Update documentation of physiologies function.

R/physiologies.R

@@ -1,8 +1,12 @@
 
-#' Physiologies
+#' Import phsiologies
 #'
 #' \code{physiologies} imports data from the
-#' Google spreadsheets (https://drive.google.com/drive/folders/1i2UAolVWAYa7UnETNnCs0BDWjKPp3ev5).
+#' Google spreadsheets at https://drive.google.com/drive/folders/1i2UAolVWAYa7UnETNnCs0BDWjKPp3ev5.
+#' This function (and its internal functions) do minimal changes to the
+#' imported data. These changes are only meant to match data coming from
+#' different sources, and attaching information needed for further processing,
+#' such as source and attribute type.
 #'
 #' @param keyword Character vector with one or more valid keywords.
 #' Valid keyboards can be checked with \code{showPhys}. If 'all', all
@@ -27,7 +31,7 @@ physiologies <- function(keyword = 'all', full_source = FALSE) {
   if (cond1 && cond2) {
     spreadsheets <- .importSpreadsheets(keyword = keyword)
     spreadsheets <- spreadsheets[names(spreadsheets) %in% keyword]
-    bacdive <- .reshapeBacDive(.getBacDive(verbose = FALSE)) ## This functions are in a different file
+    bacdive <- .reshapeBacDive(.getBacDive(verbose = FALSE))
     bacdive <- bacdive[names(bacdive) %in% keyword]
     physiologies <- vector('list', length(keyword))
     for (i in seq_along(keyword)) {
@@ -62,7 +66,7 @@ physiologies <- function(keyword = 'all', full_source = FALSE) {
       dplyr::distinct()
 
     if (full_source) {
-      df$Attribute_source <- df$full_source ## added with .addSourceInfo
+      df$Attribute_source <- df$full_source
     }
     df$full_source <- NULL
 
@@ -74,7 +78,7 @@ physiologies <- function(keyword = 'all', full_source = FALSE) {
 
     df <- as.data.frame(df[, vapply(df, \(y) !all(is.na(y)), logical(1))])
 
-    ## TODO this code should be somewhere else
+    ## TODO this code could be somewhere else
     if (unique(df$Attribute_group) == 'aerophilicity') {
       df <- .homogenizeAerophilicityAttributeNames(df)
     }