skipSpinup full solution, GLUE start.

RBBGCMuso/R/calibMuso.R

@@ -49,7 +49,7 @@ calibMuso <- function(settings=NULL,parameters=NULL, timee="d", debugging=FALSE,
     setwd(inputLoc)
 
       
-    if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
+    if(debugging){#If debugging option turned on
         #If log or ERROR directory does not exists create it!
         dirName<-file.path(inputLoc,"LOG")
         dirERROR<-file.path(inputLoc,"ERROR")
@@ -194,15 +194,15 @@ calibMuso <- function(settings=NULL,parameters=NULL, timee="d", debugging=FALSE,
         ##read the output
          
         switch(timee,
-               "d"=(Reva <- tryCatch(getdailyout(settings),
+               "d"=(Reva <- tryCatch(getdailyout(settings), #(:INSIDE: getOutput.R )
                                     error = function (e){
                                         setwd((whereAmI))
                                         stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
-               "m"=(Reva <- tryCatch(getmonthlyout(settings),
+               "m"=(Reva <- tryCatch(getmonthlyout(settings), #(:INSIDE: getOutput.R )
                                     error = function (e){
                                         setwd((whereAmI))
                                         stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
-               "y"=(Reva <- tryCatch(getyearlyout(settings),
+               "y"=(Reva <- tryCatch(getyearlyout(settings), #(:INSIDE: getOutput.R )
                                     error = function (e){
                                         setwd((whereAmI))
                                         stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")}))
@@ -221,7 +221,7 @@ calibMuso <- function(settings=NULL,parameters=NULL, timee="d", debugging=FALSE,
     logfiles <- tryCatch(getLogs(outputLoc,outputNames,type="both"),
                         error = function (e){
                             setwd(whereAmI)
-                            "Cannot find log files, something went wrong"})
+                            stop("Cannot find log files, something went wrong")})
     ## list.files(outputLoc)[grep("log$",list.files(outputLoc))]#creating a vector for logfilenames
 
 ###############################################    
@@ -262,7 +262,7 @@ calibMuso <- function(settings=NULL,parameters=NULL, timee="d", debugging=FALSE,
     
 
 
-    if(debugging==TRUE){
+    if(debugging){ #debugging is boolean
                        logfiles <- file.path(outputLoc,logfiles)
                        stampAndDir(stampDir=dirName, wrongDir=dirERROR, names=logfiles, type="general",errorsign=errorsign,logfiles=logfiles)}
   

RBBGCMuso/R/musoGLUE.R

@@ -0,0 +1,57 @@
+#' musoGlue
+#'
+#' This ...
+#' #' @author Roland Hollos
+#' @param monteCarloFile If you run musoMonte function previously, you did not have to rerun the monteCarlo, just provide the preservedEpc.csv file with its path. If you do not set this parameter, musoSensi will fun the musoMonte function to get all of the information.
+#' @param outputFile The filename in which the output of musoSensi function will be saved. It's default value is: "sensitivity.csv"
+#' @param plotName The name of the output barplot. It's default value is: "sensitivity.jpg"
+#' @param settings A list of montecarlos environmental variables. It is generated by the setupMuso() function. In default the settings parameter is generated automatically. 
+#' @param parameters This is a dataframe (heterogen data-matrix), which first column is the name of the parameters, the second is a numeric vector of the rownumbers of the given variable in the epc-fie, the last two column consist the endpont of the parameter-ranges, where the parameters will be randomized.
+#' @param calibrationPar You may want to change some parameters in your epc file, before you run the modell. You have to select the appropirate modell parameters. You can refence to these with the number of the line in the epc file where the variables are. It indexes from one. You should use a vector for this, like: c(1,5,8)
+#' @param inputDir The location of the input directory, this directory must content a viable pack of all inputfiles and the executable file. 
+#' @param iterations number of the monteCarlo run.
+#' @param preTag It will be the name of the output files. For example preTag-1.csv, pretag-2csv...
+#' @param outputType This parameter can be "oneCsv", "moreCsv", and "netCDF". If "oneCsv" is choosen the function create 1 big csv file for all of the runs, if "moreCsv" is choosen, every modell output goes to separate files, if netCDF is selected the outputs will be put in a netCDF file. The default value of the outputTypes is "moreCsv". netCDF is not implemented yet. 
+#' @param fun If you select a variable from the possible outputs (with specify the varIndex parameter), you have to provide a function which maps to a subset of real numbers. The most frequent possibilities are: mean, min, max, var, but you can define any function for your need.
+#' @param varIndex This parameter specify which parameter of the output will be used. You can extract this information from the ini-files. At the output parameter specifications, the parameters order will determine this number. For example, if you have set these output parameters: 412, 874, 926, 888, and you want to use 926, you should address varIndex with 3.
+#' @param skipSpinup With this parameter, you can turn of the spinup phase after the first spinup. I will decrease the time significantly.
+#' @import dplyr
+#' @import graphics
+#' @import grDevices
+#' @import ggplot2
+#' @export
+
+musoGLUE <- function(monteCarloFile = NULL,
+                     parameters = NULL,
+                     settings = NULL,
+                     inputDir = "./",
+                     outLoc = "./calib",
+                     iterations = 30,
+                     preTag = "mont-",
+                     outputType = "moreCsv",
+                     fun = mean,
+                     varIndex = 1,
+                     outputFile = "sensitivity.csv",
+                     plotName = "sensitivity.png",
+                     plotTitle = "Sensitivity",
+                     skipSpinup = FALSE,
+                     dpi=300){
+
+
+    rmse <- function(modelled, measured){
+        (modelled-measured) %>%
+            (function(x) {x*x}) %>% # It is more clear than `^`(.,2) form, even it is longer
+            sum %>%
+            sqrt
+    }
+
+    
+
+                     
+
+
+
+
+
+
+}

