsAsFactors = FALSE)
+ }
+ )
+ values$TAB=TAB
+ res=list(values=values,TAB=TAB)
+ return(res)
+ }
+
+ wordlist <- function(M, Field, n, measure, ngrams, remove.terms=NULL, synonyms=NULL){
+ switch(Field,
+ ID={v=tableTag(values$M,"ID", remove.terms = remove.terms, synonyms = synonyms)},
+ DE={v=tableTag(values$M,"DE", remove.terms = remove.terms, synonyms = synonyms)},
+ TI={
+ if (!("TI_TM" %in% names(M))){
+ v=tableTag(M,"TI", ngrams=ngrams, remove.terms=remove.terms, synonyms = synonyms)
+
+ }},
+ AB={if (!("AB_TM" %in% names(M))){
+ v=tableTag(M,"AB", ngrams=ngrams, remove.terms = remove.terms, synonyms = synonyms)
+ }}
+ )
+ names(v)=tolower(names(v))
+ #v=tableTag(values$M,"ID")
+ n=min(c(n,length(v)))
+ Words=data.frame(Terms=names(v)[1:n], Frequency=(as.numeric(v)[1:n]), stringsAsFactors = FALSE)
+ W=Words
+ switch(measure,
+ identity={},
+ sqrt={W$Frequency=sqrt(W$Frequency)},
+ log={W$Frequency=log(W$Frequency+1)},
+ log10={W$Frequency=log10(W$Frequency+1)}
+ )
+
+ results=list(v=v,W=W, Words=Words)
+ return(results)
+ }
+
+ readStopwordsFile <- function(file, sep=","){
+ if (!is.null(file)){
+ req(file$datapath)
+ remove.terms <- unlist(strsplit(readr::read_lines(file$datapath), sep))
+ }else{remove.terms <- NULL}
+ return(remove.terms)
+ }
+
+ readSynWordsFile <- function(file, sep=","){
+ if (!is.null(file)){
+ req(file$datapath)
+ syn.terms <- readr::read_lines(file$datapath)
+ if (sep!=";") syn.terms <- gsub(sep,";",syn.terms)
+ }else{syn.terms <- NULL}
+ return(syn.terms)
+ }
+
+ mapworld <- function(M){
+ if (!("AU_CO" %in% names(M))){M=metaTagExtraction(M,"AU_CO")}
+ CO=as.data.frame(tableTag(M,"AU_CO"),stringsAsFactors = FALSE)
+ CO$Tab=gsub("UNITED KINGDOM","UK",CO$Tab)
+ CO$Tab=gsub("KOREA","SOUTH KOREA",CO$Tab)
+
+ map.world <- map_data("world")
+ map.world$region=toupper(map.world$region)
+
+ dplyr::anti_join(CO, map.world, by = c('Tab' = 'region'))
+
+ country.prod <- dplyr::left_join( map.world, CO, by = c('region' = 'Tab'))
+
+ tab=data.frame(country.prod %>%
+ dplyr::group_by(region) %>%
+ dplyr::summarise(Freq=mean(Freq)))
+
+ tab=tab[!is.na(tab$Freq),]
+
+ tab=tab[order(-tab$Freq),]
+
+ breaks=as.numeric(round(quantile(CO$Freq,c(0.2,0.4,0.6,0.8,1))))
+ names(breaks)=breaks
+ breaks=log(breaks)
+
+ g <- ggplot(country.prod, aes( x = .data$long, y = .data$lat, group=.data$group, text=paste("Country: ",.data$region,"\nN.of Documents: ",.data$Freq))) +
+ geom_polygon(aes(fill = log(Freq), group=group)) +
+ scale_fill_continuous(low='dodgerblue', high='dodgerblue4',breaks=breaks)+
+ guides(fill = guide_legend(reverse = T)) +
+ #geom_text(data=centroids, aes(label = centroids$Tab, x = centroids$long, y = centroids$lat, group=centroids$Tab)) +
+ labs(fill = 'N.Documents'
+ ,title = 'Country Scientific Production'
+ ,x = NULL
+ ,y = NULL) +
+ theme(text = element_text(color = '#333333')
+ ,plot.title = element_text(size = 28)
+ ,plot.subtitle = element_text(size = 14)
+ ,axis.ticks = element_blank()
+ ,axis.text = element_blank()
+ ,panel.grid = element_blank()
+ ,panel.background = element_rect(fill = '#FFFFFF') #'#333333'
+ ,plot.background = element_rect(fill = '#FFFFFF')
+ ,legend.position = c(.18,.36)
+ ,legend.background = element_blank()
+ ,legend.key = element_blank()
+ ) + annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)
+
+ results=list(g=g,tab=tab)
+ return(results)
+ }
+
+ ### Structure fuctions ----
+ CAmap <- function(input, values){
+ if ((input$CSfield %in% names(values$M))){
+
+ if (input$CSfield %in% c("TI","AB")){
+ ngrams <- as.numeric(input$CSngrams)
+ }else{
+ ngrams <- 1
+ }
+
+ ### load file with terms to remove
+ if (input$CSStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$CSStop, sep=input$CSSep))
+ }else{remove.terms <- NULL}
+ values$CSremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$FASynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$FASyn, sep=input$FASynSep))
+ }else{synonyms <- NULL}
+ values$FAsyn.terms <- synonyms
+ ### end of block
+
+ tab=tableTag(values$M,input$CSfield, ngrams=ngrams)
+ if (length(tab>=2)){
+
+ minDegree=as.numeric(tab[input$CSn])
+
+ values$CS <- conceptualStructure(values$M, method=input$method , field=input$CSfield, minDegree=minDegree, clust=input$nClustersCS,
+ k.max = 8, stemming=F, labelsize=input$CSlabelsize,documents=input$CSdoc,graph=FALSE, ngrams=ngrams,
+ remove.terms=remove.terms, synonyms = synonyms)
+
+
+ }else{emptyPlot("Selected field is not included in your data collection")
+ values$CS=list("NA")}
+
+ }else{
+ emptyPlot("Selected field is not included in your data collection")
+ values$CS=list("NA")
+
+ }
+ }
+
+ historiograph <- function(input,values){
+
+ min.cit <- 1
+ # if (input$histsearch=="FAST"){
+ # min.cit=quantile(values$M$TC,0.75, na.rm = TRUE)
+ # }else{min.cit=1}
+
+ if (values$Histfield=="NA"){
+ values$histResults <- histNetwork(values$M, min.citations=min.cit, sep = ";")
+ values$Histfield="done"
+ }
+ titlelabel <- input$titlelabel=="TRUE"
+ values$histlog<- (values$histPlot <- histPlot(values$histResults, n=input$histNodes, size =input$histsize, labelsize = input$histlabelsize, title_as_label = titlelabel, verbose=FALSE))
+ return(values)
+ }
+
+
+ ### Network functions ----
+
+ degreePlot <- function(net){
+ deg <- data.frame(node = names(net$nodeDegree), x= (1:length(net$nodeDegree)), y = net$nodeDegree)
+ p <- ggplot(data = deg, aes(x=.data$x, y=.data$y,
+ text=paste("Node ",.data$x," - Degree ",.data$y, sep="")))+
+ geom_point()+
+ geom_line(aes(group="NA"),color = '#002F80', alpha = .5) +
+ theme(text = element_text(color = "#444444")
+ ,panel.background = element_rect(fill = '#FFFFFF')
+ ,panel.grid.minor = element_line(color = '#EFEFEF')
+ ,panel.grid.major = element_line(color = '#EFEFEF')
+ ,plot.title = element_text(size = 24)
+ ,axis.title = element_text(size = 14, color = '#555555')
+ ,axis.title.y = element_text(vjust = 1, angle = 0)
+ ,axis.title.x = element_text(hjust = 0)
+ ,axis.line.x = element_line(color="black",size=0.5)
+ ,axis.line.y = element_line(color="black",size=0.5)
+ ) +
+ labs(x = "Node", y="Degree", title = "Node Degrees")
+ return(p)
+ }
+
+ cocNetwork <- function(input,values){
+
+ n = input$Nodes
+ label.n = input$Labels
+
+ ### load file with terms to remove
+ if (input$COCStopFile=="Y"){
+ remove.terms <- trimws(readStopwordsFile(file=input$COCStop, sep=input$COCSep))
+ }else{remove.terms <- NULL}
+ values$COCremove.terms <- remove.terms
+ ### end of block
+ ### load file with synonyms
+ if (input$COCSynFile=="Y"){
+ synonyms <- trimws(readSynWordsFile(file=input$COCSyn, sep=input$COCSynSep))
+ }else{synonyms <- NULL}
+ values$COCsyn.terms <- synonyms
+ ### end of block
+
+ if ((input$field %in% names(values$M))){
+
+ if ((dim(values$NetWords)[1])==1 | !(input$field==values$field) | !(input$cocngrams==values$cocngrams) | ((dim(values$NetWords)[1])!=input$Nodes) ){
+
+ values$field=input$field
+ values$ngrams <- input$cocngrams
+
+ switch(input$field,
+ ID={
+ values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "keywords", n = n, sep = ";", remove.terms=remove.terms, synonyms = synonyms)
+ values$Title= "Keywords Plus Network"
+ },
+ DE={
+ values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "author_keywords", n = n, sep = ";", remove.terms=remove.terms, synonyms = synonyms)
+ values$Title= "Authors' Keywords network"
+ },
+ TI={
+ #if(!("TI_TM" %in% names(values$M))){
+ values$M=termExtraction(values$M,Field="TI",verbose=FALSE, ngrams=as.numeric(input$cocngrams), remove.terms=remove.terms, synonyms = synonyms)
+ #}
+ values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "titles", n = n, sep = ";")
+ values$Title= "Title Words network"
+ },
+ AB={
+ #if(!("AB_TM" %in% names(values$M))){
+ values$M=termExtraction(values$M,Field="AB",verbose=FALSE, ngrams=as.numeric(input$cocngrams), remove.terms=remove.terms, synonyms = synonyms)
+ #}
+ values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "abstracts", n = n, sep = ";")
+ values$Title= "Abstract Words network"
+ })
+
+ }
+
+ if (label.n>n){label.n=n}
+ if (input$normalize=="none"){normalize=NULL}else{normalize=input$normalize}
+ if (input$label.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
+ if (input$coc.curved=="Yes"){curved=TRUE}else{curved=FALSE}
+
+ #par(bg="grey92", mar=c(0,0,0,0))
+ values$cocnet=networkPlot(values$NetWords, normalize=normalize, Title = values$Title, type = input$layout,
+ size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$edgesize*3, labelsize=input$labelsize,label.cex=label.cex,
