doc: improve pkgdown content

gdrplatform · Feb 27, 2024 · baa22a2 · baa22a2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,14 +4,18 @@ Title: Package for handling the import of dose-response data
 Version: 1.1.6
 Date: 2024-02-26
 Authors@R: c(
-    person("Arkadiusz", "Gladki", role=c("aut", "cre"), email="[email protected]"),
-    person("Bartosz", "Czech", role=c("aut")), 
-    person("Marc", "Hafner", role=c("aut")),
-    person("Sergiu", "Mocanu", role=c("aut")),
-    person("Dariusz", "Scigocki", role=c("aut")),
-    person("Allison", "Vuong", role=c("aut")),
-    person("Luca", "Gerosa", role=c("aut")),
-    person("Janina", "Smola", role=c("aut")))
+    person("Arkadiusz", "Gladki", role=c("aut", "cre"), email="[email protected]",
+           comment = c(ORCID = "0000-0002-7059-6378")),
+    person("Bartosz", "Czech", role="aut", 
+           comment = c(ORCID = "0000-0002-9908-3007")),
+    person("Marc", "Hafner", role="aut",
+           comment = c(ORCID = "0000-0003-1337-7598")),
+    person("Sergiu", "Mocanu", role="aut"),
+    person("Dariusz", "Scigocki", role="aut"),
+    person("Allison", "Vuong", role="aut"),
+    person("Luca", "Gerosa", role="aut",
+           comment = c(ORCID = "0000-0001-6805-9410")),
+    person("Janina", "Smola", role="aut"))
 Description: The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats. 
 License: Artistic-2.0
 LazyLoad: yes

diff --git a/R/MAE_to_PSet.R b/R/MAE_to_PSet.R
@@ -5,7 +5,7 @@
 #'
 #' @param mae A MultiAssayExperiment object generated by gDR.
 #' @param pset_name A character string specifying the name of the resulting PharmacoSet object.
-#' @keywords mae_to_pset
+#' @keywords pset
 #' 
 #' @return A PharmacoSet object.
 #' 
@@ -130,7 +130,7 @@ convert_MAE_to_PSet <- function(mae,
 #'
 #' @param SE A SummarizedExperiment object
 #' @param assay_name A character string specifying the name of the assay to extract or create
-#' @keywords mae_to_pset
+#' @keywords pset
 #'
 #' @return A SummarizedExperiment object with the specified assay
 #'

diff --git a/R/assert_utils.R b/R/assert_utils.R
@@ -2,7 +2,7 @@
 #' Check if all paths in vector are readable
 #'
 #' @param paths a character with path(s)
-#' @keywords assert_utils
+#' @keywords utils
 #'
 #' @examples
 #' td2 <- get_test_Tecan_data()

diff --git a/R/correction.R b/R/correction.R
@@ -3,7 +3,7 @@
 #' get sheets for given set of XLS files
 #' 
 #' @param files charvec with file paths
-#' @keywords correction
+#' @keywords correction_exception
 #'
 #' @return named list where names are the excel filenames
 #' and the values are the sheets within each file
@@ -21,7 +21,7 @@ get_xl_sheets <- function(files) {
 #' 
 #' get sheets for given set of XLS files
 #' @param ts list with template sheets info
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @return logical flag
 #' 
@@ -50,7 +50,7 @@ get_xl_sheets <- function(files) {
 #' Correct names of the template sheets (if required)
 #' 
 #' @param tfiles charvec with paths to template files
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @return charvec with paths to corrected sheet names
 correct_template_sheets <- function(tfiles) {
@@ -98,7 +98,7 @@ correct_template_sheets <- function(tfiles) {
 #' Get names of the sheets expected in templates xlsx
 #'
 #' @param type charvec type of the sheets
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @return string with type of the sheets
 #' 
@@ -134,7 +134,7 @@ get_expected_template_sheets <-
 #' are template sheet valid?
 #' 
 #' @param ts list with (per file) template sheets
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @seealso get_xl_sheets
 #' 
@@ -181,7 +181,7 @@ are_template_sheets_valid <- function(ts) {
 #' 'grepl' is used to find entries from 'ref' that might be 
 #' somehow pre- or post- fixed
 #' @param fix_underscores logical flag fix the issues with underscores in data identfiers? 
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @return list or charvec with corrected data
 #' 
@@ -241,7 +241,7 @@ fix_typos_with_reference <-
 #' @param x charvec with data
 #' @param do_unlist logical_flag unlist the final results?
 #' @param ... additional argument
-#' @keywords correction
+#' @keywords correction_exception
 #' 
 #' @return list of charvec with grep output
 #' 

