Merge pull request #68 from tamnva/joss_manuscript

add vignettes run with user defined objective function
tamnva · Feb 10, 2024 · 1ac8270 · 1ac8270
2 parents a673063 + 76a1f84
commit 1ac8270
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Showing 30 changed files with 845 additions and 751 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -33,8 +33,6 @@ export(updateCalibrationFile)
 export(updateMultiFile)
 export(updateSingleFile)
 export(updatedFileContent)
-export(userObjFunction)
-export(userReadSwatOutput)
 export(yearlyOutputLoc)
 importFrom(doParallel,registerDoParallel)
 importFrom(foreach,"%dopar%")
@@ -43,7 +41,6 @@ importFrom(lhs,randomLHS)
 importFrom(magrittr,"%>%")
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
-importFrom(stats,aggregate)
 importFrom(stats,cor)
 importFrom(stats,quantile)
 importFrom(stats,rnorm)

diff --git a/R/behaSimulation.R b/R/behaSimulation.R
@@ -32,13 +32,13 @@
 #'  RMSE: "Minimize"
 #'
 #' @param samplingApproach the parameter sampling approach, possible values are:
-#' 'Sensi_Cali_(uniform_Latin_Hypercube_Sampling)',
-#' 'Cali_(from_optimization_package)',
-#' 'Cali_(from_nloptr_package)'),
-#' 'Cali_(Dynamically_Dimensioned_Search)',
-#' 'Cali_(Generalized_Likelihood_Uncertainty_Estimation)',
-#' 'Read_User_Parameter_File',
-#' 'Sensi_(from_userDefined_package)',
+#' 'Sensi_Cali_(uniform_Latin_Hypercube_Sampling)' \cr
+#' 'Cali_(from_optimization_package)'\cr
+#' 'Cali_(from_nloptr_package)')\cr
+#' 'Cali_(Dynamically_Dimensioned_Search)'\cr
+#' 'Cali_(Generalized_Likelihood_Uncertainty_Estimation)'\cr
+#' 'Read_User_Parameter_File'\cr
+#' 'Sensi_(from_userDefined_package)'\cr
 #' 'Cali_(from_userDefined_package)'
 #'
 #' @return a list of dataframes showing the 95PPU, median,
@@ -50,7 +50,6 @@
 #'
 #' \donttest{
 #' # Please see RSWAT Vignettes
-#' vignette("SUFI2_without_GUI",package="RSWAT")
 #' }
 #'
 #'
@@ -64,9 +63,9 @@ behaSimulation <- function(objValue, simData, parameterValue, behThreshold,
                            samplingApproach){
 
   # find index of simulations which are behavioral simulations
-  if ((statIndex == "NSE") | (statIndex == "KGE") | (statIndex == "R2")){
+  if (statIndex %in% c("NSE", "KGE", "R2")){
     behaIndex <- which(objValue >= behThreshold)
-  } else if(statIndex == "aBIAS" | statIndex == "RMSE") {
+  } else if(statIndex %in% c("aBIAS", "RMSE")) {
     behaIndex <- which(objValue <= abs(behThreshold))
   } else {
     if (minOrmax == "Maximize"){
@@ -114,10 +113,10 @@ behaSimulation <- function(objValue, simData, parameterValue, behThreshold,
   }
 
   # find the best simulation
-  if ((statIndex == "NSE") | (statIndex == "KGE") | (statIndex == "R2")){
+  if (statIndex %in% c("NSE", "KGE", "R2")){
     ppuSimData[,4] <- simData[[varNumber]][[which(objValue == max(objValue))[1]]]
 
-  } else if(statIndex == "aBIAS" | statIndex == "RMSE") {
+  } else if(statIndex %in% c("aBIAS","RMSE")) {
     ppuSimData[,4] <- simData[[varNumber]][[which (objValue == min(objValue))[1]]]
 