RBBGCMuso/R/musoMonte.R

@@ -11,10 +11,12 @@
 #' @param outputType  This parameter can be "oneCsv", "moreCsv", and "netCDF". If "oneCsv" is choosen the function create 1 big csv file for all of the runs, if "moreCsv" is choosen, every modell output goes to separate files, if netCDF is selected the outputs will be put in a netCDF file. The default value of the outputTypes is "moreCsv". netCDF is not implemented yet. 
 #' @param fun If you select a variable from the possible outputs (with specify the varIndex parameter), you have to provide a function which maps to a subset of real numbers. The most frequent possibilities are: mean, min, max, var, but you can define any function for your need.
 #' @param varIndex This parameter specify which parameter of the output will be used. You can extract this information from the ini-files. At the output parameter specifications, the parameters order will determine this number. For example, if you have set these output parameters: 412, 874, 926, 888, and you want to use 926, you should address varIndex with 3.
+#' @param debugging If you set this parameter, you can save every logfile, and RBBGCMuso will select those which contains errors.
+#' @param keepEpc if you set keepEpc also true, it will save every selected epc file, and put the wrong ones in the WRONGEPC directory.
 #' @export
 
 musoMonte <- function(settings=NULL,
-                     parameters,
+                     parameters=NULL,
                      inputDir = "./",
                      outLoc = "./calib",
                      iterations = 10,
@@ -23,8 +25,22 @@ musoMonte <- function(settings=NULL,
                      fun=mean,
                      varIndex = 1,
                      silent = TRUE,
+                     skipSpinup = FALSE,
+                     debugging = FALSE,
+                     keepEpc = FALSE,
                      ...){
 
+    if(is.null(parameters)){
+        parameters <- tryCatch(read.csv("parameters.csv"), error = function (e) {
+            stop("You need to specify a path for the parameters.csv, or a matrix.")
+        })
+    } else {
+        if((!is.list(parameters)) & (!is.matrix(parameters))){
+             parameters <- tryCatch(read.csv(parameters), error = function (e){
+                                         stop("Cannot find neither parameters file neither the parameters matrix")
+                                     })
+        }}
+    
     outLocPlain <- basename(outLoc)
     currDir <- getwd()
     inputDir <- normalizePath(inputDir)
@@ -91,10 +107,31 @@ musoMonte <- function(settings=NULL,
     