diff --git a/R/exceptions.R b/R/exceptions.R
@@ -48,7 +48,7 @@ EXCEPTION_TABLE <- tibble::tribble(
 #' @examples
 #' get_exception_data(1)
 #' get_exception_data()
-#' @keywords exceptions
+#' @keywords correction_exception
 #' 
 #' @return A tibble row with exception data or all exceptions
 #' @export

diff --git a/R/load_files.R b/R/load_files.R
@@ -7,6 +7,7 @@
 #' or character with file path of templates file(s)
 #' @param results_file  data.table, with datapaths and names of results file(s)
 #' or character with file path of results file(s)
+#' @param instrument character
 #' @keywords load_files
 #'
 #' @examples
@@ -1134,7 +1135,7 @@ read_in_results_Tecan <- function(results_file, results_sheets, headers) {
 #' @param col_df a character with colnames of df
 #' @param df_name a name of data.table ("" by default)
 #' @param df_type a type of a data.table (NULL by default)
-#' @keywords load_files
+#' @keywords correction_exception
 #'
 #' @examples
 #'  td <- get_test_data()
@@ -1168,7 +1169,7 @@ check_metadata_names <-
 #' @param col_df a charvec with corrected colnames of df
 #' @param df_name a name of data.table ("" by default)
 #' @param df_type a type of a data.table (NULL by default)
-#' @keywords load_files
+#' @keywords correction_exception
 #'
 #'
 #' @return \code{NULL} invisibly.
@@ -1225,7 +1226,7 @@ check_metadata_req_col_names <- function(col_df, df_name, df_type) {
 #
 #' @param corrected_names a charvec with corrected colnames of df
 #' @param df_name a name of data.table ("" by default)
-#' @keywords load_files
+#' @keywords correction_exception
 #'
 #' @return a charvec with corrected colnames of df
 #'
@@ -1249,7 +1250,7 @@ check_metadata_field_names <- function(corrected_names, df_name) {
 #
 #' @param corrected_names a charvec with corrected colnames of df
 #' @param df_name a name of data.table ("" by default)
-#' @keywords load_files
+#' @keywords correction_exception
 #'
 #' @return a charvec with corrected colnames of df
 #'
@@ -1278,7 +1279,7 @@ check_metadata_against_spaces <- function(corrected_names, df_name) {
 #
 #' @param corrected_names a charvec with corrected colnames of df
 #' @param df_name a name of data.table ("" by default)
-#' @keywords load_files
+#' @keywords correction_exception
 #'
 #' @return a charvec with corrected colnames of df
 #'

diff --git a/R/pset_to_gdrDF.R b/R/pset_to_gdrDF.R
@@ -3,7 +3,7 @@
 #' @param pharmacoset PharmacoSet object
 #' @param run_parallel logical, TRUE (default) if to run functions in Parallel, FALSE to run in serial
 #' @param workers integer, number of workers defaults to 2L if run_parallel is TRUE
-#' @keywords pset_to_gdr
+#' @keywords pset
 #' @return data.table of PharmacoSet's dose response data with column names aligned with gDR standard
 #' 
 #' @examples
@@ -47,7 +47,7 @@ convert_pset_to_df <- function(pharmacoset,
 #' setEnvForPSet()
 #' gDRutils::reset_env_identifiers()
 #' 
-#' @keywords pset_to_gdr
+#' @keywords pset
 #' @return \code{NULL}
 #' @export
 setEnvForPSet <- function() {
@@ -76,7 +76,7 @@ setEnvForPSet <- function() {
 #' @param timeout maximum number of seconds allowed for PSet download
 #' @param use_local_PSets_list logical flag if PSets list should be used from 
 #' local. If FALSE PSets list will be taken from web.
-#' @keywords pset_to_gdr
+#' @keywords pset
 #' 
 #' @examples  
 #' suppressMessages(getPSet(

