fix: bugs in readAllOutVar function

DESCRIPTION

@@ -19,7 +19,7 @@ Imports:
     stats (>= 4.1.2),
     utils (>= 4.1.2),
     foreach (>= 1.2.0),
-	  htmltools (>= 0.5.7),
+    htmltools (>= 0.5.7),
     parallel (>= 4.1.2),
     lhs (>= 1.1.4),
     plotly (>= 4.10.0),

R/readAllOutVar.R

@@ -17,7 +17,8 @@
 #'
 #' @return a list of data frame for each output variable. Each data frame has n
 #' rows (number of rows are number of time steps) and m columns (m is the number
-#' of iterations)
+#' of iterations: column 1 = result from iteration 1 and column i = result from
+#' iteration i)
 #'
 #' @examples
 #'
@@ -29,39 +30,59 @@
 #' #  if you have two output variables with different number of time steps
 #' #  numTimesteps <- c(3000, 4000)
 #'
-#' readAllOutVar("C:/data/workingFolder")
+#' output <- readAllOutVar("C:/data/workingFolder", numTimesteps)
 #'}
 #'
 #' @export
 #'
 #'
+
 readAllOutVar <- function(workingFolder, numTimesteps){
 
-  # List of folders with Core_ where output_var_xx.txt files are stored
-  coreFolders <- dir(file.path(workingFolder, "Output"), pattern = "Core_",
-                    full.names = TRUE)
+  # Find number of cores
+  numberOfCores <- length(dir(file.path(workingFolder, "Output"),
+                              pattern = "Core_"))
+
+  # List of folder names starts with "Core_1" in the Workingfolder/Output
+  coreFolders <- paste0("Core_", c(1:numberOfCores))
 
-  # List of files in each coreFolders (all coreFolders have the same file list)
-  outVarFiles <- list.files(coreFolders[1], full.names = TRUE)
+  # Number of output variables = number of files in  Workingfolder/Output/Core_1
+  numOuputVariables <- length(list.files(file.path(workingFolder,
+                                                   "Output",
+                                                   coreFolders[1])
+                                         )
+                              )
+  # List of output files starts in  Workingfolder/Output/Core_1
+  outVarFiles <- paste0("out_var_",
+                        c(1:numOuputVariables),
+                        ".txt")
 
+  # Now read all output files (out_var_xx.txt) in all Core_xx folders
   output <- list()
   for (ifolder in 1:length(coreFolders)){
+
     # Loop over each outVarfiles
     for (var in 1:length(outVarFiles)){
+
       # Read content of each file and store
-      data <- read.table(outVarFiles[var], header = FALSE, sep="")
+      outFile <- file.path(workingFolder,
+                           "Output",
+                           coreFolders[ifolder],
+                           outVarFiles[var])
+
+      data <- read.table(outFile, header = FALSE, sep="")
 
       # convert to matrix
       data <- matrix(data[,1], nrow = numTimesteps[var] + 1)
 
       # Remove the first rows
       data <- data[-c(1),]
 
-      if ((var == 1) & (ifolder == 1)){
+      if (ifolder == 1){
         output[[var]] <- list()
         output[[var]] <- data
       } else {
-        output[[var]] <- cbind(output[[var]],data)
+        output[[var]] <- cbind(output[[var]], data)
       }
     }
   }

vignettes/SUFI2_without_GUI.R

@@ -1,4 +1,4 @@
-## ----include = FALSE----------------------------------------------------------
+## ---- include = FALSE---------------------------------------------------------
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
@@ -8,15 +8,15 @@ knitr::opts_chunk$set(
 # Load require packages
 library(RSWAT)
 
-## ----message=FALSE, eval = FALSE----------------------------------------------
+## ---- message=FALSE, eval = FALSE---------------------------------------------
 #  # Extract all of examples data to the temporal working directory
 #  extracExampleData(exampleData, "all", tempdir())
 #  
 #  # This is the path the temporal folder
 #  tempdir()
 #  
 
-## ----message=FALSE, eval = FALSE----------------------------------------------
+## ---- message=FALSE, eval = FALSE---------------------------------------------
 #  #
 #  # 1. Set SWATproject is TRUE if you run SWAT, set to FALSE if you run SWAT+
 #  SWATproject <- TRUE
@@ -117,7 +117,7 @@ library(RSWAT)
 #  # observedDataFile <- c("D:/example/obs_var_1.txt", "D:/example/obs_var_2.txt")
 #  
 
-## ----message=FALSE, eval = FALSE----------------------------------------------
+## ---- message=FALSE, eval = FALSE---------------------------------------------
 #  
 #  # Generate parameter samples using Latin Hypercube Sampling
 #  parameterValue <- lhsRange(sensCaliCommand, getParamRange(paraSelection))
@@ -150,7 +150,7 @@ library(RSWAT)
 #             dateRangeCali,firstRun)
 #  
 
-## ----message=FALSE, eval = FALSE----------------------------------------------
+## ---- message=FALSE, eval = FALSE---------------------------------------------
 #  # Number of output variables (from the output extraction data frame)
 #  OutputVar <- getNumberOutputVar(outputExtraction)
 #  nOutputVar <- OutputVar$nOutputVar