diff --git a/RBBGCMuso/DESCRIPTION b/RBBGCMuso/DESCRIPTION
index af838a1..88e6627 100644
--- a/RBBGCMuso/DESCRIPTION
+++ b/RBBGCMuso/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RBBGCMuso
 Title: An R package for BiomeBGC-MuSo ecosystem modelling
-Version: 0.3.3.0-0
+Version: 0.4.0.0-0
 Authors@R: person("Roland", "Hollo's", , "hollorol@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 Depends: R (>= 2.10)
diff --git a/RBBGCMuso/R/calibMuso.R b/RBBGCMuso/R/calibMuso.R
index 9757361..076b1ce 100644
--- a/RBBGCMuso/R/calibMuso.R
+++ b/RBBGCMuso/R/calibMuso.R
@@ -20,7 +20,7 @@
 #' @export
 
 
-calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE){
+calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE,keepBinary=FALSE, binayPlace="./"){
 
 
 ##########################################################################
@@ -29,12 +29,12 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     
     Linuxp <-(Sys.info()[1]=="Linux")
     ##Copy the variables from settings
-    inputloc <- settings$inputloc
-    outputloc <- settings$outputloc
+    inputLoc <- settings$inputLoc
+    outputLoc <- settings$outputLoc
     executable <- settings$executable
-    ininput <- settings$ininput
-    epc <- settings$epcinput
-    calibrationpar <- settings$calibrationpar
+    iniInput <- settings$iniInput
+    epc <- settings$epcInput
+    calibrationPar <- settings$calibrationPar
     whereAmI<-getwd()
 
 
@@ -57,7 +57,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 ##alma    
 
     if(silent!=TRUE){
-        if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){    
+        if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){    
             cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
 
         }
@@ -65,19 +65,19 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
     
     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc,deep = TRUE)
+        cleanupMuso(location=outputLoc,deep = TRUE)
     }
     
     ##change the epc file if and only if there are given parameters
     if(!is.null(parameters)){
-        changemulline(filename=epc[2],calibrationpar,parameters)
+        changemulline(filename=epc[2],calibrationPar,parameters)
     }
 
     ##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)
+    ## Set the working directory to the inputLoc temporary.
+    setwd(inputLoc)
 
 
     ##Run the model for the spinup run.
@@ -85,19 +85,19 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     if(silent){#silenc mode
         if(Linuxp){
             #In this case, in linux machines
-            system(paste(executable,ininput[1],"> /dev/null",sep=" "))
+            system(paste(executable,iniInput[1],"> /dev/null",sep=" "))
         } else {
             #In windows machines there is a show.output.on.console option
-            system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
+            system(paste(executable,iniInput[1],sep=" "),show.output.on.console = FALSE)
         }
         
     } else {
-        system(paste(executable,ininput[1],sep=" "))
+        system(paste(executable,iniInput[1],sep=" "))
     }
 
     
     
-    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
+    logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
     if(length(logspinup)==0){
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
@@ -105,10 +105,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     if(length(logspinup)>1){
         spincrash<-TRUE
     } else {
-        if(identical(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1),character(0))){
+        if(identical(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1),character(0))){
             spincrash<-TRUE
         } else {
-            spincrash<-(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)!=1)
+            spincrash<-(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1)!=1)
         }
     }
     
@@ -121,17 +121,17 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
       #################################################################
 
         ##for the sake of safe we set the location again
-        setwd(inputloc)
+        setwd(inputLoc)
 
         if(silent){
             if(Linuxp){
-                system(paste(executable,ininput[2],"> /dev/null",sep=" "))
+                system(paste(executable,iniInput[2],"> /dev/null",sep=" "))
             } else {
-                system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
+                system(paste(executable,iniInput[2],sep=" "),show.output.on.console = FALSE)
             }
             
         } else {
-            system(paste(executable,ininput[2],sep=" "))
+            system(paste(executable,iniInput[2],sep=" "))
         }
 
 
@@ -142,10 +142,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
                "m"=(Reva<-getmonthlyout(settings)),
                "y"=(Reva<-getyearlyout(settings))
                )
+        if(keepBinary){
+            file.copy(grep("out$",list.files(outputLoc),value=TRUE)
+                    ,file.path(binaryPlace,paste0(stamp(binaryPlace),"-",grep("out$",list.files(outputLoc),value=TRUE))))
+        }
     }
-
     
-    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
+    logfiles <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]#creating a vector for logfilenames
 