   } else {

diff --git a/R/calObjFunction.R b/R/calObjFunction.R
@@ -3,7 +3,7 @@
 #' calibration and validation period and for each variable
 #'
 #' @inheritParams runSWATpar
-#' @param nOutputVar number of output variables
+#' @param nOutputVar integer - number of output variables
 #' @param userReadSwatOutput TODO
 #' @param observedData list of observed data, each observed data is a data frame
 #' @param index performance criteria (NSE, KGE, RMSE, R2, or aBIAS)
@@ -14,7 +14,6 @@
 #'
 #' \donttest{
 #' # Please see RSWAT Vignettes
-#' vignette("SUFI2_without_GUI",package="RSWAT")
 #' }
 #'
 #' @export
@@ -35,7 +34,7 @@ calObjFunction <- function(parameterValue, ncores,
   simData <- list()
 
   counter <- rep(0, nOutputVar)
-  output$objValueCali <-  rep(0, nrow(parameterValue))
+  output$objValueCali <- rep(0, nrow(parameterValue))
   output$objValueValid <-  rep(0, nrow(parameterValue))
   output$error <- FALSE
 
@@ -55,8 +54,8 @@ calObjFunction <- function(parameterValue, ncores,
       }
 
       #Loop over number of simulation
-      fileNameSimData <- paste(workingDirectory, "/Output/Core_",
-                               i, "/out_var_", j, ".txt", sep = "")
+      fileNameSimData <- file.path(workingDirectory, "Output", paste0("Core_", i),
+                                   paste0("out_var_", j, ".txt"))
       tempSimData <- read.table(fileNameSimData, header = FALSE, sep = "")
 
       #Check if length of observed and simulated data are the same or not

diff --git a/R/extractExampleData.R b/R/extractExampleData.R
@@ -29,7 +29,7 @@
 
 extracExampleData <- function(exampleData, dataName, toDir){
 
-  if(dataName =="swatTxtInOut" | dataName =="all"){
+  if(dataName %in% c("swatTxtInOut", "all")){
     dir.create(file.path(toDir, "swatTxtInOut"))
     for (i in 1:length(exampleData$swatTxtInOut)){
       writeLines(exampleData$swatTxtInOut[[i]],
@@ -45,7 +45,7 @@ extracExampleData <- function(exampleData, dataName, toDir){
   }
 
 
-  if(dataName =="swatPlusTxtInOut" | dataName =="all"){
+  if(dataName %in% c("swatPlusTxtInOut", "all")){
     dir.create(file.path(toDir, "swatPlusTxtInOut"))
     for (i in 1:length(exampleData$swatPlusTxtInOut)){
       writeLines(exampleData$swatPlusTxtInOut[[i]],
@@ -60,13 +60,13 @@ extracExampleData <- function(exampleData, dataName, toDir){
 
   }
 
-  if(dataName =="swatParam" | dataName =="all"){
+  if(dataName %in% c("swatParam", "all")){
     writeLines(exampleData$swatParam, file.path(toDir, "swatParam.txt"))
     message("Created swatParam.txt file in  ", file.path(toDir, "swatParam.txt"))
 
   }
 
-  if(dataName =="swatObservedData" | dataName =="all"){
+  if(dataName %in% c("swatObservedData", "all")){
     dir.create(file.path(toDir, "observedSWAT"))
     writeLines(exampleData$swatObservedData, file.path(toDir,
                                                        "observedSWAT",
@@ -77,7 +77,7 @@ extracExampleData <- function(exampleData, dataName, toDir){
 
   }
 
-  if(dataName =="swatPlusObservedData" | dataName =="all"){
+  if(dataName %in% c("swatPlusObservedData", "all")){
     dir.create(file.path(toDir, "observedSWATPlus"))
     writeLines(exampleData$swatPlusObservedData, file.path(toDir,
                                                            "observedSWATPlus",
@@ -88,7 +88,7 @@ extracExampleData <- function(exampleData, dataName, toDir){
 