     ## Creating function for generating separate
     ## csv files for each run
+
     progBar <- txtProgressBar(1,iterations,style=3)
+
+    modelRun <- function(settings, debugging, parameters, keepEpc, silent, skipSpinup){
+        if(!skipSpinup){
+            calibMuso(settings, debugging = debugging, parameters = parameters, keepEpc = keepEpc, silent = silent)        
+        } else {
+            normalMuso(settings, debugging = debugging, parameters = parameters, keepEpc = keepEpc, silent = silent)
+        } 
+        
+    }
+    
     moreCsv <- function(){
+
+        if(skipSpinup){#skipSpinup is boolean
+            spinupMuso(settings = settings , silent = silent)
+        }
         a <- numeric(iterations+1)
-        tempData <- calibMuso(settings, debugging = "stamplog", parameters = origEpc,keepEpc = TRUE,silent = silent)
+        tempData <- modelRun(settings=settings,
+                             debugging = debugging,
+                             parameters = origEpc,
+                             keepEpc = keepEpc,
+                             silent = silent,
+                             skipSpinup = skipSpinup)
+        ## tempData <- calibMuso(settings, debugging = "stamplog", parameters = origEpc,keepEpc = TRUE,silent = silent)
         a[1] <- tryCatch(fun(tempData[,varIndex]),error=function(e){return(NA)})
         preservedEpc[1,(npar+1)] <- a[1]
         write.table(t(preservedEpc[1,]),row.names = FALSE,"preservedEpc.csv",sep=",")
@@ -103,10 +140,12 @@ musoMonte <- function(settings=NULL,
             parVar <- musoRandomizer(A,B)[,2]
             preservedEpc[(i+1),] <- c(parVar,NA)
             exportName <- paste0(preTag,(i+1),".csv")
-            tempData <- calibMuso(settings,debugging = "stamplog",
+            tempData <- modelRun(settings = settings,
+                                 debugging = debugging,
                                  parameters = parVar,
-                                 keepEpc = TRUE,
-                                 silent=silent)
+                                 keepEpc = keepEpc,
+                                 silent=silent,
+                                 skipSpinup =skipSpinup)
             write.csv(x=tempData,file=exportName)
             
             preservedEpc[(i+1),(npar+1)] <- a[i+1]<- tryCatch(fun(tempData[,varIndex]),error=function(e){return(NA)})

RBBGCMuso/R/musoSensi.R

@@ -14,6 +14,7 @@
 #' @param outputType This parameter can be "oneCsv", "moreCsv", and "netCDF". If "oneCsv" is choosen the function create 1 big csv file for all of the runs, if "moreCsv" is choosen, every modell output goes to separate files, if netCDF is selected the outputs will be put in a netCDF file. The default value of the outputTypes is "moreCsv". netCDF is not implemented yet. 
 #' @param fun If you select a variable from the possible outputs (with specify the varIndex parameter), you have to provide a function which maps to a subset of real numbers. The most frequent possibilities are: mean, min, max, var, but you can define any function for your need.
 #' @param varIndex This parameter specify which parameter of the output will be used. You can extract this information from the ini-files. At the output parameter specifications, the parameters order will determine this number. For example, if you have set these output parameters: 412, 874, 926, 888, and you want to use 926, you should address varIndex with 3.
+#' @param skipSpinup With this parameter, you can turn of the spinup phase after the first spinup. I will decrease the time significantly.
 #' @import dplyr
 #' @import graphics
 #' @import grDevices
@@ -21,9 +22,8 @@
 #' @export
 
 musoSensi <- function(monteCarloFile = NULL,
-                     parameters=NULL,
+                     parameters = NULL,
                      settings = NULL,
-                     parametersFromFile=FALSE,
                      inputDir = "./",
                      outLoc = "./calib",
                      iterations = 30,
@@ -34,17 +34,19 @@ musoSensi <- function(monteCarloFile = NULL,
                      outputFile = "sensitivity.csv",
                      plotName = "sensitivity.png",
                      plotTitle = "Sensitivity",
+                     skipSpinup = FALSE,
                      dpi=300){
 
     if(is.null(parameters)){
-        parameters <- read.csv("parameters.csv")
+        parameters <- tryCatch(read.csv("parameters.csv"), error = function (e) {
+            stop("You need to specify a path for the parameters.csv, or a matrix.")
+        })
     } else {
-        if(parametersFromFile){
-            parameters <- read.csv(parameters,stringsAsFactors=FALSE)
-        } else {
-            parameters <- parameters
-        }
-    }
+        if((!is.list(parameters)) & (!is.matrix(parameters))){
+             parameters <- tryCatch(read.csv(parameters), error = function (e){
+                                         stop("Cannot find neither parameters file neither the parameters matrix")
+                                     })
+        }}
 
     doSensi <- function(M){
         npar <- ncol(M)-1
@@ -90,7 +92,8 @@ musoSensi <- function(monteCarloFile = NULL,
                       preTag = preTag,
                       outputType = outputType,
                       fun = fun,
-                      varIndex = varIndex
+                      varIndex = varIndex,
+                      skipSpinup = skipSpinup
                       )
         return(doSensi(M))
         