 ###############################################    
 #############LOG SECTION#######################
@@ -153,13 +156,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
 
     
-    perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1))))                                      #vector of spinup and normalrun error
+    perror<-as.numeric(as.vector(lapply(paste(outputLoc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1))))                                      #vector of spinup and normalrun error
     
     
     if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
         #If log or ERROR directory does not exists create it!
-        dirName<-paste(inputloc,"LOG",sep="") 
-        dirERROR<-paste(inputloc,"ERROR",sep="")
+        dirName<-paste(inputLoc,"LOG",sep="") 
+        dirERROR<-paste(inputLoc,"ERROR",sep="")
         
         if(!dir.exists(dirName)){
             dir.create(dirName)
@@ -190,8 +193,8 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
         } else {
             epcdir <- dirname(epc[1])
             
-            WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
-            EPCS<-paste(inputloc,"EPCS",sep="")
+            WRONGEPC<-paste(inputLoc,"WRONGEPC",sep="")
+            EPCS<-paste(inputLoc,"EPCS",sep="")
             
             if(!dir.exists(WRONGEPC)){
                 dir.create(WRONGEPC)
@@ -216,11 +219,11 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
     if(debugging=="stamplog"){
         stampnum<-stamp(dirName)
-        if(inputloc==outputloc){
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+        if(inputLoc==outputLoc){
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
             
         } else {
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
         }
         
         if(errorsign==1){
@@ -229,10 +232,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     } else { if(debugging){
                  if(is.null(logfilename)){
 
-                     if(inputloc==outputloc){
-                          lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
+                     if(inputLoc==outputLoc){
+                          lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName,"/", x, sep="")))
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
                      }
 
                      if(errorsign==1){
@@ -241,10 +244,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
                  } else {
 
-                     if(inputloc==outputloc){#These are very ugly solutions for a string problem: inputloc: "./", if outputloc equalent of inputloc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
+                     if(inputLoc==outputLoc){#These are very ugly solutions for a string problem: inputLoc: "./", if outputLoc equalent of inputLoc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
                      }
                      
                      if(errorsign==1){
@@ -254,16 +257,16 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
                  
              }}
     
-    cleanupMuso(location=outputloc,deep = TRUE)
+    cleanupMuso(location=outputLoc,deep = TRUE)
     if(errorsign==1){
         return("Modell Failure")
     }
 
     if(timee=="d"){
-        colnames(Reva) <- unlist(settings$outputvars[[1]])
+        colnames(Reva) <- unlist(settings$outputVars[[1]])
     } else {
         if(timee=="y")
-            colnames(Reva) <- unlist(settings$outputvars[[2]])
+            colnames(Reva) <- unlist(settings$outputVars[[2]])
     }
 
 
diff --git a/RBBGCMuso/R/changeMuso.R b/RBBGCMuso/R/changeMuso.R
index 11f7f61..c9c1edc 100644
--- a/RBBGCMuso/R/changeMuso.R
+++ b/RBBGCMuso/R/changeMuso.R
@@ -6,11 +6,11 @@
 #' @author Roland Hollos
 #' @keywords internal
 
-changemulline <- function(filename,calibrationpar,contents){
+changemulline <- function(filename,calibrationPar,contents){
     ##This is the function which is capable change multiple specific lines to other using their row numbers.
     ##The function uses the previous changspecline function to operate.
     ##From now changespecline is in the forarcheologist file, because its no longer needed
-    varnum <- length(calibrationpar)
+    varnum <- length(calibrationPar)
     contents <- as.list(contents)
     if(length(contents)!=varnum)
     {
@@ -20,7 +20,7 @@ changemulline <- function(filename,calibrationpar,contents){
     readedFile = readLines(filename,-1)
 
     for(i in 1:varnum){
-        readedFile[calibrationpar[i]] <- paste(contents[[i]],collapse = " ")
+        readedFile[calibrationPar[i]] <- paste(contents[[i]],collapse = " ")
     }
     
     writeLines(unlist(readedFile),filename)
diff --git a/RBBGCMuso/R/getOutput.R b/RBBGCMuso/R/getOutput.R
index 9436a82..24d6486 100644
--- a/RBBGCMuso/R/getOutput.R
+++ b/RBBGCMuso/R/getOutput.R
@@ -12,9 +12,9 @@ getthespecdata<-function(settings,colnumbers){
 }
 