   }
 
-  if(dataName =="swatPlusParam" | dataName =="all"){
+  if(dataName %in% c("swatPlusParam", "all")){
     writeLines(exampleData$swatPlusParam, file.path(toDir, "cal_parms.cal"))
     message("Created cal_parms.cal file in ", file.path(toDir, "cal_parms.cal"))
   }

diff --git a/R/getNumberOutputVar.R b/R/getNumberOutputVar.R
@@ -19,8 +19,18 @@
 #' @export
 #'
 getNumberOutputVar <- function(outputExtraction){
+
   nOutputVar <- 0
   userReadSwatOutput <- c()
+
+  # output.rch file tpye
+  outputRchType <- c("output.rch", "channel_sd_day.txt", 'channel_sd_mon.txt', 
+                     'channel_sd_yr.txt', 'channel_sdmorph_day.txt',
+                     'channel_sdmorph_mon.txt','channel_sdmorph_yr.txt',
+                     'lsunit_wb_day.txt','lsunit_wb_mon.txt','lsunit_wb_yr.txt', 
+                     'basin_wb_day.txt','basin_wb_mon.txt','basin_wb_yr.txt',
+                     "output.hru","output.sub","output.rsv")
+
   for (i in 1:nrow(outputExtraction)) {
     if (outputExtraction[i,1] == "watout.dat"){
       temp <- length(strsplit(as.character(outputExtraction[i,3]), ",")[[1]])
@@ -34,22 +44,7 @@ getNumberOutputVar <- function(outputExtraction){
         }
       }
 
-    } else if(outputExtraction[i,1] == "output.rch" |
-              outputExtraction[i,1] == "channel_sd_day.txt" |
-              outputExtraction[i,1] == 'channel_sd_mon.txt' |
-              outputExtraction[i,1] == 'channel_sd_yr.txt'  |
-              outputExtraction[i,1] == 'channel_sdmorph_day.txt' |
-              outputExtraction[i,1] == 'channel_sdmorph_mon.txt' |
-              outputExtraction[i,1] == 'channel_sdmorph_yr.txt'  |
-              outputExtraction[i,1] == 'lsunit_wb_day.txt' |
-              outputExtraction[i,1] == 'lsunit_wb_mon.txt' |
-              outputExtraction[i,1] == 'lsunit_wb_yr.txt'  |
-              outputExtraction[i,1] == 'basin_wb_day.txt' |
-              outputExtraction[i,1] == 'basin_wb_mon.txt' |
-              outputExtraction[i,1] == 'basin_wb_yr.txt'  |
-              outputExtraction[i,1] == "output.hru" |
-              outputExtraction[i,1] == "output.sub" |
-              outputExtraction[i,1] == "output.rsv"){
+    } else if(outputExtraction[i,1] %in% outputRchType){
       if ((nchar(outputExtraction[i,3]) > 0) & (nchar(outputExtraction[i,4]) > 0)){
         temp <- sum(lengths(getRchNumber(outputExtraction[i,4])))
         nOutputVar <- nOutputVar + temp

diff --git a/R/getSimTime.R b/R/getSimTime.R
@@ -29,7 +29,7 @@ getSimTime <- function(TxtInOut){
   if(substr(TxtInOut,(nchar(TxtInOut)-3), nchar(TxtInOut)) == ".cio"){
     fileCio <- readLines(TxtInOut, 60)
   } else {
-    fileCio <- readLines(paste(TxtInOut, "/file.cio", sep = ""), 60)
+    fileCio <- readLines(file.path(TxtInOut, "file.cio"), 60)
   }
 
   # Check whether this is TxtInOut of SWAT or SWAT+
@@ -73,7 +73,7 @@ getSimTime <- function(TxtInOut){
   } else {
 
     # Read simulation time information from the time.sim file
-    simTime <- read.table(paste(TxtInOut, "/", "time.sim", sep = ""), skip = 2, sep = "")
+    simTime <- read.table(file.path(TxtInOut, "time.sim"), skip = 2, sep = "")
 