+ label.n=label.n,edges.min=input$edges.min,label.color = F, curved=curved,alpha=input$cocAlpha,
+ cluster=input$cocCluster, remove.isolates = (input$coc.isolates=="yes"),
+ community.repulsion = input$coc.repulsion/2, verbose = FALSE)
+ if (input$cocyears=="Yes"){
+ Y=fieldByYear(values$M, field = input$field, graph=FALSE)
+ g=values$cocnet$graph
+ label=igraph::V(g)$name
+ ind=which(tolower(Y$df$item) %in% label)
+ df=Y$df[ind,]
+
+ #bluefunc <- colorRampPalette(c("lightblue", "darkblue"))
+ #col=bluefunc((diff(range(df$year))+1)*10)
+ col=heat.colors((diff(range(df$year))+1)*10)
+ igraph::V(g)$color=col[(max(df$year)-df$year+1)*10]
+ igraph::V(g)$year=df$year
+ values$cocnet$graph=g
+ }
+
+ }else{
+ emptyPlot("Selected field is not included in your data collection")
+ }
+ return(values)
+ }
+
+ intellectualStructure <- function(input,values){
+ n = input$citNodes
+ label.n = input$citLabels
+
+ if ((dim(values$NetRefs)[1])==1 | !(input$citField==values$citField) | !(input$citSep==values$citSep) | !(input$citShortlabel==values$citShortlabel) | ((dim(values$NetRefs)[1])!=input$citNodes)){
+
+ values$citField=input$citField
+ values$citSep=input$citSep
+ if (input$citShortlabel=="Yes"){shortlabel=TRUE}else{shortlabel=FALSE}
+ values$citShortlabel=input$citShortlabel
+ switch(input$citField,
+ CR={
+ values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "references", n = n, sep = input$citSep, shortlabel=shortlabel)
+ values$Title= "Cited References network"
+
+ },
+ CR_AU={
+ if(!("CR_AU" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="CR_AU", sep = input$citSep)}
+ values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "authors", n = n, sep = input$citSep)
+ values$Title= "Cited Authors network"
+ },
+ CR_SO={
+ if(!("CR_SO" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="CR_SO", sep = input$citSep)}
+ values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "sources", n = n, sep = input$citSep)
+ values$Title= "Cited Sources network"
+ })
+
+ }
+
+ if (label.n>n){label.n=n}
+ if (input$citlabel.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
+ if (input$cocit.curved=="Yes"){curved=TRUE}else{curved=FALSE}
+
+ values$cocitnet=networkPlot(values$NetRefs, normalize=NULL, Title = values$Title, type = input$citlayout,
+ size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$citedgesize*3,
+ labelsize=input$citlabelsize,label.cex=label.cex, curved=curved,
+ label.n=label.n,edges.min=input$citedges.min,label.color = F,remove.isolates = (input$cit.isolates=="yes"),
+ alpha=0.7, cluster=input$cocitCluster,
+ community.repulsion = input$cocit.repulsion/2, verbose = FALSE)
+ return(values)
+ }
+
+ socialStructure<-function(input,values){
+ n = input$colNodes
+ label.n = input$colLabels
+
+ if ((dim(values$ColNetRefs)[1])==1 | !(input$colField==values$colField) | ((dim(values$ColNetRefs)[1])!=input$colNodes)){
+
+ values$colField=input$colField
+
+
+ values$cluster="walktrap"
+ switch(input$colField,
+ COL_AU={
+ values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "authors", n = n, sep = ";")
+ values$Title= "Author Collaboration network"
+
+ },
+ COL_UN={
+ if(!("AU_UN" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_UN", sep=";")}
+ values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "universities", n = n, sep = ";")
+ values$Title= "Edu Collaboration network"
+ },
+ COL_CO={
+ if(!("AU_CO" %in% names(values$M))){values$M=metaTagExtraction(values$M,Field="AU_CO", sep=";")}
+ values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "countries", n = n, sep = ";")
+ values$Title= "Country Collaboration network"
+ #values$cluster="none"
+ })
+
+ }
+
+ if (label.n>n){label.n=n}
+ if (input$colnormalize=="none"){normalize=NULL}else{normalize=input$colnormalize}
+ if (input$collabel.cex=="Yes"){label.cex=TRUE}else{label.cex=FALSE}
+ if (input$soc.curved=="Yes"){curved=TRUE}else{curved=FALSE}
+
+ type=input$collayout
+ if (input$collayout=="worldmap"){type="auto"}
+
+ values$colnet=networkPlot(values$ColNetRefs, normalize=normalize, Title = values$Title, type = type,
+ size.cex=TRUE, size=5 , remove.multiple=F, edgesize = input$coledgesize*3,
+ labelsize=input$collabelsize,label.cex=label.cex, curved=curved,
+ label.n=label.n,edges.min=input$coledges.min,label.color = F,alpha=input$colAlpha,
+ remove.isolates = (input$col.isolates=="yes"), cluster=input$colCluster,
+ community.repulsion = input$col.repulsion/2, verbose = FALSE)
+
+ return(values)
+
+ }
+
+ countrycollaboration <- function(M,label,edgesize,min.edges){
+ M=metaTagExtraction(M,"AU_CO")
+ net=biblioNetwork(M,analysis="collaboration",network="countries")
+ CO=data.frame(Tab=rownames(net),Freq=diag(net),stringsAsFactors = FALSE)
+ bsk.network=igraph::graph_from_adjacency_matrix(net,mode="undirected")
+ COedges=as.data.frame(igraph::ends(bsk.network,igraph::E(bsk.network),names=TRUE),stringsAsFactors = FALSE)
+
+ map.world <- map_data("world")
+ map.world$region=toupper(map.world$region)
+ map.world$region=gsub("UK","UNITED KINGDOM",map.world$region)
+ map.world$region=gsub("SOUTH KOREA","KOREA",map.world$region)
+
+ country.prod <- dplyr::left_join( map.world, CO, by = c('region' = 'Tab'))
+
+ breaks=as.numeric(round(quantile(CO$Freq,c(0.2,0.4,0.6,0.8,1))))
+ names(breaks)=breaks
+ breaks=log(breaks)
+ data("countries",envir=environment())
+ names(countries)[1]="Tab"
+
+ COedges=dplyr::inner_join(COedges,countries, by=c('V1'='Tab'))
+ COedges=dplyr::inner_join(COedges,countries, by=c('V2'='Tab'))
+ COedges=COedges[COedges$V1!=COedges$V2,]
+ COedges=count.duplicates(COedges)
+ tab=COedges
+ COedges=COedges[COedges$count>=min.edges,]
+
+ g=ggplot(country.prod, aes( x = .data$long, y = .data$lat, group = .data$group )) +
+ geom_polygon(aes(fill = log(Freq))) +
+ scale_fill_continuous(low='dodgerblue', high='dodgerblue4',breaks=breaks)+
+ #guides(fill = guide_legend(reverse = T)) +
+ guides(colour=FALSE, fill=FALSE)+
+ geom_curve(data=COedges, aes(x = .data$Longitude.x , y = .data$Latitude.x, xend = .data$Longitude.y, yend = .data$Latitude.y, # draw edges as arcs
+ color = "firebrick4", size = .data$count, group=.data$continent.x),
+ curvature = 0.33,
+ alpha = 0.5) +
+ scale_size_continuous(guide = FALSE, range = c(0.25, edgesize))+
+ labs(title = NULL, x = "Latitude", y = "Longitude") +
+ theme(text = element_text(color = '#333333')
+ ,plot.title = element_text(size = 28)
+ ,plot.subtitle = element_text(size = 14)
+ ,axis.ticks = element_blank()
+ ,axis.text = element_blank()
+ ,panel.grid = element_blank()
+ ,panel.background = element_rect(fill = '#FFFFFF') #'#333333'
+ ,plot.background = element_rect(fill = '#FFFFFF')
+ ,legend.position = c(.18,.36)
+ ,legend.background = element_blank()
+ ,legend.key = element_blank()
+ ) + annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)
+ if (isTRUE(label)){
+ CO=dplyr::inner_join(CO,countries, by=c('Tab'='Tab'))
+ g=g+
+ ggrepel::geom_text_repel(data=CO, aes(x = .data$Longitude, y = .data$Latitude, label = .data$Tab, group=.data$continent), # draw text labels
+ hjust = 0, nudge_x = 1, nudge_y = 4,
+ size = 3, color = "orange", fontface = "bold")
+ }
+
+ results=list(g=g,tab=tab)
+ return(results)
+ }
+ ### visNetwork tools ----
+ netLayout <- function(type){
+ switch(type,
+ auto={l <- "layout_nicely"},
+ circle={l <- "layout_in_circle"},
+ mds={l <- "layout_with_mds"},
+ star={l <- "layout_as_star"},
+
+ sphere={l <- "layout_on_sphere"},
+ fruchterman={l <- "layout_with_fr"},
+ kamada={l <- "layout_with_kk"}
+ )
+ return(l)
+ }
+
+ savenetwork <- function(con){
+ vn=values$network$vn
+ visNetwork(nodes = vn$nodes, edges = vn$edges, type="full", smooth=TRUE, physics=FALSE, height = "2000px",width = "2000px" ) %>%
+ visNodes(shape="box", font=list(color="black"),scaling=list(label=list(enables=TRUE))) %>%
+ visIgraphLayout(layout = values$network$l) %>%
+ visEdges(smooth = values$network$curved) %>%
+ visOptions(highlightNearest =list(enabled = T, hover = T, degree=1), nodesIdSelection = T) %>%
+ visInteraction(dragNodes = TRUE, navigationButtons = TRUE, hideEdgesOnDrag = TRUE) %>% visExport() %>%
+ visPhysics(enabled = FALSE) %>% visSave(con)
+ }
+
+ igraph2vis<-function(g,curved,labelsize,opacity,type,shape, net, shadow=TRUE){
+
+ LABEL=igraph::V(g)$name
+
+ LABEL[igraph::V(g)$labelsize==0]=""
+
+ vn <- toVisNetworkData(g)
+
+ vn$nodes$label=LABEL
+ vn$edges$num=1
+ vn$edges$dashes=FALSE
+ vn$edges$dashes[vn$edges$lty==2]=TRUE