RBBGCMuso/R/normalMuso.R

@@ -30,9 +30,9 @@ normalMuso<- function(settings=NULL,parameters=NULL,timee="d",debugging=FALSE,lo
 ########################################################################
 
     if(is.null(settings)){
-        settings <- setupMuso()
+        settings <- setupMuso() #( :INSIDE: setupMuso.R)
     }
-    
+        # The software works on Linux or Windows, Mac is not implemented yet, so with this simple dichotomy we can determine wich syste is running
     Linuxp <-(Sys.info()[1]=="Linux")
     ##Copy the variables from settings
     inputLoc <- settings$inputLoc
@@ -42,28 +42,65 @@ normalMuso<- function(settings=NULL,parameters=NULL,timee="d",debugging=FALSE,lo
     iniInput <- settings$iniInput
     epc <- settings$epcInput
     calibrationPar <- settings$calibrationPar
+    
+    ## We want to minimize the number of sideeffects so we store the state to restore in the end.
     whereAmI<-getwd()
 
+    
+    ## Optionally the user may want to store the original binary file. At default we set it to the output location. 
+    
     if(is.null(binaryPlace)){
         binaryPlace <- outputLoc
     }
 
+    ## Now we create a directories for the debugging files if these are not exists, and if debugging or keepEpc options are set to true. 
+
+        if(debugging){ #debugging is boolean, so we dont write debugging == TRUE for the sake of faster model run
+        #If log or ERROR directory does not exists create it!
+        dirName<-file.path(inputLoc,"LOG")
+        dirERROR<-file.path(inputLoc,"ERROR")
+        
+        if(!dir.exists(dirName)){
+            dir.create(dirName)
+        }
+
+        if(!dir.exists(dirERROR)){
+            dir.create(dirERROR)
+        }
+    }
+    
+    if(keepEpc) {#keepEpc is boolean
+        epcdir <- dirname(epc[1])
+        print(epcdir)
+        WRONGEPC<-file.path(inputLoc,"WRONGEPC")
+        EPCS<-file.path(inputLoc,"EPCS")
+        
+        if(!dir.exists(WRONGEPC)){
+            dir.create(WRONGEPC)
+        }
+        
+        if(!dir.exists(EPCS)){
+            dir.create(EPCS)
+        }
+    }
+    
 
 
     
     
     if(!is.null(parameters)){
-
         switch(fileToChange,
-               "epc"=(changemulline(filename=epc[2],calibrationPar,parameters)), #(:TODO: trycatch /p4/)
-               "ini"=(changemulline(filename=iniInput[2],calibrationPar,parameters)),
-               "both"=(stop("This option is not implemented yet, please choose epc or ini"))
+               "epc" = tryCatch(changemulline(filename = epc[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
+                                error = function (e) {stop("Cannot change the epc file")}),
+               "ini" = tryCatch(changemulline(filename = iniInput[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
+                                error = function (e) {stop("Cannot change the ini file")}),
+               "both" = (stop("This option is not implemented yet, please choose epc or ini"))
                )
     }
 
 
 