     # Find the starting date of simulation
     startSim <- as.Date(paste(toString(as.numeric(simTime[2])),"0101",
@@ -93,7 +93,7 @@ getSimTime <- function(TxtInOut){
     timeStepCode <- as.numeric(simTime[5])
 
     # Find start of eval or printing
-    printTime <- readLines(paste(TxtInOut, "/print.prt", sep = ""), 3)
+    printTime <- readLines(file.path(TxtInOut, "print.prt"), 3)
     printTime <- as.numeric(strsplit(trimws(printTime[3]), " +")[[1]])
 
     startPrint <- max(printTime[1] + as.numeric(simTime[2]) , printTime[3])

diff --git a/R/readChannelFile.R b/R/readChannelFile.R
@@ -38,8 +38,7 @@ readChannelFile <- function(workingDirectory,
                 "lsunit_wb_mon.txt",
                 "lsunit_wb_yr.txt")
 
-  filePath <- paste(workingDirectory, "/TxtInOut_", coreNumber, "/",
-                    fileName, sep = "")
+  filePath <- file.path(workingDirectory, paste0("TxtInOut_", coreNumber), fileName)
 
   # Get file content/data
   channelData <- read.table(filePath, header = FALSE, sep = "", skip = 3)

diff --git a/R/readFileContent.R b/R/readFileContent.R
@@ -16,7 +16,7 @@
 
 readFileContent <- function(fileDirectory, files){
 
-  files <- paste(fileDirectory, "/", files, sep = "")
+  files <- file.path(fileDirectory, files)
   fileContent <- list()
 
   for (i in 1:length(files)){

diff --git a/R/readSaveOutput.R b/R/readSaveOutput.R
@@ -23,8 +23,7 @@ readOutputRchFile <- function(workingDirectory,
                            output){
 
 
-  fileName <- paste(workingDirectory, "/TxtInOut_", coreNumber, "/",
-                    fileName, sep = "")
+  fileName <- file.path(workingDirectory, paste0("TxtInOut_", coreNumber), fileName)
 
   getOutputRsvData <- read.table(fileName, header = FALSE, sep = "", skip = 9)
 
@@ -111,4 +110,4 @@ readOutputRchFile <- function(workingDirectory,
   }
 
   return(output)
-}
+}
diff --git a/R/readWatoutFile.R b/R/readWatoutFile.R
@@ -18,8 +18,7 @@ readWatoutFile <- function(workingDirectory,
                            fileCioInfo,
                            output){
 
-  fileName <- paste(workingDirectory, "/TxtInOut_",
-                    coreNumber, "/", fileName, sep = "")
+  fileName <- file.path(workingDirectory, paste0("TxtInOut_", coreNumber), fileName)
 
   getWatoutData <- read.table(fileName, header = FALSE, sep = "", skip = 6)
 

diff --git a/R/runSWATpar.R b/R/runSWATpar.R
@@ -156,13 +156,7 @@ runSWATSequential <- function(coreNumber,
                               firstRun){
 
   # Set working directory
-  setwd(paste(workingDirectory,
-              '/',
-              'TxtInOut',
-              '_',
-              coreNumber,
-              sep = ""))
-
+  setwd(file.path(workingDirectory, paste0('TxtInOut_', coreNumber)))
   # Get directory where new TxtInOut files are saved
   toDir <- getwd()
 
@@ -222,10 +216,7 @@ runSWATSequential <- function(coreNumber,
                 Sys.time(),
                 sep =''
     ),
-    file= paste(workingDirectory,
-                '/Output/CurrentSimulationReport.log',
-                sep =''
-    ),
+    file= file.path(workingDirectory, 'Output', 'CurrentSimulationReport.log'),
     append=TRUE
     )
   }

diff --git a/R/saveOutput.R b/R/saveOutput.R
@@ -43,6 +43,14 @@ saveOutput <- function(workingDirectory,
   # Set output as list object
   output <- list()
 
