fully packages

.Rbuildignore

@@ -1,2 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.github
+aws
+docs
+scripts
+app.R
+LICENSE
+^LICENSE\.md$

DESCRIPTION

@@ -1,31 +1,37 @@
 Package: straf
-Title: STR Analysis For Forensics
-Version: 1.5.0
+Title: STR Analysis for Forensics
+Version: 2.0.0
 Authors@R: 
     person(given = "Alexandre",
            family = "Gouy",
            role = c("aut", "cre"),
-           email = "[email protected]")
-Description: straf is a Shiny application to perform STR / microsatellite data analysis.
-License: `use_gpl3_license()`
+           email = "[email protected]", 
+           comment = c(ORCID = "0000-0002-2478-8475"))
+Description: A 'shiny' application to perform Short Tandem Repeats (STRs, also 
+    known as microsatellites) data analysis. The application allows one to 
+    compute forensic parameters, population genetics indices, and investigate 
+    population structure through various methods and generate relevant data 
+    visualisations. It also implements file conversion to other popular formats.
+Depends: R (>= 3.5.0)
+License: GPL-3
 Encoding: UTF-8
-LazyData: true
+BugReports: https://github.com/agouy/straf/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1.9000
 Imports:
   shiny (>= 1.5.0),
+  shinyWidgets,
   colourpicker,
   DT,
   plotly,
-  shinyWidgets,
-  ade4,
-  adegenet,
-  pegas,
-  hierfstat,
-  car,
   openxlsx,
   reshape2,
   dplyr,
   tidyr,
   ggplot2,
-  ggrepel
+  ggrepel,
+  car,
+  ade4,
+  adegenet,
+  pegas,
+  hierfstat

NAMESPACE

@@ -1,17 +1,48 @@
 # Generated by roxygen2: do not edit by hand
 
-import(ade4)
-import(adegenet)
-import(car)
-import(colourpicker)
+export(runStraf)
 import(dplyr)
 import(ggplot2)
-import(ggrepel)
-import(hierfstat)
-import(openxlsx)
-import(pegas)
-import(plotly)
-import(reshape2)
-import(shiny)
-import(shinyWidgets)
-import(tidyr)
+import(shiny, except = c(dataTableOutput, renderDataTable))
+importClassesFrom(adegenet,genind)
+importFrom(DT,dataTableOutput)
+importFrom(DT,datatable)
+importFrom(DT,renderDataTable)
+importFrom(ade4,dudi.pca)
+importFrom(adegenet,"pop<-")
+importFrom(adegenet,as.genind)
+importFrom(adegenet,df2genind)
+importFrom(adegenet,dist.genpop)
+importFrom(adegenet,funky)
+importFrom(adegenet,genind2genpop)
+importFrom(adegenet,loadingplot)
+importFrom(adegenet,locNames)
+importFrom(adegenet,makefreq)
+importFrom(adegenet,pop)
+importFrom(adegenet,transp)
+importFrom(colourpicker,colourInput)
+importFrom(ggrepel,geom_text_repel)
+importFrom(graphics,abline)
+importFrom(graphics,axis)
+importFrom(graphics,barplot)
+importFrom(graphics,hist)
+importFrom(graphics,image)
+importFrom(graphics,legend)
+importFrom(graphics,par)
+importFrom(hierfstat,genind2hierfstat)
+importFrom(hierfstat,pairwise.WCfst)
+importFrom(openxlsx,write.xlsx)
+importFrom(pegas,genind2loci)
+importFrom(reshape2,acast)
+importFrom(shinyWidgets,awesomeCheckbox)
+importFrom(shinyWidgets,pickerInput)
+importFrom(stats,as.dist)
+importFrom(stats,cmdscale)
+importFrom(stats,cov)
+importFrom(stats,frequency)
+importFrom(stats,ks.test)
+importFrom(stats,qqplot)
+importFrom(stats,qunif)
+importFrom(tidyr,gather)
+importFrom(utils,read.table)
+importFrom(utils,write.table)

R/doc_tabs.R

@@ -1,4 +1,3 @@
-### documentation tab
 documentation_tab <- function() {
   tabPanel(
     "Documentation",
@@ -10,7 +9,6 @@ documentation_tab <- function() {
   )
 }
 
-
 about_tab <- function() {
   tabPanel(
     "About STRAF",