+
+ ## opacity
+ vn$nodes$color=adjustcolor(vn$nodes$color,alpha=min(c(opacity+0.2,1)))
+ vn$edges$color=adjustcolor(vn$edges$color,alpha=opacity)
+
+ ## removing multiple edges
+ vn$edges=unique(vn$edges)
+
+ ## labelsize
+ scalemin=20
+ scalemax=150
+ Min=min(vn$nodes$font.size)
+ Max=max(vn$nodes$font.size)
+ if (Max>Min){
+ size=(vn$nodes$font.size-Min)/(Max-Min)*15*labelsize+10
+ } else {size=10*labelsize}
+ size[sizescalemax]=scalemax
+ vn$nodes$font.size=size
+ l<-netLayout(type)
+
+ ### TO ADD SHAPE AND FONT COLOR OPTIONS
+ coords <- net$layout
+
+ vn$nodes$size <- vn$nodes$font.size*0.8
+
+ if (shape %in% c("text")){
+ vn$nodes$font.color <- vn$nodes$color
+ }else{
+ vn$nodes$font.color <- "black"
+ }
+
+ if (shape %in% c("dot","square")){
+ vn$nodes$font.vadjust <- -0.7*vn$nodes$font.size
+ }else{
+ vn$nodes$font.vadjust <-0
+ }
+
+ VIS<-
+ visNetwork(nodes = vn$nodes, edges = vn$edges, type="full", smooth=TRUE, physics=FALSE) %>%
+ #visNodes(shape=shape, font=list(color="black")) %>%
+ visNodes(shadow=shadow, shape=shape, font=list(color="black", size=vn$nodes$font.size,vadjust=vn$nodes$font.vadjust)) %>%
+ visIgraphLayout(layout = "layout.norm", layoutMatrix = coords) %>%
+ visEdges(smooth = curved) %>%
+ visOptions(highlightNearest =list(enabled = T, hover = T, degree=1), nodesIdSelection = T) %>%
+ visInteraction(dragNodes = TRUE, navigationButtons = TRUE, hideEdgesOnDrag = TRUE) %>%
+ visOptions(manipulation = TRUE) %>%
+ visExport(type = "png", name = "network",
+ label = paste0("Export graph as png"), background = "#fff",
+ float = "right", style = NULL, loadDependencies = TRUE)
+ values$COCVIS=VIS
+ return(list(VIS=VIS,vn=vn, type=type, l=l, curved=curved))
+ }
+
+ #### Common functions ----
+
+ notifications <- function(){
+
+ ## check connection and download notifications
+ online <- is_online()
+ location <- "https://www.bibliometrix.org/bs_notifications/biblioshiny_notifications.csv"
+ if (isTRUE(is_online())){
+ suppressWarnings(notifOnline <- read.csv(location, header=TRUE, sep=","))
+ #notifOnline <- notifOnline[nchar(notifOnline)>2]
+ #n <- strsplit(notifOnline,",")
+ #notsOnline <- unlist(lapply(n,function(l) l[1]))
+ #linksOnline <- unlist(lapply(n,function(l) l[2]))
+ notifOnline$href[nchar(notifOnline$href)<6] <- NA
+ }
+
+ ## check if a file exists on the local machine and load it
+ switch(Sys.info()[['sysname']],
+ Windows= {home <- Sys.getenv('R_USER')},
+ Linux = {home <- Sys.getenv('HOME')},
+ Darwin = {home <- Sys.getenv('HOME')})
+
+ file <- paste(home,"/biblioshiny_notifications.csv", sep="")
+ fileTrue <- file.exists(file)
+ if (isTRUE(fileTrue)){
+ suppressWarnings(notifLocal <- read.csv(file, header=TRUE, sep=","))
+ #notifLocal <- readLines(file)
+ #linksLocal[nchar(linksLocal)<6] <- NA
+ }
+
+
+ A <- c("noA","A")
+ B <- c("noB","B")
+ status <- paste(A[online+1],B[fileTrue+1],sep="")
+
+ switch(status,
+ # missing both files (online and local)
+ noAnoB={
+ notifTot <- data.frame(nots="No notifications", href=NA, status="info") %>% mutate(status = "info")
+ },
+ # missing online file. The local one exists.
+ noAB={
+ notifTot <- notifLocal %>% filter(.data$action == TRUE) %>% mutate(status = "info")
+ },
+ # missing the local file. The online one exists.
+ AnoB={
+ notifOnline <- notifOnline %>%
+ dplyr::slice_head(n=5)
+ notifTot <- notifOnline %>% filter(.data$action == TRUE) %>% mutate(status = "danger")
+ notifOnline %>% filter(.data$action == TRUE) %>% write.csv(file=file, quote = FALSE, row.names = FALSE)
+ },
+ # both files exist.
+ AB={
+ notifTot <- left_join(notifOnline %>% mutate(status = "danger"),
+ notifLocal%>% mutate(status = "info"), by="nots") %>%
+ mutate(status = replace_na(.data$status.y,"danger")) %>%
+ rename(href = .data$href.x,
+ action = .data$action.x) %>%
+ select(nots, href, action, status) %>%
+ arrange(.data$status) %>%
+ filter(.data$action == TRUE) %>%
+ dplyr::slice_head(n=5)
+ notifTot %>% select(-.data$status) %>% write.csv(file=file, quote = FALSE, row.names = FALSE)
+
+ })
+
+ #notifTot <- notifTot[1:(min(5,nrow(notifTot))),]
+ return(notifTot)
+ }
+
+
+ is_online <- function(site="https://www.bibliometrix.org/") {
+ tryCatch({
+ readLines(site,n=1)
+ TRUE
+ },
+ warning = function(w) invokeRestart("muffleWarning"),
+ error = function(e) FALSE)
+ }
+
+ getFileNameExtension <- function (fn) {
+ # remove a path
+ splitted <- strsplit(x=fn, split='/')[[1]]
+ # or use .Platform$file.sep in stead of '/'
+ fn <- splitted [length(splitted)]
+ ext <- ''
+ splitted <- strsplit(x=fn, split='\\.')[[1]]
+ l <-length (splitted)
+ if (l > 1 && sum(splitted[1:(l-1)] != '')) ext <-splitted [l]
+ # the extention must be the suffix of a non-empty name
+ ext
+ }
+
+ # string preview (stopwords)
+ strPreview <- function(string, sep=","){
+ str1 <- unlist(strsplit(string, sep))
+ str1 <- str1[1:min(c(length(str1),5))]
+ str1 <- paste(str1, collapse=sep)
+ HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
+ }
+
+ # string preview (synonyms)
+ strSynPreview <- function(string){
+ string <- string[1]
+ str1 <- unlist(strsplit(string, ";"))
+ str1 <- str1[1:min(c(length(str1),5))]
+ str1 <- paste(paste(str1[1], " <- ",collapse=""),paste(str1[-1], collapse=";"), collapse="")
+ HTML(paste("", "File Preview: ", str1,"
", sep = '
'))
+ }
+
+ # from ggplot to plotly
+ plot.ly <- function(g, flip=FALSE, side="r", aspectratio=1, size=0.15,data.type=2, height=0){
+
+ g <- g + labs(title = NULL)
+ # a <- ggplot_build(g)$data
+ #
+ # ymin <- unlist(lapply(a, function(l){
+ # if ("y" %in% names(l)){
+ # min(l["y"])
+ # }
+ # })) %>% min(na.rm=TRUE)
+ #
+ # ymax <- unlist(lapply(a, function(l){
+ # if ("y" %in% names(l)){
+ # max(l["y"])
+ # }
+ # })) %>% max(na.rm=TRUE)
+ #
+ # xmin <- unlist(lapply(a, function(l){
+ # if ("x" %in% names(l)){
+ # min(l["x"])
+ # }
+ # })) %>% min(na.rm=TRUE)
+ #
+ # xmax <- unlist(lapply(a, function(l){
+ # if ("x" %in% names(l)){
+ # max(l["x"])
+ # }
+ # })) %>% max(na.rm=TRUE)
+ #
+ # if (isTRUE(flip)){
+ # xrange <- c(ymin,ymax)
+ # yrange <- c(xmin,xmax)
+ # }else{
+ # yrange <- c(ymin,ymax)
+ # xrange <- c(xmin,xmax)
+ # }
+ #
+ #
+ # sizex = diff(xrange)*size
+ # sizey = diff(yrange)*size*aspectratio
+ #
+ # y <- min(yrange)+0.2
+ #
+ # if (side=="l"){
+ # x <- min(xrange)+0.2
+ # }else{
+ # x <- max(xrange)-0.2-sizex
+ # }
+
+ ggplotly(g, tooltip = "text") %>%
+ config(displaylogo = FALSE,
+ modeBarButtonsToRemove = c(
+ 'sendDataToCloud',
+ 'pan2d',
+ 'select2d',
+ 'lasso2d',
+ 'toggleSpikelines',
+ 'hoverClosestCartesian',
+ 'hoverCompareCartesian',
+ 'toImage'
+ )) #%>%
+ # layout(
+ # images = list(
+ # source = raster2uri(as.raster(values$logo)),
+ # x = x, y = y+height,
+ # sizex = sizex, sizey = sizey,
+ # xref = "x", yref = "y",
+ # xanchor = "left", yanchor = "bottom",
+ # sizing = "stretch"
+ # )
+ # )
+ }
+
+ freqPlot <- function(xx,x,y, textLaby,textLabx, title){
+
+
+ xl <- c(max(xx[,x])-0.02-diff(range(xx[,x]))*0.125, max(xx[,x])-0.02)+0.5
+ yl <- c(1,1+length(unique(xx[,y]))*0.125)
+
+ Text <- paste(textLaby,": ",xx[,y],"\n",textLabx, ": ",xx[,x])
+
+ g <- ggplot(xx, aes(x =xx[,x], y = xx[,y], label = xx[,x], text=Text)) +
+ geom_segment(aes(x = 0, y = xx[,y], xend = xx[,x], yend = xx[,y]), color = "grey50") +
+ geom_point(aes(color=-xx[,x], size=xx[,x]), show.legend = FALSE) +
+ scale_radius(range=c(7, 15))+
+ geom_text(color = "white", size = 3) +
+ scale_y_discrete(limits = rev(xx[,y])) +
+ scale_fill_continuous(type = "gradient")+
+ labs(title=title, y = textLaby)+
+ labs(x = textLabx)+
+ expand_limits(y= c(1, length(xx[,y]) + 1))+
+ theme_minimal()+
+ theme(axis.text.y = element_text(angle=0, hjust=0)) +
+ annotation_custom(values$logoGrid, xmin = xl[1], xmax = xl[2], ymin = yl[1], ymax = yl[2])
+
+ return(g)
+ }
+
+ emptyPlot<-function(errortext){
+ g=ggplot()+
+ theme_void() + theme(legend.position="none")+
+ annotate("text", x = 4, y = 25, label = errortext, size=10)
+ plot(g)
+ }
+
+ count.duplicates <- function(DF){
+ x <- do.call('paste', c(DF, sep = '\r'))
+ ox <- order(x)
+ rl <- rle(x[ox])
+ cbind(DF[ox[cumsum(rl$lengths)],,drop=FALSE],count = rl$lengths)
+
+ }
+
+ reduceRefs<- function(A){
+
+ ind=unlist(regexec("*V[0-9]", A))
+ A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
+ ind=unlist(regexec("*DOI ", A))
+ A[ind>-1]=substr(A[ind>-1],1,(ind[ind>-1]-1))
+ return(A)
+ }
+
+
+ initial <- function(values){
+ values$results <- list("NA")
+ values$log <- "working..."