diff --git a/R/testdata.R b/R/testdata.R
@@ -3,7 +3,7 @@
 #' @examples 
 #' get_test_data()
 #' 
-#' @keywords test_data
+#' @keywords test_data_class
 #' @export
 #'
 #' @return object class "gdr_test_data" with with input data (manifest/template/result paths)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -3,33 +3,24 @@ template:
   bootstrap: 5
 
 reference:
+- title: Load files
+- contents:
+  - has_keyword("load_files")
+- title: Pset conversion
+- contents:
+  - has_keyword("pset")
 - title: Import D300
 - contents:
   - has_keyword("D300")
-- title: Convert MAE to PSet object
+- title: Input data validation/correction
 - contents:
-  - has_keyword("mae_to_pset")
-- title: Correction helpers
-- contents:
-  - has_keyword("correction")
-- title: Exception helpers
+  - has_keyword("correction_exception")
+- title: Utils
 - contents:
-  - has_keyword("exceptions")
+  - has_keyword("utils")
 - title: Test data class
 - contents:
   - has_keyword("test_data_class")
-- title: Load files
-- contents:
-  - has_keyword("load_files")
-- title: Convert Pset object to gDR object
-- contents:
-  - has_keyword("pset_to_gdr")
 - title: Test data
 - contents:
   - has_keyword("test_data")
-- title: Assert utils
-- contents:
-  - has_keyword("assert_utils")
-- title: Utils
-- contents:
-  - has_keyword("utils")
diff --git a/man/are_template_sheets_valid.Rd b/man/are_template_sheets_valid.Rd
diff --git a/man/check_metadata_against_spaces.Rd b/man/check_metadata_against_spaces.Rd
diff --git a/man/check_metadata_field_names.Rd b/man/check_metadata_field_names.Rd
diff --git a/man/check_metadata_headers.Rd b/man/check_metadata_headers.Rd
diff --git a/man/check_metadata_names.Rd b/man/check_metadata_names.Rd
diff --git a/man/check_metadata_req_col_names.Rd b/man/check_metadata_req_col_names.Rd
diff --git a/man/convert_MAE_to_PSet.Rd b/man/convert_MAE_to_PSet.Rd
diff --git a/man/convert_pset_to_df.Rd b/man/convert_pset_to_df.Rd
diff --git a/man/correct_template_sheets.Rd b/man/correct_template_sheets.Rd
diff --git a/man/dot-check_against_single_template_sheet.Rd b/man/dot-check_against_single_template_sheet.Rd
diff --git a/man/dot-extract_or_create_assay.Rd b/man/dot-extract_or_create_assay.Rd
diff --git a/man/fix_typos_with_reference.Rd b/man/fix_typos_with_reference.Rd
diff --git a/man/gDRimport-package.Rd b/man/gDRimport-package.Rd
diff --git a/man/getPSet.Rd b/man/getPSet.Rd
diff --git a/man/get_exception_data.Rd b/man/get_exception_data.Rd
diff --git a/man/get_expected_template_sheets.Rd b/man/get_expected_template_sheets.Rd
diff --git a/man/get_test_data.Rd b/man/get_test_data.Rd
diff --git a/man/get_xl_sheets.Rd b/man/get_xl_sheets.Rd
diff --git a/man/is_readable_v.Rd b/man/is_readable_v.Rd
diff --git a/man/load_data.Rd b/man/load_data.Rd