 getdailyout<-function(settings){
-  binaryname<-paste(settings$inputloc,settings$outputnames,".dayout",sep="")
+  binaryname<-paste(settings$inputLoc,settings$outputNames,".dayout",sep="")
   d<-file(binaryname,"rb")
-  dayoutput<-matrix(readBin(d,"double",size=8,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE)
+  dayoutput<-matrix(readBin(d,"double",size=8,n=(settings$numData[1])),(settings$numYears*365),byrow=TRUE)
   close(d) 
   return(dayoutput)
 }
diff --git a/RBBGCMuso/R/musoTime.R b/RBBGCMuso/R/musoTime.R
index 5318a0b..65f3d83 100644
--- a/RBBGCMuso/R/musoTime.R
+++ b/RBBGCMuso/R/musoTime.R
@@ -86,6 +86,7 @@ sumDaysOfPeriod <- function(year, periodlen, corrigated=TRUE){
         return(days)
     } else {
         days <- periodlen*365
+        return(days)
     }
 }
 
@@ -121,7 +122,7 @@ musoDate <- function(settings,timestep="d",combined=TRUE, corrigated=TRUE, forma
     
 
     
-    days <- sumDaysOfPeriod(settings$startyear,settings$numyears, corrigated=corrigated)
+    days <- sumDaysOfPeriod(settings$startyear,settings$numYears, corrigated=corrigated)
     dates <- matrix(rep(NA,days*3),ncol=3)
 
         dates[1,] <- c(1,1,settings$startyear)    
diff --git a/RBBGCMuso/R/outputMapping.R b/RBBGCMuso/R/outputMapping.R
index 6abb859..7e26a19 100644
--- a/RBBGCMuso/R/outputMapping.R
+++ b/RBBGCMuso/R/outputMapping.R
@@ -9,7 +9,7 @@
 
 updateMusoMapping<-function(output_map_init="output_map_init.c"){
     
-    outputRaw<-grep("\\[",readLines("output_map_init",-1),value=TRUE)
+    outputRaw<-grep("\\[",readLines(output_map_init,-1),value=TRUE)
 
     codes <- as.vector(lapply(outputRaw, function (x)  as.numeric(unlist(strsplit(unlist(strsplit(x,"\\["))[2],"\\]"))[1])))
     names <- unlist(lapply(outputRaw, function (x) unlist(strsplit(unlist(strsplit(x,">"))[2],";"))[1]))
@@ -31,9 +31,9 @@ updateMusoMapping<-function(output_map_init="output_map_init.c"){
 
 musoMapping <- function(code, mapData=NULL){
     if(is.null(mapData)){
-        return(unlist(mMapping[which(mMapping[,1]==code),2])) #mMapping is package-scoped system variable generated by uudateMusoMapping
+        return(unlist(mMapping[which(mMapping[,1]==code),2])) #mMapping is package-scoped system variable generated by udateMusoMapping
     } else {
-        return(unlist(mapData[which(mapData[,1]==650),2]))
+        return(unlist(mapData[which(mapData[,1]==code),2]))
     }
 }
 
diff --git a/RBBGCMuso/R/rungetMuso.R b/RBBGCMuso/R/rungetMuso.R
index 57e91d3..c6bad88 100644
--- a/RBBGCMuso/R/rungetMuso.R
+++ b/RBBGCMuso/R/rungetMuso.R
@@ -31,12 +31,12 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     
     Linuxp <-(Sys.info()[1]=="Linux")
     ##Copy the variables from settings
-    inputloc <- settings$inputloc
-    outputloc <- settings$outputloc
+    inputLoc <- settings$inputLoc
+    outputLoc <- settings$outputLoc
     executable <- settings$executable
-    ininput <- settings$ininput
-    epc <- settings$epcinput
-    calibrationpar <- settings$calibrationpar
+    iniInput <- settings$iniInput
+    epc <- settings$epcInput
+    calibrationPar <- settings$calibrationPar
     whereAmI<-getwd()
         
 #############################################################
@@ -48,7 +48,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     
 
     if(silent!=TRUE){
-        if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){    
+        if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){    
             cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
 
         }
@@ -56,13 +56,13 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     }
     
     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc, deep=TRUE)
+        cleanupMuso(location=outputLoc, deep=TRUE)
     }
 
     ##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)
+    ## Set the working directory to the inputLoc temporary.
+    setwd(inputLoc)
 