+ values$load <- "FALSE"
+ values$field = values$cocngrams = "NA"
+ values$citField = values$colField = values$citSep= "NA"
+ values$NetWords = values$NetRefs = values$ColNetRefs=matrix(NA,1,1)
+ values$Title <- "Network"
+ values$Histfield <- "NA"
+ values$histlog <- "working..."
+ values$kk <- 0
+ values$histsearch <- "NA"
+ values$citShortlabel <- "NA"
+ values$S <- list("NA")
+ values$GR <- "NA"
+
+ return(values)
+ }
+
+
+
+
+ observe({
+ if (!(input$sidebarmenu %in% c("biblioshinyy","mainInfo")) & !isTRUE(values$checkControlBar)){
+ updateControlbar("controlbar2")
+ values$checkControlBar <- TRUE
+ #updateControlbarMenu("item_controlbar")
+ }
+ if ((input$sidebarmenu %in% c("biblioshinyy","mainInfo")) & isTRUE(values$checkControlBar)){
+ updateControlbar("controlbar2")
+ values$checkControlBar <- FALSE
+ }
+ })
+
+ # observe({
+ # if( input$sidebarmenu != "biblioshinyy"){
+ # shinyjs::addCssClass(selector = "aside.control-sidebar", class = "control-sidebar-collapse")
+ # } else{
+ # shinyjs::removeCssClass(selector = "aside.control-sidebar", class = "control-sidebar-collapse")
+ # }
+ # })
+
+ output$controlbar <- renderUI({
+ controlbarMenu(
+ controlbarItem(
+ h2(strong("Options"),align="center"),
+ fluidPage(
+ fluidRow(
+ column(width = 1),
+ column(width=11,
+ ## Load Data ----
+ conditionalPanel(condition = 'input.sidebarmenu == "loadData"',
+ h3(strong("Import or Load ")),
+ #br(),
+ selectInput(
+ "load",
+ label = "Please, choose what to do",
+ choices = c(
+ " " = "null",
+ "Import raw file(s)" = "import",
+ "Load bibliometrix file(s)" = "load",
+ "Use a sample collection" = "demo"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(
+ condition = "input.load == 'demo'",
+ helpText(h4(strong("The use of bibliometric approaches in business and management disciplines.")),
+ h5(strong("Dataset 'Management'")),
+ em("A collection of scientific articles about the use of bibliometric approaches",
+ "in business and management disciplines."),
+ br(),
+ em("Period: 1985 - 2020
+ , Source WoS.")
+ )
+ ),
+ #br(),
+ conditionalPanel(
+ condition = "input.load == 'import'",
+ selectInput(
+ "dbsource",
+ label = "Database",
+ choices = c(
+ "Web of Science (WoS/WoK)" = "isi",
+ "Scopus" = "scopus",
+ "Dimensions" = "dimensions",
+ "Lens.org" = "lens",
+ "PubMed" = "pubmed",
+ "Cochrane Library" = "cochrane"
+ ),
+ selected = "isi"
+ )
+ ),
+ conditionalPanel(
+ condition = "input.load != 'null' & input.load != 'demo'",
+ conditionalPanel(
+ condition = "input.load == 'load'",
+ helpText(em("Load a collection in XLSX or R format previously exported from bibliometrix")
+ )),
+ fileInput(
+ "file1",
+ "Choose a file",
+ multiple = FALSE,
+ accept = c(
+ ".csv",
+ ".txt",
+ ".ciw",
+ ".bib",
+ ".xlsx",
+ ".zip",
+ ".xls",
+ ".rdata",
+ ".rda",
+ ".rds"
+ )
+ )
+ ),
+ #h6("Here accept single .txt/.bib/.csv/.xslx/.RData files, or multiple .txt/.bib/.csv files compressed in a single .zip archive."),
+ conditionalPanel(condition = "input.load != 'null'",
+ actionButton("applyLoad", strong("START"),
+ style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%"),
+ width = "100%"),
+ tags$hr(),
+
+ uiOutput("textLog"),
+ #shinycssloaders::withSpinner(verbatimTextOutput("log")),
+
+ tags$hr(),
+
+ h3(strong(
+ "Export collection"
+ )),
+ #br(),
+
+ selectInput(
+ 'save_file',
+ 'Save as:',
+ choices = c(
+ ' ' = 'null',
+ 'Excel' = 'xlsx',
+ 'R Data Format' = 'RData'
+ ),
+ selected = 'null'
+ ),
+ conditionalPanel(condition = "input.save_file != 'null'",
+ downloadButton("collection.save", strong("Export"),
+ style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Gathering Data ----
+ conditionalPanel(condition = 'input.sidebarmenu == "gathData"',
+ h3(strong(
+ "Gather data using APIs "
+ )),
+ br(),
+
+ selectInput(
+ "dbapi",
+ label = "Database",
+ choices = c("DS Dimensions" = "ds",
+ "PubMed" = "pubmed"),
+ selected = "pubmed"
+ ),
+ ## Dimenions API
+ conditionalPanel(
+ condition = "input.dbapi == 'ds'",
+ br(),
+ actionButton("dsShow", h5(strong("1. Configure API request")),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ h5(tags$b("Your Query")),
+ verbatimTextOutput("queryLog2", placeholder = FALSE),
+ h5(tags$b("Documents returned using your query")),
+ verbatimTextOutput("sampleLog2", placeholder = FALSE),
+ #
+ #
+ # uiOutput("sliderLimit"),
+
+
+ ),
+ ### Pubmed API
+ conditionalPanel(
+ condition = "input.dbapi == 'pubmed'",
+ br(),
+ actionButton("pmShow", h5(strong("1. Configure API request")),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ h5(tags$b("Your Query")),
+ verbatimTextOutput("pmQueryLog2", placeholder = FALSE),
+ h5(tags$b("Documents returned using your query")),
+ verbatimTextOutput("pmSampleLog2", placeholder = FALSE),
+
+ ),
+ tags$hr(),
+ #h4(em(strong("Gather metadata"))),
+ actionButton("apiApply", h5(strong("2. Download metadata")),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ tags$hr(),
+
+ h3(strong(
+ "Export a bibliometrix file "
+ )),
+ br(),
+
+ selectInput(
+ 'save_file_api',
+ 'Save as:',
+ choices = c(
+ ' ' = 'null',
+ 'Excel' = 'xlsx',
+ 'R Data Format' = 'RData'
+ ),
+ selected = 'null'
+ ),
+ conditionalPanel(condition = "input.save_file_api != 'null'",
+ downloadButton("collection.save_api", strong("Export"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Filters ----
+ conditionalPanel(condition = 'input.sidebarmenu == "filters"',
+ h3(strong("Filters")),
+ br(),
+ actionButton("applyFilter", strong("Run"),style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%",
+ icon = fa_i(name ="play")),
+ h5(" "),
+ #br(),
+ #span(h5((strong("Dataset Overview "))),style="color:CornflowerBlue"),
+ box(h6(htmlOutput("textDim")),
+ width = "100%"),
+ # box(h5(htmlOutput("textDim")),
+ # width = "100%"),
+ #htmlOutput("textDim"),
+ br(),
+ #uiOutput("textDim"),
+ uiOutput("selectLA"),
+ uiOutput("sliderPY"),
+ uiOutput("selectType"),
+ uiOutput("sliderTCpY"),
+ #uiOutput("selectSource"),
+ selectInput("bradfordSources",
+ label = "Source by Bradford Law Zones",
+ choices = c("Core Sources"="core",
+ "Core + Zone 2 Sources"="zone2",
+ "All Sources"="all"),
+ selected = "all")
+ ),
+ ## Annual Scientific Prod ----
+ conditionalPanel(condition = 'input.sidebarmenu == "annualScPr"',
+ br(),
+ h4(strong("Annual Growth Rate")),
+ br(),
+ verbatimTextOutput("CAGR", placeholder = TRUE)
+ ),
+ br(),
+ br(),
+ conditionalPanel(condition = 'input.sidebarmenu == "annualScPr"',
+ selectInput(
+ 'ASPdpi',
+ label = h4(strong("Export plot")),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ )
+ ),
+ br(),
+ br(),
+ conditionalPanel(condition = 'input.sidebarmenu == "annualScPr" & input.ASPdpi != "null"',
+ #h4(em(strong("Height (in inches)")), align="center"),
+ sliderInput(
+ 'ASPh',
+ label =h4(em(strong("Height (in inches)"))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("ASPplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px; vertical-align: 'middle';font-size: 20px;",
+ width = "100%")
+ ),
+ ## Average Cit Per Year ----
+ conditionalPanel(condition = 'input.sidebarmenu == "averageCitPerYear"',
+ selectInput(
+ 'ACpYdpi',
+ h4(strong("Export plot"), align ="center"),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.ACpYdpi != 'null'",
+ sliderInput(
+ 'ACpYh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("ACpYplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Three field Plot ----
+ conditionalPanel(condition = 'input.sidebarmenu == "threeFieldPlot"',
+ # actionButton("apply3F", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ #collapsed = TRUE,
+ fluidRow(
+ (column(6, selectInput("CentralField",
+ label = "Middle Field",
+ choices = c("Authors" = "AU",
+ "Affiliations" = "AU_UN",
+ "Countries"="AU_CO",
+ "Keywords" = "DE",
+ "Keywords Plus" = "ID",
+ "Titles" = "TI_TM",
+ "Abstract" = "AB_TM",
+ "Sources" = "SO",
+ "References" = "CR",
+ "Cited Sources" = "CR_SO"),
+ selected = "AU"))),
+ (column(6,numericInput("CentralFieldn",
+ label=("Number of items"),
+ min = 1, max = 50, step = 1, value = 20)))),
+ fluidRow(
+ (column(6,selectInput("LeftField",
+ label = "Left Field",
+ choices = c("Authors" = "AU",
+ "Affiliations" = "AU_UN",
+ "Countries"="AU_CO",
+ "Keywords" = "DE",
+ "Keywords Plus" = "ID",
+ "Titles" = "TI_TM",
+ "Abstract" = "AB_TM",
+ "Sources" = "SO",
+ "References" = "CR",
+ "Cited Sources" = "CR_SO"),
+ selected = "CR"))),
+ (column(6, numericInput("LeftFieldn",
+ label=("Number of items"),
+ min = 1, max = 50, step = 1, value = 20)))),
+ fluidRow(
+ (column(6,selectInput("RightField",
+ label = "Right Field",
+ choices = c("Authors" = "AU",
+ "Affiliations" = "AU_UN",
+ "Countries"="AU_CO",
+ "Keywords" = "DE",
+ "Keywords Plus" = "ID",
+ "Titles" = "TI_TM",
+ "Abstract" = "AB_TM",
+ "Sources" = "SO",
+ "References" = "CR",
+ "Cited Sources" = "CR_SO"),
+ selected = "DE"))),
+ (column(6,numericInput("RightFieldn",
+ label=("Number of items"),
+ min = 1, max = 50, step = 1, value = 20))))
+ )),
+ ## Relevant Sources ----
+ conditionalPanel(condition = 'input.sidebarmenu == "relevantSources"',
+ # actionButton("applyMRSources", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ h4(strong("Parameters: ")),
+ " ",
+ numericInput("MostRelSourcesK",
+ label=("Number of Sources"),
+ value = 10),
+ selectInput(
+ 'MRSdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MRSdpi != 'null'",
+ sliderInput(
+ 'MRSh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MRSplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Local Cited Sources ----
+ conditionalPanel(condition ='input.sidebarmenu == "localCitedSources"',
+ # actionButton("applyMLCSources", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%")
+ h4(strong("Parameters: ")),
+ " ",
+ numericInput("MostRelCitSourcesK",
+ label=("Number of Sources"),
+ value = 10),
+ selectInput(
+ 'MLCSdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MLCSdpi != 'null'",
+ sliderInput(
+ 'MLCSh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MLCSplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px; font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Bradford Law ----
+ conditionalPanel(condition ='input.sidebarmenu == "bradford"',
+ selectInput(
+ 'BLdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.BLdpi != 'null'",
+ sliderInput(
+ 'BLh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("BLplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )),
+ ## Source Impact ----
+ conditionalPanel(condition ='input.sidebarmenu == "sourceImpact"',
+ # actionButton("applyHsource", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput("HmeasureSources",
