Added dec_sep in collate_*

NEWS.md

@@ -1,3 +1,7 @@
+# vortexR 1.1.8
+collate_* functions gain dec_sep argument to control decimal separator charcter in order to solve reading numerical data on European machines
+Minor edits to help files
+
 # vortexR 1.1.7
 Ensured copatibility with R 4.*
 fit_regression gains a new argument: `links`, which allows for a better control

R/data_handling.R

@@ -11,6 +11,7 @@
 #' @param filename The fully qualified filename of a Vortex .dat or .stdat file
 #' @param runs The number of simulation runs
 #' @param verbose Progress messages, default: FALSE
+#' @param dec_sep Decimal separator (default ".")
 #' @return A data.frame with data from one .dat or .stdat file and
 #'  population/scenario names as factors
 #' @import vortexRdata
@@ -21,7 +22,7 @@
 #' pac.dir <- system.file('extdata', 'pacioni', package='vortexRdata')
 #' f <- file.path(pac.dir, 'Pacioni_et_al_ST_Classic(Base).stdat')
 #' one.st.classic <- collate_one_dat(f, 3)
-collate_one_dat <- function(filename, runs, verbose = FALSE) {
+collate_one_dat <- function(filename, runs, dec_sep=".", verbose = FALSE) {
 
     if (verbose) message(cat("INFO vortexR::collate_one_dat parsing", filename))
     lines <- readLines(filename)
@@ -59,6 +60,7 @@ collate_one_dat <- function(filename, runs, verbose = FALSE) {
                           sep = ";",
                           nrows = readFor,
                           skip = readAfter,
+                          dec = dec_sep,
                           colClasses = "numeric",
                           comment.char = "")
         colnames(tmp) <- h
@@ -114,12 +116,12 @@ collate_one_dat <- function(filename, runs, verbose = FALSE) {
 #'
 #' @param project The Vortex project name to be imported
 #' @param scenario The scenario name if ST, default: NULL
-#' @param runs The number of Vortex simulation runs
 #' @param dir_in The local folder containing Vortex files, default: NULL. If
 #'   not specified, will fall back to use current working directory.
 #' @param save2disk Whether to save the data as rda and csv, default: TRUE
 #' @param dir_out The local path to store the output. Default: ProcessedData
 #' @param verbose Progress messages, default: TRUE
+#' @inheritParams collate_one_dat
 #' @return a data.frame with data from all matching Vortex files or NULL
 #' @import vortexRdata
 #' @export
@@ -152,6 +154,7 @@ collate_dat <- function(project,
                         runs,
                         scenario = NULL,
                         dir_in = NULL,
+                        dec_sep = ".",
                         save2disk = TRUE,
                         dir_out = "ProcessedData",
                         verbose = TRUE) {
@@ -176,7 +179,7 @@ collate_dat <- function(project,
     if (verbose) message("vortexR::collate_dat is parsing:")
     for (filename in files) {
         if (verbose) message(filename, "\r")
-        d <- rbind(d, collate_one_dat(filename, runs))
+        d <- rbind(d, collate_one_dat(filename, runs, dec_sep = dec_sep))
     }
     if (save2disk) df2disk(d, dir_out, fname, "_data")
     return(d)
@@ -219,6 +222,7 @@ collate_dat <- function(project,
 collate_run <- function(project,
                         scenario,
                         npops = 1,
+                        dec_sep = ".",
                         dir_in = NULL,
                         save2disk = TRUE,
                         dir_out = "ProcessedData",
@@ -250,7 +254,8 @@ collate_run <- function(project,
                            sep = ";",
                            skip = 3,
                            colClasses = "numeric",
-                           comment.char = "")
+                           comment.char = "",
+                           dec=dec_sep)
         colnames(trun) <- h
 
         Scenario <- read.table(filename,
@@ -343,6 +348,7 @@ collate_run <- function(project,
 collate_yr <- function(project,
                        scenario,
                        npops_noMeta = 1,
+                       dec_sep = ".",
                        dir_in = NULL,
                        save2disk = TRUE,
                        dir_out = "ProcessedData",
@@ -391,7 +397,8 @@ collate_yr <- function(project,
                          n_rows,
                          iter_ln,
                          lines,
-                         header)
+                         header,
+                         dec_sep = dec_sep)
 
         censusData[[i]] <- rbindlist(one_yr)
     }

R/helper_fun.R

@@ -111,10 +111,13 @@ PrefixAndRepeat <- function(chars, times = 1, prefix = "") {
 #' @param iter_ln The number of rows to skip from the file
 #' @param lines An object returned from readLines()
 #' @param header A character vector of column names
+#' @param dec_sep Decimal separator (default ".")
 #' @return A data.frame
-CompileIter <- function(iter, filename, n_rows, iter_ln, lines, header) {
+CompileIter <- function(iter, filename, n_rows, iter_ln, lines, header,
+                        dec_sep = ".") {
     temp.df <- read.table(filename, header = FALSE, sep = ";", nrows = n_rows,
-                          skip = iter_ln[iter], colClasses = "numeric",
+                          skip = iter_ln[iter],
+                          dec = dec_sep, colClasses = "numeric",
                           comment.char = "")
     colnames(temp.df) <- header
     Iteration <- rep(iter, length = length(temp.df$Year))

vignettes/vortexRguide.Rmd

@@ -360,7 +360,7 @@ You can access the help file for all functions typing ```?function_name```, wher
 
 ## Data handling
 
-As for the vortexR output files, the input files in all ```collate``` functions are searched in the working directory unless an alternative path is provided with ```dir_in```. In all ```collate```, the argument ```verbose=TRUE``` will result in R printing on the screen the number and progress of files found/read.
+As for the vortexR output files, the input files in all ```collate``` functions are searched in the working directory unless an alternative path is provided with ```dir_in```. In all ```collate```, the argument ```verbose=TRUE``` will result in R printing on the screen the number and progress of files found/read. By default, the decimal separator character is ".". In cases where the operating system uses a different separator (e.g. most of European countries use ","), this can be changed with the argument ```dec_sep``` (e.g. ```dec_sep=","```). This is omitted in all examples below for brevity, but is present in all ```collate``` functions.
 
 ### *collate_one_dat & collate_dat*
 These functions collate one or all the .dat or .stdat files within a folder. ```collate_one_dat```  takes only two arguments: the name of the file (```filename```) and the number of runs or iterations (```runs```) that were conducted, while ```collate_dat``` has three arguments (in addition to the standard ```dir_in```, ```dir_out```, ```verbose```, and ```save2disk```): the name of the project (```project```), the name of the scenario (```scenario```) and the number of runs or iterations (```runs```) that were conducted. There is no need to pass the number of populations or their names as vortexR will automatically detect these information from the files.