 
     ##Run the model for the spinup run.
@@ -70,19 +70,19 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     if(silent){#silenc mode
         if(Linuxp){
                                         #In this case, in linux machines
-            system(paste(executable,ininput[1],"> /dev/null",sep=" "))
+            system(paste(executable,iniInput[1],"> /dev/null",sep=" "))
         } else {
                                         #In windows machines there is a show.output.on.console option
-            system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
+            system(paste(executable,iniInput[1],sep=" "),show.output.on.console = FALSE)
         }
         
     } else {
-        system(paste(executable,ininput[1],sep=" "))
+        system(paste(executable,iniInput[1],sep=" "))
     }
 
     
     
-    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
+    logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
     if(length(logspinup)==0){
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
@@ -91,10 +91,10 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     if(length(logspinup)>1){
         spincrash<-TRUE
     } else {
-        if(identical(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1),character(0))){
+        if(identical(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1),character(0))){
             spincrash<-TRUE
         } else {
-            spincrash<-(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)!=1)
+            spincrash<-(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1)!=1)
         }
     }
     
@@ -107,17 +107,17 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
 #################################################################
 
         ##for the sake of safe we set the location again
-        setwd(inputloc)
+        setwd(inputLoc)
 
         if(silent){
             if(Linuxp){
-                system(paste(executable,ininput[2],"> /dev/null",sep=" "))
+                system(paste(executable,iniInput[2],"> /dev/null",sep=" "))
             } else {
-                system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
+                system(paste(executable,iniInput[2],sep=" "),show.output.on.console = FALSE)
             }
             
         } else {
-            system(paste(executable,ininput[2],sep=" "))
+            system(paste(executable,iniInput[2],sep=" "))
         }
 
 
@@ -131,18 +131,18 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     }
 
     
-    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
+    logfiles <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]#creating a vector for logfilenames
 
 ###############################################    
 #############LOG SECTION#######################
 ###############################################
     
-    perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
+    perror<-as.numeric(as.vector(lapply(paste(outputLoc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
     
     if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
                                         ##If log or ERROR directory does not exists create it!
-        dirName<-paste(inputloc,"LOG",sep="") 
-        dirERROR<-paste(inputloc,"ERROR",sep="")
+        dirName<-paste(inputLoc,"LOG",sep="") 
+        dirERROR<-paste(inputLoc,"ERROR",sep="")
         
         if(!dir.exists(dirName)){
             dir.create(dirName)
@@ -173,8 +173,8 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
         } else {
             epcdir <- dirname(epc[1])
             
-            WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
-            EPCS<-paste(inputloc,"EPCS",sep="")
+            WRONGEPC<-paste(inputLoc,"WRONGEPC",sep="")
+            EPCS<-paste(inputLoc,"EPCS",sep="")
             
             if(!dir.exists(WRONGEPC)){
                 dir.create(WRONGEPC)
@@ -200,11 +200,11 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
 
     if(debugging=="stamplog"){
         stampnum<-stamp(dirName)
-        if(inputloc==outputloc){
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+        if(inputLoc==outputLoc){
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
             
         } else {
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
         }
         
         if(errorsign==1){
@@ -213,10 +213,10 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     } else { if(debugging){
                  if(is.null(logfilename)){
 
-                     if(inputloc==outputloc){
-                          lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
+                     if(inputLoc==outputLoc){
+                          lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName,"/", x, sep="")))
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
                      }
 
                      if(errorsign==1){
@@ -225,10 +225,10 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
 
                  } else {
 
-                     if(inputloc==outputloc){#These are very ugly solutions for a string problem: inputloc: "./", if outputloc equalent of inputloc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
+                     if(inputLoc==outputLoc){#These are very ugly solutions for a string problem: inputLoc: "./", if outputLoc equalent of inputLoc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
                      }
                      
                      if(errorsign==1){
@@ -238,16 +238,16 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
                  
              }}
     
-    cleanupMuso(location=outputloc)
+    cleanupMuso(location=outputLoc)
     if(errorsign==1){
         return("Modell Failure")
     }
 
     if(timee=="d"){
-        colnames(Reva) <- unlist(settings$outputvars[[1]])
+        colnames(Reva) <- unlist(settings$outputVars[[1]])
     } else {
         if(timee=="y")
-            colnames(Reva) <- unlist(settings$outputvars[[2]])
+            colnames(Reva) <- unlist(settings$outputVars[[2]])
     }
 
     if(leapYear){
diff --git a/RBBGCMuso/R/rungettanul.R b/RBBGCMuso/R/rungettanul.R
index 480aaf1..ff38c2d 100644
--- a/RBBGCMuso/R/rungettanul.R
+++ b/RBBGCMuso/R/rungettanul.R
@@ -14,7 +14,7 @@
 ##     executable <- settings$executable
 ##     ininput <- settings$ininput
 ##     epc <- settings$epcinput
-##     calibrationpar <- settings$calibrationpar
+##     calibrationPar <- settings$calibrationPar
 ##     whereAmI<-getwd()
         