+ label = "Impact measure",
+ choices = c("H-Index"="h",
+ "G-Index"="g",
+ "M-Index"="m",
+ "Total Citation"="tc"),
+ selected = "h"),
+ " ",
+ numericInput("Hksource",
+ label=("Number of sources"),
+ value = 10)),
+ selectInput(
+ 'SIdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.SIdpi != 'null'",
+ sliderInput(
+ 'SIh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("SIplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Source Dynamics ----
+ conditionalPanel(condition ='input.sidebarmenu == "sourceDynamics"',
+ # actionButton("applySOGrowth", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput("cumSO", "Occurrences",
+ choices = c("Cumulate" = "Cum",
+ "Per year" = "noCum"),
+ selected = "Cum"),
+ # selectInput("SOse", "Confidence Interval",
+ # choices = c("Yes" = "Yes",
+ # "No" = "No"),
+ # selected = "No"),
+ hr(),
+ sliderInput("topSO", label = "Number of Sources", min = 1, max = 50, step = 1, value = c(1,5))),
+ selectInput(
+ 'SDdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.SDdpi != 'null'",
+ sliderInput(
+ 'SDh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("SDplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )),
+ ## Most relevant Authors ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostRelAuthors"',
+ # actionButton("applyMRAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ numericInput("MostRelAuthorsK",
+ label=("Number of Authors"),
+ value = 10),
+ " ",
+ selectInput("AuFreqMeasure",
+ label = "Frequency measure",
+ choices = c("N. of Documents "="t",
+ "Percentage"="p",
+ "Fractionalized Frequency"="f"),
+ selected = "t")),
+ selectInput(
+ 'MRAdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MRAdpi != 'null'",
+ sliderInput(
+ 'MRAh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MRAplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Local Cited Authors ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitedAuthors"',
+ # actionButton("applyMLCAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(strong("Parameters: ")),
+ " ",
+ numericInput("MostCitAuthorsK",
+ label=("Number of Authors"),
+ value = 10),
+ selectInput(
+ 'MLCAdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MLCAdpi != 'null'",
+ sliderInput(
+ 'MLCAh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MLCAplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Authors production over time ----
+ conditionalPanel(condition = 'input.sidebarmenu == "authorsProdOverTime"',
+ # actionButton("applyAUoverTime", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(strong("Parameters: ")),
+ " ",
+ numericInput("TopAuthorsProdK",
+ label=("Number of Authors"),
+ value = 10),
+ selectInput(
+ 'APOTdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.APOTdpi != 'null'",
+ sliderInput(
+ 'APOTh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("APOTplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Lotka law ----
+ conditionalPanel(condition = 'input.sidebarmenu == "lotka"',
+ selectInput(
+ 'LLdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.LLdpi != 'null'",
+ sliderInput(
+ 'LLh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("LLplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Author Impact ----
+ conditionalPanel(condition = 'input.sidebarmenu == "authorImpact"',
+ # actionButton("applyHAuthors", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput("HmeasureAuthors",
+ label = "Impact measure",
+ choices = c("H-Index"="h",
+ "G-Index"="g",
+ "M-Index"="m",
+ "Total Citation"="tc"),
+ selected = "h"),
+ " ",
+ numericInput("Hkauthor",
+ label=("Number of authors"),
+ value = 10)),
+ selectInput(
+ 'AIdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.AIdpi != 'null'",
+ sliderInput(
+ 'AIh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("AIplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Relevant Affiliations ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostRelAffiliations"',
+ # actionButton("applyMRAffiliations", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput("disAff",
+ label = "Affiliation Name Disambiguation",
+ choices = c("Yes"="Y",
+ "No"="N"),
+ selected = "Y"),
+ " ",
+ numericInput("MostRelAffiliationsK",
+ label=("Number of Affiliations"),
+ value = 10)),
+ selectInput(
+ 'AFFdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.AFFdpi != 'null'",
+ sliderInput(
+ 'AFFh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("AFFplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Corresponding Author country ----
+ conditionalPanel(condition = 'input.sidebarmenu == "correspAuthorCountry"',
+ # actionButton("applyCAUCountries", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(strong("Parameters: ")),
+ numericInput("MostRelCountriesK",
+ label=("Number of Countries"),
+ value = 20),
+ selectInput(
+ 'MRCOdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MRCOdpi != 'null'",
+ sliderInput(
+ 'MRCOh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MRCOplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Country Scientific Production ----
+ conditionalPanel(condition = 'input.sidebarmenu == "countryScientProd"',
+ selectInput(
+ 'CSPdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.CSPdpi != 'null'",
+ sliderInput(
+ 'CSPh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("CSPplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Cited Countries ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostCitedCountries"',
+ # actionButton("applyMCCountries", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput("CitCountriesMeasure",
+ label = "Measure",
+ choices = c("Total Citations"="TC",
+ "Average Citations per Year"="TCY"),
+ selected = "TC"),
+ " ",
+ numericInput("MostCitCountriesK",
+ label=("Number of Countries"),
+ value = 10)),
+ selectInput(
+ 'MCCdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MCCdpi != 'null'",
+ sliderInput(
+ 'MCCh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MCCplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Global Cited Documents
+ conditionalPanel(condition = 'input.sidebarmenu == "mostGlobalCitDoc"',
+ # actionButton("applyMGCDocuments", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ br(),
+ br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ numericInput("MostCitDocsK",
+ label=("Number of Documents"),
+ value = 10),
+ " ",
+ selectInput("CitDocsMeasure",
+ label = "Measure",
+ choices = c("Total Citations"="TC",
+ "Total Citations per Year"="TCY"),
+ selected = "TC")),
+ selectInput(
+ 'MGCDdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MGCDdpi != 'null'",
+ sliderInput(
+ 'MGCDh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MGCDplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ # Most Local Cited Document
+ conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitDoc"',
+ # actionButton("applyMLCDocuments", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ br(),
+ br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ numericInput("MostLocCitDocsK",
+ label=("Number of Documents"),
+ value = 10),
+ " ",
+ selectInput(inputId = "LocCitSep",
+ label = "Field separator character",
+ choices = c(";" = ";",
+ ". " = ". ",
+ "," = ","),
+ selected = ";")),
+ selectInput(
+ 'MLCDdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MLCDdpi != 'null'",
+ sliderInput(
+ 'MLCDh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MLCDplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Most Local Cited References ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostLocalCitRef"',
+ # actionButton("applyMLCReferences", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ numericInput("MostCitRefsK",
+ label=("Number of Documents"),
+ value = 10),
+ " ",
+ selectInput(inputId = "CitRefsSep",
+ label = "Field separator character",
+ choices = c(";" = ";",
+ ". " = ". ",
+ "," = ","),
+ selected = ";")),
+ selectInput(
+ 'MLCRdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MLCRdpi != 'null'",
+ sliderInput(
+ 'MLCRh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MLCRplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Reference spectroscopy
+ conditionalPanel(condition = 'input.sidebarmenu == "ReferenceSpect"',
+ # actionButton("applyRPYS", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ br(),
+ br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput(inputId = "rpysSep",
+ label = "Field separator character",
+ choices = c(";" = ";",
+ ". " = ". ",
+ "," = ","),
+ selected = ";"),
+ h4(em(strong("Time slice"))),
+ fluidRow(column(6,
+ numericInput(inputId = "rpysMinYear",
+ label = "Starting Year",
+ value = NA,
+ step = 1)),
+ column(6,
+ numericInput(inputId = "rpysMaxYear",
+ label = "End Year",
+ value = NA,
+ step = 1)
+ ))),
+ selectInput(
+ 'RSdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.RSdpi != 'null'",
+ sliderInput(
+ 'RSh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("RSplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+
+ )
+ ),
+ ## Most Frequent Words ----
+ conditionalPanel(condition = 'input.sidebarmenu == "mostFreqWords"',
+ # actionButton("applyMFWords", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ selectInput("MostRelWords", "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.MostRelWords == 'AB' |input.MostRelWords == 'TI'",
+ selectInput("MRWngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ numericInput("MostRelWordsN", label = "Number of words", min = 2, max = 100, step = 1, value = 10),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("MostRelWordsStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.MostRelWordsStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("MostRelWordsStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("MostRelWordsSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("MostRelWordsStopPreview"))
+ ),
+ selectInput("MRWSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.MRWSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("MRWSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("MRWSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("MRWSynPreview"))
+ )),
+ selectInput(
+ 'MRWdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.MRWdpi != 'null'",
+ sliderInput(
+ 'MRWh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("MRWplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"))
+ ),
+ ## Word cloud ----
+ conditionalPanel(condition = 'input.sidebarmenu == "wcloud"',
+ # actionButton("applyWordCloud", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(em(strong(" "))),
+ " ",
+ selectInput("summaryTerms", "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.summaryTerms == 'AB' |input.summaryTerms == 'TI'",