-    setwd(inputLoc)
+   
                                         #normal run
 
     ## if(silent){
@@ -106,63 +143,51 @@ normalMuso<- function(settings=NULL,parameters=NULL,timee="d",debugging=FALSE,lo
         ##read the output
 
             switch(timee,
-               "d"=(Reva <- tryCatch(getdailyout(settings),
-               error = function (e) {stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
-               "m"=(Reva <- tryCatch(getmonthlyout(settings),
-               error = function (e) {stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
-               "y"=(Reva <- tryCatch(getyearlyout(settings),
-               error = function (e) {stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")}))
+               "d"=(Reva <- tryCatch(getdailyout(settings), #(:INSIDE: getOutput.R ) 
+                                    error = function (e){
+                                        setwd((whereAmI))
+                                        stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
+               "m"=(Reva <- tryCatch(getmonthlyout(settings), #(:INSIDE: getOutput.R )
+                                    error = function (e){
+                                        setwd((whereAmI))
+                                        stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})),
+               "y"=(Reva <- tryCatch(getyearlyout(settings), #(:INSIDE: getOutput.R )
+                                    error = function (e){
+                                        setwd((whereAmI))
+                                        stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")}))
                )
 
+
+
         if(keepBinary){
-            possibleNames <- getOutFiles(outputLoc = outputLoc,outputNames = outputNames)
-            stampAndDir(outputLoc = outputLoc,names = possibleNames,stampDir=binaryPlace,type="output")
+            possibleNames <- getOutFiles(outputLoc = outputLoc,outputNames = outputNames) #(:INSIDE: assistantFunctions.R)
+            stampAndDir(outputLoc = outputLoc,names = possibleNames,stampDir=binaryPlace,type="output") #(:INSIDE: assistantFunctions.R)
         }
     
 
 
-    logfiles <- getLogs(outputLoc,outputNames,type = "normal")
+    logfiles <- getLogs(outputLoc,outputNames,type = "normal") #(:INSIDE: assistantFunctions.R)
+    
 
 #############LOG SECTION#######################
-    errorsign <- readErrors(outputLoc = outputLoc,logfiles = logfiles,type="normal")
-    dirName<-paste(inputloc,"/LOG",sep="")
-    dirERROR<-paste(inputloc,"/ERROR",sep="")
-    ERROR_EPC<-paste(inputloc,"/ERROR_EPC",sep="")
+    errorsign <- readErrors(outputLoc = outputLoc,logfiles = logfiles,type="normal") #(:INSIDE: assistantFunctions.R)
 
-    if(!dir.exists(dirName)){
-        dir.create(dirName)
-    }
-
-    if(!dir.exists(dirERROR)){
-        dir.create(dirERROR)
-    }
-
-
-
-
-    if(debugging=="stamplog"){
-        stampnum<-stamp(dirName)
-        lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
-        if(errorsign==1){
-            lapply( logfiles, function (x) file.copy(from=paste(dirName, "/",(stampnum+1),"-",x,sep=""), to=dirERROR  ))}
-
-    } else { if(debugging){
-                 if(is.null(logfilename)){
-                     lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
-                     if(errorsign==1){
-                         lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
-                     }
+    if(keepEpc){#if keepepc option turned on
 
+        if(length(unique(dirname(epc)))>1){
+            stop("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
         } else {
-                     lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))
-                     if(errorsign==1){
-                         lapply( logfiles, function (x) file.rename(from=paste(dirName, "/",logfilename,"-",x,sep=""), to=dirERROR))
+
+            stampAndDir(stampDir=EPCS, wrongDir=WRONGEPC, names=epc[2], type="general", errorsign=errorsign, logfiles=logfiles)
+
         }
     }
         
-             }}
 
     
+        if(debugging){ #debugging is boolean
+                       logfiles <- file.path(outputLoc,logfiles)
+                       stampAndDir(stampDir=dirName, wrongDir=dirERROR, names=logfiles, type="general",errorsign=errorsign,logfiles=logfiles)}
     cleanupMuso()
     if(errorsign==1){
         return("Modell Failure")

RBBGCMuso/R/setupMuso.R

@@ -122,7 +122,6 @@ setupMuso <- function(executable=NULL,
 
 
     
-    
     inputs <- lapply(1:nrow(grepHelper), function (x) {
 
         outMaker(grepHelper[x,1],grepHelper[x,2],grepHelper[x,3])
@@ -149,14 +148,17 @@ setupMuso <- function(executable=NULL,
     
     if(is.null(mapData)){
         
-        c<-grep("DAILY_OUTPUT",iniFiles[[2]])+1
-        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
-        dailyVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
+        outIndex<-grep("DAILY_OUTPUT",iniFiles[[2]])+1
+        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][outIndex],"[\ \t]"))[1])
+        dailyVarCodes<-tryCatch(iniFiles[[2]][(outIndex+1):(outIndex+numVar)],
+                                error = function(e){
+        stop("Cannot read indexes of output variables from the normal ini file, please make sure you have not skiped a line after the flag: \"DAILY_OUTPUT\"")    
+        })
         dailyVarnames<-lapply(dailyVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1]))
 