+  # SWAT+ output files
+  swatPlusFiles <- c("channel_sd_day.txt", "channel_sd_mon.txt",
+                     "channel_sd_yr.txt", "channel_sdmorph_day.txt",
+                     "channel_sdmorph_mon.txt", "channel_sdmorph_yr.txt",
+                     "lsunit_wb_day.txt", "lsunit_wb_mon.txt",
+                     "lsunit_wb_yr.txt","basin_wb_day.txt",
+                     "basin_wb_mon.txt", "basin_wb_yr.txt")
+
   for (i in 1:length(fileType)){
 
     if (fileType[i] == "watout.dat"){
@@ -56,9 +64,7 @@ saveOutput <- function(workingDirectory,
                                fileCioInfo,
                                output)
 
-    } else if (fileType[i] == "output.rch" |
-               fileType[i] == "output.sub" |
-               fileType[i] == "output.hru" ){
+    } else if (fileType[i] %in% c("output.rch", "output.sub", "output.hru")){
       output <- readOutputRchFile(workingDirectory,
                                   coreNumber,
                                   fileName[i],
@@ -68,18 +74,8 @@ saveOutput <- function(workingDirectory,
                                   getRchNumber(rchNumber[i]),
                                   output)
 
-    } else if (fileType[i] == "channel_sd_day.txt"      |
-               fileType[i] == "channel_sd_mon.txt"      |
-               fileType[i] == "channel_sd_yr.txt"       |
-               fileType[i] == "channel_sdmorph_day.txt" |
-               fileType[i] == "channel_sdmorph_mon.txt" |
-               fileType[i] == "channel_sdmorph_yr.txt"  |
-               fileType[i] == "lsunit_wb_day.txt"       |
-               fileType[i] == "lsunit_wb_mon.txt"       |
-               fileType[i] == "lsunit_wb_yr.txt"        |
-               fileType[i] == "basin_wb_day.txt"       |
-               fileType[i] == "basin_wb_mon.txt"       |
-               fileType[i] == "basin_wb_yr.txt"){
+    } else if (fileType[i] %in% swatPlusFiles){
+
       output <- readChannelFile(workingDirectory,
                                 coreNumber,
                                 fileName[i],
@@ -90,7 +86,7 @@ saveOutput <- function(workingDirectory,
                                 output)
 
     } else if (fileType[i] == "userReadSwatOutput"){
-      workingDir <- paste(workingDirectory, "/TxtInOut_", coreNumber, sep = "")
+      workingDir <- file.path(workingDirectory, paste0("TxtInOut_", coreNumber))
       setwd(workingDir)
       userExtractData <- userReadSwatOutput()
       output <- c(output, userExtractData)
@@ -101,14 +97,13 @@ saveOutput <- function(workingDirectory,
   }
 
   # Save output
-  outputDirectory <- paste(workingDirectory, "/Output/Core_", coreNumber, sep = "")
+  outputDirectory <- file.path(workingDirectory, "Output", paste0("Core_", coreNumber))
 
   # Create directory if it does not exist
   if(!dir.exists(outputDirectory)) dir.create(outputDirectory)
 
   for (i in 1:length(output)){
-    OutputFileName <- paste(outputDirectory, '/out_var_', i,
-                            '.txt', sep ='')
+    OutputFileName <- file.path(outputDirectory, paste0('out_var_', i, '.txt'))
 
     if (firstRun){file.create(OutputFileName)}
 

diff --git a/R/updateTxtInOut.R b/R/updateTxtInOut.R
@@ -175,5 +175,5 @@ updateCalibrationFile <- function(paraSelection, parameterValue, currentDirector
 
   }
 
-  writeLines(fileContent, paste(currentDirectory, "/", "calibration.cal", sep = ""))
+  writeLines(fileContent, file.path(currentDirectory, "calibration.cal"))
 }
-Original file line number
+Diff line change
@@ Expand Up @@
       }
-      writeLines(fileContent, paste(currentDirectory, "/", "calibration.cal", sep = ""))
+      writeLines(fileContent, file.path(currentDirectory, "calibration.cal"))
     }