+ selectInput("summaryTermsngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ #hr(),
+ numericInput("n_words", label = "Number of words", min = 10, max = 500, step = 1, value = 50),
+ #hr(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("WCStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.WCStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("WCStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+ selectInput("WCSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ",")
+ #,h5(htmlOutput("WCStopPreview"))
+ ),
+ selectInput("WCSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.WCSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("WCSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("WCSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ",")
+ #,h5(htmlOutput("WCSynPreview"))
+ )),
+ hr(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ selectInput("measure", "Word occurrence by",
+ choices = c("Frequency" = "freq",
+ "Square root" = "sqrt",
+ "Log" = "log",
+ "Log10" = "log10"),
+ selected = "freq")
+ ),
+ column(6,
+ selectInput("wcShape", "Shape",
+ choices = c("Circle" = "circle",
+ "Cardiod" = "cardioid",
+ "Diamond" = "diamond",
+ "Pentagon" = "pentagon",
+ "Star" = "star",
+ "Triangle-forward" = "triangle-forward"
+ ,"Triangle" = "triangle"),
+ selected = "circle")
+ )),
+ fluidRow(column(6,
+ selectInput("font", label = "Font type",
+ choices = c("Impact", "Comic Sans MS (No plz!)" = "Comic Sans MS",
+ "Arial", "Arial Black", "Tahoma", "Verdana", "Courier New",
+ "Georgia", "Times New Roman", "Andale Mono"))
+ ),
+ column(6,
+ selectInput("wcCol", "Text colors",
+ choices = c("Random Dark" = "random-dark",
+ "Random Light" = "random-light"),
+ selected = "random-dark")
+ )),
+ fluidRow(column(6,
+ numericInput("scale", label = "Font size", min=0.2,max=5,step=0.1,value=1)
+ ),
+ column(6,
+ numericInput("ellipticity", label = "Ellipticity", min=0,max=1,step=0.05,value=0.65)
+ )),
+ fluidRow(column(6,
+ numericInput("padding", label = "Padding", min = 0, max = 5, value = 1, step = 1)
+ ),
+ column(6,
+ numericInput("rotate", label = "Rotate", min = 0, max = 20, value = 0, step = 1)
+ ))
+ )
+ ),
+ ## Tree Map ----
+ conditionalPanel(condition = 'input.sidebarmenu == "treemap"',
+ # actionButton("applyTreeMap", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ selectInput("treeTerms", "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.treeTerms == 'AB' |input.treeTerms == 'TI'",
+ selectInput("treeTermsngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ numericInput("treen_words", label = "Number of words", min = 10, max = 200, step = 5, value = 50),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("TreeMapStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TreeMapStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("TreeMapStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TreeMapSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TreeMapStopPreview"))
+ ),
+ selectInput("TreeMapSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TreeMapSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("TreeMapSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TreeMapSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TreeMapSynPreview"))
+ )
+ )
+ ),
+ ## Word dynamics ----
+ conditionalPanel(condition = 'input.sidebarmenu == "wordDynamics"',
+ # actionButton("applyWD", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ selectInput("growthTerms", "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("cumTerms", "Occurrences",
+ choices = c("Cumulate" = "Cum",
+ "Per year" = "noCum"),
+ selected = "Cum"),
+ conditionalPanel(condition = "input.growthTerms == 'AB' |input.growthTerms == 'TI'",
+ selectInput("growthTermsngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ sliderInput("topkw", label = "Number of words", min = 1, max = 100, step = 1, value = c(1,10))),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("WDStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.WDStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("WDStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("WDSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("WDStopPreview"))
+ ),
+ selectInput("WDSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.WDSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("WDSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("WDSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("WDSynPreview"))
+ )),
+ hr(),
+ selectInput(
+ 'WDdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.WDdpi != 'null'",
+ sliderInput(
+ 'WDh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("WDplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+
+ )
+ ),
+ ## Trend Topic ----
+ conditionalPanel(condition = 'input.sidebarmenu == "trendTopic"',
+ # actionButton("applyTrendTopics", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ #h4(em(strong("Method Parameters:"))),
+ selectInput("trendTerms", "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.trendTerms == 'TI' | input.trendTerms == 'AB'",
+ selectInput("trendTermsngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ conditionalPanel(
+ condition = "input.trendTerms == 'TI' | input.trendTerms == 'AB'",
+ selectInput("trendStemming", label="Word Stemming",
+ choices = c("Yes" = TRUE,
+ "No" = FALSE),
+ selected = FALSE)),
+ uiOutput("trendSliderPY"),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("TTStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TTStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("TTStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TTSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TTStopPreview"))
+ ),
+ selectInput("TTSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TTSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("TTSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TTSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TTSynPreview"))
+ )),
+ hr(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ #uiOutput("trendMinFreq"),
+ fluidRow(column(6,
+ numericInput("trendMinFreq", label = "Word Minimum Frequency", min = 0, max = 100, value = 5, step = 1),
+ ),
+ column(6,
+ numericInput("trendNItems", label = "Number of Words per Year", min = 1, max = 20, step = 1, value = 5)
+ ))),
+ #sliderInput("trendSize", label = "Word label size", min = 0, max = 20, step = 1, value = 5),
+ selectInput(
+ 'TTdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "Please select a dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.TTdpi != 'null'",
+ sliderInput(
+ 'TTh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("TTplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Coupling ----
+ conditionalPanel(condition = 'input.sidebarmenu == "coupling"',
+ # actionButton("applyCM", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(em(strong(" "))),
+ " ",
+ selectInput("CManalysis",
+ label = "Unit of Analysis",
+ choices = c("Documents" = "documents",
+ "Authors" = "authors",
+ "Sources" = "sources"),
+ selected = "documents"),
+ " ",
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ #selectInput("cmNP",
+ # label = h4(em(strong("Parameters: "))),
+ # choices = c("Hide Parameters" = "hide",
+ # "Show Parameters" = "show"),
+ # selected = "hide"),
+ #conditionalPanel(condition = "input.cmNP == 'show'",
+ #" ",
+ selectInput("CMfield",
+ label = "Coupling measured by",
+ choices = c("References" ="CR",
+ "Keywords Plus" = "ID",
+ "Author's Keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "CR"),
+ conditionalPanel(condition = "input.CMfield == 'TI' | input.CMfield == 'AB'",
+ selectInput("CMstemming", label="Word Stemming",
+ choices = c("Yes" = TRUE,
+ "No" = FALSE),
+ selected = FALSE)),
+ selectInput("CMimpact",
+ label = "Impact measure",
+ choices = c("Local Citation Score" = "local",
+ "Global Citation Score" = "global"),
+ selected = "local"),
+ selectInput("CMlabeling",
+ label = "Cluster labeling by",
+ choices = c("None" = "none",
+ "Keyword Plus" = "ID",
+ "Authors' keywords" = "DE",
+ "Title terms" = "TI",
+ "Abstract terms" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.CMlabeling == 'TI' | input.CMlabeling == 'AB'",
+ selectInput("CMngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ fluidRow(column(6,
+ numericInput("CMn", label="Number of Units\n ",value=250,min=50,max=5000,step=1)),
+ column(6,
+ numericInput("CMfreq", label="Min Cluster Freq. ",value=5,min=1,max=100,step=1))),
+ fluidRow(column(6,
+ numericInput("CMn.labels", label="Labels per cluster",value=3,min=1,max=10,step=1)),
+ column(6,
+ numericInput("sizeCM", label="Label size",value=0.3,min=0.0,max=1,step=0.05)))
+ ),
+
+ selectInput(
+ 'CMdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "Dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.CMdpi != 'null'",
+ sliderInput(
+ 'CMh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("CMplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Co-Occurence Network ----
+ conditionalPanel(condition = 'input.sidebarmenu == "coOccurenceNetwork"',
+ # actionButton("applyCoc", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ #" ",
+ #h4(em(strong("Network Parameters: "))),
+ selectInput("field",
+ "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's Keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.field == 'TI' | input.field == 'AB'",
+ selectInput("cocngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("COCStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.COCStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("COCStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("COCSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("COCStopPreview"))
+ ),
+ selectInput("COCSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.COCSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("COCSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("COCSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("COCSynPreview"))
+ )),
+ br(),
+ box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ selectInput("layout",
+ label = "Network Layout",
+ choices = c("Automatic layout"="auto",
+ "Circle"="circle",
+ "Fruchterman & Reingold"="fruchterman",
+ "Kamada & Kawai"="kamada",
+ "MultiDimensional Scaling"="mds",
+ "Sphere"="sphere",
+ "Star"="star"),
+ selected = "auto")
+ ),
+ column(6,
+ selectInput("cocCluster",
+ label = "Clustering Algorithm",
+ choices = c("None" = "none",
+ "Edge Betweenness" = "edge_betweenness",
+ "InfoMap" = "infomap",
+ "Leading Eigenvalues" = "leading_eigen",
+ "Louvain" = "louvain",