-        c<-grep("ANNUAL_OUTPUT",iniFiles[[2]])+1
-        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
-        annualVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
+        outIndex<-grep("ANNUAL_OUTPUT",iniFiles[[2]])+1
+        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][outIndex],"[\ \t]"))[1])
+        annualVarCodes<-iniFiles[[2]][(outIndex+1):(outIndex+numVar)]
         annualVarnames<-lapply(annualVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1]))
         outputVars<-list(dailyVarnames,annualVarnames)} else {
 

RBBGCMuso/R/spinupMuso.R

@@ -22,11 +22,12 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
 ########################################################################
 
     if(is.null(settings)){
-        settings <- setupMuso()
-    }
+        settings <- setupMuso() #(:INSIDE: setupMuso.R)
         
+    }
+    # The software works on Linux or Windows, Mac is not implemented yet, so with this simple dichotomy we can determine wich system is running
     Linuxp <-(Sys.info()[1]=="Linux")
-    ##Copy the variables from settings
+    ##Copy the variables from settings for the sake of easy
     inputLoc <- settings$inputLoc
     outputLoc <- settings$outputLoc
     outputNames <- settings$outputNames
@@ -34,6 +35,8 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
     iniInput <- settings$iniInput
     epc <- settings$epcInput
     calibrationPar <- settings$calibrationPar
+
+    ## We want to minimize the number of sideeffects so we store the state to restore in the end.
     whereAmI<-getwd()
 
 
@@ -41,26 +44,28 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
 ############################spinup run############################
 ########################################################## 
 
+    ## obsolete feature, but there can be cases in wich this option is helpfull
     if(aggressive==TRUE){
-        cleanupMuso(location=outputLoc,deep=TRUE)}
+        cleanupMuso(location=outputLoc,deep=TRUE)} #(:INSIDE: cleanup.R)
+
+    ## If parameters given, use changemulline, else leave this steps
     
      if(!is.null(parameters)){
         switch(fileToChange,
-               "epc"=tryCatch(changemulline(filename=epc[2],calibrationPar,parameters),
+               "epc" = tryCatch(changemulline(filename = epc[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
                               error = function (e) {stop("Cannot change the epc file")}),
-               "ini"=tryCatch(changemulline(filename=iniInput[2],calibrationPar,parameters),
+               "ini" = tryCatch(changemulline(filename = iniInput[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
                               error = function (e) {stop("Cannot change the ini file")}),
-               "both"=(stop("This option is not implemented yet, please choose epc or ini"))
+               "both" = (stop("This option is not implemented yet, please choose epc or ini"))
                )
     }
     
-    ##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
-    
     ## Set the working directory to the inputLoc temporary.
     setwd(inputLoc)
-    ##Run the spinup
 
     
+    ##Run the spinup modell
+    
     if(silent){#silenc mode
         if(Linuxp){
             #In this case, in linux machines
@@ -76,7 +81,8 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
 ###############################################
 #############LOG SECTION#######################
 ###############################################
-      logspinup <- getLogs(outputLoc,outputNames,type="spinup")
+    
+      logspinup <- getLogs(outputLoc,outputNames,type="spinup") #(:INSIDE: assistantFunctions.R)
  
   if(length(logspinup)==0){
         if(keepEpc){
@@ -101,7 +107,7 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
     }
 
     dirName<-normalizePath(paste(inputLoc,"/LOG",sep=""))
-    dirERROR<-paste(inputLoc,"/ERROR",sep="")
+    dirERROR<-paste0(inputLoc,"/ERROR")
     
     if(!dir.exists(dirName)){
         dir.create(dirName)}
@@ -117,7 +123,7 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
 
 
     if(debugging==TRUE){
-        stampAndDir(outputLoc=outputLoc,stampDir=dirName, names=logspinup, type="output")
+        stampAndDir(outputLoc=outputLoc,stampDir=dirName, names=logspinup, type="output") #(:INSIDE: assistantFunctions.R)
     }