+ "Spinglass" = "spinglass",
+ "Walktrap" = "walktrap"),
+ selected = "louvain")
+ )),
+ fluidRow(column(6,
+ selectInput("normalize",
+ label = "Normalization",
+ choices = c("none",
+ "association",
+ "jaccard",
+ "salton",
+ "inclusion",
+ "equivalence"),
+ selected = "association")
+ ),
+ column(6,
+ selectInput("cocyears",
+ label = "Node Color by Year",
+ choices = c("No" = "No",
+ "Yes"= "Yes"),
+ selected = "No")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "Nodes",
+ label = "Number of Nodes",
+ min = 5,
+ max = 1000,
+ value = 50,
+ step = 1)
+ ),
+ column(6,
+ numericInput(inputId = "coc.repulsion",
+ label = "Repulsion Force",
+ min = 0,
+ max = 1,
+ value = 0.1,
+ step = 0.1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="coc.isolates",
+ label = "Remove Isolated Nodes",
+ choices = c("Yes" = "yes",
+ "No" = "no"),
+ selected = "yes")
+ ),
+ column(6,
+ numericInput("edges.min",
+ label=("Minimum Number of Edges"),
+ value = 2,
+ step = 1,
+ min = 0)
+ )
+ )),
+ #uiOutput("Focus"),
+ br(),
+ #h4(em(strong("Graphical Parameters: "))),
+ #br(),
+ box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ numericInput(inputId = "cocAlpha",
+ label = "Opacity",
+ min = 0,
+ max = 1,
+ value = 0.7,
+ step=0.05)
+ ),
+ column(6,
+ numericInput(inputId = "Labels",
+ label = "Number of labels",
+ min = 0,
+ max = 1000,
+ value = 50,
+ step = 1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="label.cex",
+ label = "Label cex",
+ choices = c("Yes",
+ "No"),
+ selected = "Yes")
+ ),
+ column(6,
+ selectInput(inputId ="coc.shape",
+ label = "Node Shape",
+ choices = c(
+ "Box"="box",
+ "Circle"="circle",
+ "Dot"="dot",
+ "Ellipse"="ellipse",
+ "Square"="square",
+ "Text"="text"),
+ selected = "dot")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "labelsize",
+ label = "Label size",
+ min = 0.0,
+ max = 20,
+ value = 6,
+ step = 0.10)
+ ),
+ column(6,
+ numericInput(
+ inputId = "edgesize",
+ label = "Edge size",
+ min = 0.5,
+ max = 20,
+ value = 5,
+ step=0.5)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="coc.shadow",
+ label = "Node shadow",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+ ),
+ column(6,
+ selectInput(inputId ="coc.curved",
+ label = "Curved edges",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+
+ )
+ )
+ ),
+ br(),
+ fluidRow(column(6,
+ downloadButton("network.coc", strong("Save Pajek"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ ),
+ column(6,
+ downloadButton("networkCoc.fig", strong("Save HTML"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ )
+ )
+ ),
+ ## Thematic Map ----
+ conditionalPanel(condition = 'input.sidebarmenu == "thematicMap"',
+ # actionButton("applyTM", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(em(strong(" "))),
+ " ",
+ selectInput("TMfield",
+ label = "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's Keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.TMfield == 'TI' | input.TMfield == 'AB'",
+ selectInput("TMngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ conditionalPanel(
+ condition = "input.TMfield == 'TI' | input.TMfield == 'AB'",
+ selectInput("TMstemming", label="Word Stemming",
+ choices = c("Yes" = TRUE,
+ "No" = FALSE),
+ selected = FALSE)),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("TMStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TMStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("TMStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TMSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TMStopPreview"))
+ ),
+ selectInput("TMapSynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TMapSynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("TMapSyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TMapSynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TMapSynPreview"))
+ )),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ numericInput("TMn", label="Number of Words",value=250,min=50,max=5000,step=1)
+ ),
+ column(6,
+ numericInput("TMfreq", label="Min Cluster Frequency (per thousand docs)",value=5,min=1,max=100,step=1)
+ )),
+ fluidRow(column(6,
+ numericInput("TMn.labels", label="Number of Labels",value=3,min=0,max=10,step=1)
+ ),
+ column(6,
+ numericInput("sizeTM", label="Label size",value=0.3,min=0.0,max=1,step=0.05)
+ ))
+ ),
+ selectInput(
+ 'TMdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.TMdpi != 'null'",
+ sliderInput(
+ 'TMh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("TMplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Thematic Evolution ----
+ conditionalPanel(condition = 'input.sidebarmenu == "thematicEvolution"',
+ # actionButton("applyTE", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(em(strong(" "))),
+ " ",
+ selectInput("TEfield",
+ label = "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's Keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts
+ " = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.TEfield == 'TI' | input.TEfield == 'AB'",
+ selectInput("TEngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("TEStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TEStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("TEStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TESep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TEStopPreview"))
+ ),
+ selectInput("TESynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.TESynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("TESyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("TESynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("TESynPreview"))
+ )),
+ br(),
+ box(title = p(strong("Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ numericInput("nTE", label="Number of Words",value=250,min=50,max=5000,step=1)
+ ),
+ column(6,
+ numericInput("fTE", label="Min Cluster Frequency (per thousand docs)",value=5,min=1,max=100,step=1)
+ )),
+ fluidRow(column(6,
+ selectInput("TEmeasure",
+ label = "Weight index",
+ choices = c("Inclusion Index" = "inclusion",
+ "Inclusion Index weighted by Word-Occurrences" = "weighted",
+ "Stability Index" = "stability"
+ ),
+ selected = "weighted")
+ ),
+ column(6,
+ numericInput("minFlowTE", label="Min Weight Index",value=0.1,min=0.02,max=1,step=0.02)
+ )),
+ fluidRow(column(6,
+ numericInput("sizeTE", label="Label size",value=0.3,min=0.0,max=1,step=0.05)
+ ),
+ column(6,
+ numericInput("TEn.labels", label="Number of Labels (for each cluster)",value=1,min=1,max=5,step=1)
+ ))
+ ),
+ br(),
+ box(title = p(strong("Time Slices"),style='font-size:16px;color:black;'),
+ collapsible = FALSE, width = 15,
+ solidHeader = FALSE, collapsed = FALSE,
+ numericInput("numSlices", label="Number of Cutting Points",min=1,max=4,value=1),
+ "Please, write the cutting points (in year) for your collection",
+ uiOutput("sliders")
+ )
+ ),
+ ## Factorial Analysis
+ conditionalPanel(condition = 'input.sidebarmenu == "factorialAnalysis"',
+ # actionButton("applyCA", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ br(),
+ br(),
+ selectInput("method",
+ label = "Method",
+ choices = c("Correspondence Analysis" = "CA",
+ "Multiple Correspondence Analysis" = "MCA",
+ "Multidimensional Scaling"= "MDS"),
+ selected = "MCA"),
+ selectInput("CSfield",
+ label = "Field",
+ choices = c("Keywords Plus" = "ID",
+ "Author's Keywords" = "DE",
+ "Titles" = "TI",
+ "Abstracts" = "AB"),
+ selected = "ID"),
+ conditionalPanel(condition = "input.CSfield == 'TI' | input.CSfield == 'AB'",
+ selectInput("CSngrams",'N-Grams',
+ choices = c("Unigrams" = "1",
+ "Bigrams" = "2",
+ "Trigrams" = "3"),
+ selected = 1)),
+ br(),
+ box(title = p(strong("Text Editing"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ selectInput("CSStopFile", "Load a list of terms to remove",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.CSStopFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing a list of terms you want to remove from the analysis.")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator)."))
+ ),
+ fileInput("CSStop", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("CSSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("CSStopPreview"))
+ ),
+ selectInput("FASynFile", "Load a list of synonyms",
+ choices = c("Yes" = "Y",
+ "No" = "N"),
+ selected = "N"),
+ conditionalPanel(condition = "input.FASynFile == 'Y'",
+ helpText(h5(strong("Upload a TXT or CSV file containing, in each row, a list of synonyms, that will be merged into a single term (the first word contained in the row)")),
+ h5(("Terms have to be separated by a standard separator (comma, semicolon or tabulator).
+ Rows have to be separated by return separator (\\n)."))
+ ),
+ fileInput("FASyn", "",
+ multiple = FALSE,
+ accept = c("text/csv",
+ "text/comma-separated-values,text/plain",
+ ".csv",
+ ".txt")),
+
+ selectInput("FASynSep", "File Separator",
+ choices = c('Comma ","' = ",",
+ 'Semicolon ";"' = ";",
+ 'Tab '= "\t"),
+ selected = ","),
+ h5(htmlOutput("FASynPreview"))
+ )),
+ #h4(em(strong("FA Parameters: "))),
+ br(),
+ box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ numericInput("CSn",
+ label=("Number of terms"),
+ value = 50, step = 1)),
+ column(6,
+ selectInput("nClustersCS",
+ label = "N. of Clusters",
+ choices = c("Auto" = "0",
+ "2" = "2",
+ "3" = "3",
+ "4" = "4",
+ "5" = "5",
+ "6" = "6",
+ "7" = "7",
+ "8" = "8"),
+ selected = "0")))
+ ),
+ br(),
+ box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ #h4(em(strong("Graphical Parameters: "))),
+ fluidRow(column(6,
+ numericInput(
+ inputId = "CSlabelsize",
+ label = "Label size",
+ min = 5,
+ max = 30,
+ value = 10)),
+ column(6,
+ numericInput("CSdoc",
+ label=("Num. of documents"),
+ value = 5)))
+ ),
+ selectInput(
+ 'FAdpi',
+ h4(strong(
+ "Export plots as png"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.FAdpi != 'null'",
+ sliderInput(
+ 'FAh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("FA1plot.save", strong("Term Factorial Map "),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ h4(" "),
+ downloadButton("FA2plot.save", strong("Topic Dendrogram "),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ h4(" "),
+ downloadButton("FA3plot.save", strong("Most Contributing Map "),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%"),
+ h4(" "),
+ downloadButton("FA4plot.save", strong("Most Cited Map "),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Co-citation Network ----
+ conditionalPanel(condition = 'input.sidebarmenu == "coCitationNetwork"',
+ # actionButton("applyCocit", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ #" ",
+ #h4(em(strong("Network Parameters: "))),
+ selectInput("citField",
+ label = "Field",
+ choices = c("Papers" = "CR",
+ "Authors" = "CR_AU",
+ "Sources" = "CR_SO"),
+ selected = "CR"),
+ selectInput(inputId = "citSep",
+ label = "Field separator character",
+ choices = c('";" (Semicolon)' = ";",
+ '". " (Dot and 3 or more spaces)' = ". ",
+ '"," (Comma)' = ","),
+ selected = "';'"),
+ box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ selectInput("citlayout",
+ label = "Network Layout",
+ choices = c("Automatic layout"="auto",
+ "Circle"="circle",
+ "Fruchterman & Reingold"="fruchterman",
+ "Kamada & Kawai"="kamada",
+ "MultiDimensional Scaling"="mds",
+ "Sphere"="sphere",
+ "Star"="star"),
+ selected = "auto")
+ ),
+ column(6,
+ selectInput("cocitCluster",
+ label = "Clustering Algorithm",
+ choices = c("None" = "none",
+ "Edge Betweenness" = "edge_betweenness",
+ "InfoMap" = "infomap",
+ "Leading Eigenvalues" = "leading_eigen",
+ "Louvain" = "louvain",
+ "Spinglass" = "spinglass",
+ "Walktrap" = "walktrap"),
+ selected = "louvain")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "citNodes",
+ label = "Number of Nodes",
+ min = 5,
+ max = 1000,
+ value = 50,
+ step = 1)
+ ),
+ column(6,
+ numericInput(inputId = "cocit.repulsion",
+ label = "Repulsion Force",
+ min = 0,
+ max = 1,
+ value = 0.1,
+ step = 0.1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="cit.isolates",
+ label = "Remove Isolated Nodes",
+ choices = c("Yes" = "yes",
+ "No" = "no"),
+ selected = "yes")
+ ),
+ column(6,
+ numericInput("citedges.min",
+ label=("Minimum Number of Edges"),
+ value = 2,
+ step = 1,
+ min = 0)
+ )
+ )),
+ #uiOutput("Focus"),
+ #br(),
+ #h4(em(strong("Graphical Parameters: "))),
+ #br(),
+ box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ selectInput(inputId ="citShortlabel",
+ label = "Short Label",
+ choices = c("Yes",
+ "No"),
+ selected = "Yes"),
+
+ ),
+ column(6,
+ numericInput(inputId = "citLabels",
+ label = "Number of labels",
+ min = 0,
+ max = 1000,
+ value = 50,
+ step = 1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="citlabel.cex",
+ label = "Label cex",
+ choices = c("Yes",
+ "No"),
+ selected = "Yes")
+ ),
+ column(6,
+ selectInput(inputId ="cocit.shape",
+ label = "Node Shape",
+ choices = c(
+ "Box"="box",
+ "Circle"="circle",
+ "Dot"="dot",
+ "Ellipse"="ellipse",
+ "Square"="square",
+ "Text"="text"),
+ selected = "dot")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "citlabelsize",
+ label = "Label size",
+ min = 0.0,
+ max = 20,
+ value = 2,
+ step = 0.10)
+ ),
+ column(6,
+ numericInput(
+ inputId = "citedgesize",
+ label = "Edge size",
+ min = 0.5,
+ max = 20,
+ value = 5,
+ step=0.5)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="cocit.shadow",
+ label = "Node shadow",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+ ),
+ column(6,
+ selectInput(inputId ="cocit.curved",
+ label = "Curved edges",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+
+ )
+ )
+ ),
+ br(),
+ fluidRow(column(6,
+ downloadButton("network.cocit", strong("Save Pajek"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ ),
+ column(6,
+ downloadButton("networkCocit.fig", strong("Save HTML"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ )
+ )
+ ),
+ ## Historiograph ----
+ conditionalPanel(condition = 'input.sidebarmenu == "historiograph"',
+ # actionButton("applyHist", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ #selectInput('save_colnet', 'Save network as:', choices = c('No, thanks!' = 'no_thanks', 'Pajek format' = 'pajek')),
+ #conditionalPanel(condition = "input.save_colnet == 'pajek'"
+ # br(),
+ # br(),
+ numericInput(inputId = "histNodes",
+ label = "Number of Nodes",
+ min = 5,
+ max = 100,
+ value = 20,
+ step = 1),
+ " ",
+ br(),
+ box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE,
+ collapsed = FALSE,
+ selectInput(inputId = "titlelabel",
+ label = "Node label",
+ choices = c("Short id (1st Author, Year)" = "FALSE",
+ "Document Title" = "TRUE"),
+ selected = "FALSE"),
+ fluidRow(column(6,
+ numericInput(inputId = "histlabelsize",
+ label = "Label size",
+ min = 0.0,
+ max = 20,
+ value = 3, step = 1)),
+ column(6,
+ numericInput(inputId = "histsize",
+ label = "Node size",
+ min = 0,
+ max = 20,
+ value = 4, step = 1)))
+ ),
+ selectInput(
+ 'HGdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.HGdpi != 'null'",
+ sliderInput(
+ 'HGh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("HGplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ ),
+ ## Collaboration Network ----
+ conditionalPanel(condition = 'input.sidebarmenu == "collabNetwork"',
+ # actionButton("applyCol", strong("Run"),style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ #" ",
+ #h4(em(strong("Network Parameters: "))),
+ selectInput("colField",
+ label = "Field",
+ choices = c("Authors" = "COL_AU",
+ "Institutions" = "COL_UN",
+ "Countries" = "COL_CO"),
+ selected = "COL_AU"),
+ br(),
+ box(title = p(strong("Method Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ selectInput("collayout",
+ label = "Network Layout",
+ choices = c("Automatic layout"="auto",
+ "Circle"="circle",
+ "Fruchterman & Reingold"="fruchterman",
+ "Kamada & Kawai"="kamada",
+ "MultiDimensional Scaling"="mds",
+ "Sphere"="sphere",
+ "Star"="star"),
+ selected = "auto")
+ ),
+ column(6,
+ selectInput("colCluster",
+ label = "Clustering Algorithm",
+ choices = c("None" = "none",
+ "Edge Betweenness" = "edge_betweenness",
+ "InfoMap" = "infomap",
+ "Leading Eigenvalues" = "leading_eigen",
+ "Louvain" = "louvain",
+ "Spinglass" = "spinglass",
+ "Walktrap" = "walktrap"),
+ selected = "louvain")
+ )),
+ fluidRow(column(6,
+ selectInput("colnormalize",
+ label = "Normalization",
+ choices = c("none",
+ "association",
+ "jaccard",
+ "salton",
+ "inclusion",
+ "equivalence"),
+ selected = "association")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "colNodes",
+ label = "Number of Nodes",
+ min = 5,
+ max = 1000,
+ value = 50,
+ step = 1)
+ ),
+ column(6,
+ numericInput(inputId = "col.repulsion",
+ label = "Repulsion Force",
+ min = 0,
+ max = 1,
+ value = 0.1,
+ step = 0.1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="col.isolates",
+ label = "Remove Isolated Nodes",
+ choices = c("Yes" = "yes",
+ "No" = "no"),
+ selected = "yes")
+ ),
+ column(6,
+ numericInput("coledges.min",
+ label=("Minimum Number of Edges"),
+ value = 1,
+ step = 1,
+ min = 0)
+ )
+ )),
+ #uiOutput("Focus"),
+ #h4(em(strong("Graphical Parameters: "))),
+ br(),
+ box(title = p(strong("Graphical Parameters"),style='font-size:16px;color:black;'),
+ collapsible = TRUE, width = 15,
+ solidHeader = FALSE, collapsed = TRUE,
+ fluidRow(column(6,
+ numericInput(inputId = "colAlpha",
+ label = "Opacity",
+ min = 0,
+ max = 1,
+ value = 0.7,
+ step=0.05)
+ ),
+ column(6,
+ numericInput(inputId = "colLabels",
+ label = "Number of labels",
+ min = 0,
+ max = 1000,
+ value = 50,
+ step = 1)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="collabel.cex",
+ label = "Label cex",
+ choices = c("Yes",
+ "No"),
+ selected = "Yes")
+ ),
+ column(6,
+ selectInput(inputId ="col.shape",
+ label = "Node Shape",
+ choices = c(
+ "Box"="box",
+ "Circle"="circle",
+ "Dot"="dot",
+ "Ellipse"="ellipse",
+ "Square"="square",
+ "Text"="text"),
+ selected = "dot")
+ )),
+ fluidRow(column(6,
+ numericInput(inputId = "collabelsize",
+ label = "Label size",
+ min = 0.0,
+ max = 20,
+ value = 2,
+ step = 0.10)
+ ),
+ column(6,
+ numericInput(
+ inputId = "coledgesize",
+ label = "Edge size",
+ min = 0.5,
+ max = 20,
+ value = 5,
+ step=0.5)
+ )),
+ fluidRow(column(6,
+ selectInput(inputId ="col.shadow",
+ label = "Node shadow",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+ ),
+ column(6,
+ selectInput(inputId ="soc.curved",
+ label = "Curved edges",
+ choices = c("Yes",
+ "No"),
+ selected = "No")
+
+ ))
+ ),
+ br(),
+ fluidRow(column(6,
+ downloadButton("network.col", strong("Save Pajek"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ ),
+ column(6,
+ downloadButton("networkCol.fig", strong("Save HTML"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 15px;",
+ width = "100%")
+ )
+ )
+ ),
+ ## Collaboration World Map ----
+ conditionalPanel(condition = 'input.sidebarmenu == "collabWorldMap"',
+ # actionButton("applyWM", strong("Run"),
+ # style ="border-radius: 10px; border-width: 3px;",
+ # width = "100%"),
+ # br(),
+ # br(),
+ h4(strong("Method Parameters: ")),
+ " ",
+ numericInput("WMedges.min",
+ label=("Min edges"),
+ value = 2,
+ step = 1),
+ " ",
+ br(),
+ h4(strong("Graphical Parameters: ")),
+ " ",
+ sliderInput(inputId = "WMedgesize",
+ label = "Edge size",
+ min = 0.1,
+ max = 20,
+ value = 5),
+ br(),
+ selectInput(
+ 'CCdpi',
+ h4(strong(
+ "Export plot"
+ )),
+ choices=c(
+ "dpi value" = "null",
+ "75 dpi" = "75",
+ "150 dpi" = "150",
+ "300 dpi" = "300",
+ "600 dpi" = "600"
+ ),
+ selected = "null"
+ ),
+ conditionalPanel(condition = "input.CCdpi != 'null'",
+ sliderInput(
+ 'CCh',
+ h4(em(strong(
+ "Height (in inches)"
+ ))),
+ value = 7, min = 1, max = 20, step = 1),
+ downloadButton("CCplot.save", strong("Export plot as png"),
+ style ="border-radius: 10px; border-width: 3px;font-size: 20px;",
+ width = "100%")
+ )
+ )
+ )
+ )
+ )
+ )
+ )
+ })
+
+}
#### END ####
\ No newline at end of file
diff --git a/inst/biblioshiny/utils.R b/inst/biblioshiny/utils.R
index f943c9af..c8dc3132 100644
--- a/inst/biblioshiny/utils.R
+++ b/inst/biblioshiny/utils.R
@@ -59,6 +59,28 @@ ValueBoxes <- function(M){
## VB 12 - Average citations per doc
df[12,] <- c("Average citations per doc", format(mean(M$TC, na.rm=T), digit = 4))
+ DT <- M %>% mutate(DT = tolower(.data$DT)) %>%
+ count(.data$DT) %>%
+ rename(Description = .data$DT,
+ Results = .data$n)
+
+ # Indexed Keywords (ID)
+ ID <- unique(trimws(gsub("\\s+|\\.|\\,"," ",unlist(strsplit(M$ID, ";")))))
+ ID <- ID[!is.na(ID)]
+ df[nrow(df)+1,] <- c("Keywords Plus (ID)",length(ID))
+
+ # Single authored docs
+
+ df[nrow(df)+1,] <- c("Single-authored docs",sum(nAU==1))
+
+ df2 <- data.frame(Description = c("MAIN INFORMATION ABOUT DATA","Timespan","Sources (Journals, Books, etc)","Documents",
+ "Annual Growth Rate %","Document Average Age","Average citations per doc","References",
+ "DOCUMENT CONTENTS","Keywords Plus (ID)","Author's Keywords (DE)","AUTHORS","Authors","Authors of single-authored docs",
+ "AUTHORS COLLABORATION","Single-authored docs","Co-Authors per Doc","International co-authorships %", "DOCUMENT TYPES"))
+
+ df <- left_join(df2,df,by = "Description") %>% rbind(DT) %>%
+ mutate(Results = replace_na(.data$Results, ""))
+
return(df)
}
@@ -80,5 +102,5 @@ countryCollab<-function(M){
rename(Country = .data$AU1_CO) %>%
arrange(desc(.data$Articles))
- return(df)
+ return(df)
}