 ## #############################################################
diff --git a/RBBGCMuso/R/setupMuso.R b/RBBGCMuso/R/setupMuso.R
index de32f83..8204ca8 100644
--- a/RBBGCMuso/R/setupMuso.R
+++ b/RBBGCMuso/R/setupMuso.R
@@ -5,253 +5,168 @@
 #' @author Roland Hollos
 #' @param parallel Do you want to run multiple modell paralelly, if yes, set this variable to TRUE
 #' @param executable This parameter stores the place of the modell-executable file. In normal usage, you don't have to be set this, because a RBBgcmuso package contains allways the latest modell executable. In spite of this, if you would like to use this package for modell development or just want to use different models (for example for comparison), you will find it useful
-#' @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 outputloc Where should the modell puts its outputs. You should give a location for it via this variable, for example: outputloc="/place/of/the/outputs/"
-#' @param inputloc Usually it is the root directory, where you put the inifiles for the modell
-#' @param metinput Via metinput parameter, you can tell the modell where are the meteorological files. As default it reads this from the inifiles.
-#' @param CO2input Via CO2 parameter, you can tell the modell where are the CO2 data files. As default it reads this from the inifiles.
-#' @param plantinput Via planting parameter, you can tell the modell where are the data files, which contains the planting informations. As default it reads this from the inifiles.
-#' @param thininput Via thining parameter, you can tell the modell where are the data files, which contains the thining informations. As default it reads this from the inifiles.
-#' @param mowinput Via mowing parameter, you can tell the modell where are the data files, which contains the mowing informations. As default it reads this from the inifiles.
-#' @param grazinput Via grazing parameter, you can tell the modell where are the data files, which contains the grazing informations. As default it reads this from the inifiles.
-#' @param harvinput Via harvesting parameter, you can tell the modell where are the data files, which contains the harvesting informations. As default it reads this from the inifiles.
-#' @param plouginput Via ploughing parameter, you can tell the modell where are the data files, which contains the ploughing informations. As default it reads this from the inifiles.
-#' @param fertinput Via fertilizing parameter, you can tell the modell where are the fertilizing data files, which contains the fertilizing informations. As default it reads this from the inifiles.
-#' @param irrinput Via irrigation parameter, you can tell the modell where are the data files, which contains the irrigation informations. As default it reads this from the inifiles.
-#' @param nitinput Via this parameter, you can tell the modell where are the NO2 data files. As default it reads this from the inifiles.
-#' @param ininput Via this parameter, you can tell the modell where are the ini files. As default it reads this from the inifiles.
-#' @param epcinput Via this parameter, you can tell the modell where are the epc data files. As default it reads this from the inifiles.
-#' @usage setupMuso(executable=NULL, parallel = F, calibrationpar =c(1),
-#' outputloc=NULL, inputloc=NULL,
-#' metinput=NULL, CO2input=NULL,
-#' plantinput=NULL, thininput=NULL,
-#' mowinput=NULL, grazinput=NULL,
-#' harvinput=NULL, plouginput=NULL,
-#' fertinput=NULL, irrinput=NULL,
-#' nitinput=NULL, ininput=NULL, epcinput=NULL)
+#' @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 outputLoc Where should the modell puts its outputs. You should give a location for it via this variable, for example: outputLoc="/place/of/the/outputs/"
+#' @param inputLoc Usually it is the root directory, where you put the iniFiles for the modell
+#' @param metInput Via metInput parameter, you can tell the modell where are the meteorological files. As default it reads this from the iniFiles.
+#' @param CO2Input Via CO2 parameter, you can tell the modell where are the CO2 data files. As default it reads this from the iniFiles.
+#' @param plantInput Via planting parameter, you can tell the modell where are the data files, which contains the planting informations. As default it reads this from the iniFiles.
+#' @param thinInput Via thining parameter, you can tell the modell where are the data files, which contains the thining informations. As default it reads this from the iniFiles.
+#' @param mowInput Via mowing parameter, you can tell the modell where are the data files, which contains the mowing informations. As default it reads this from the iniFiles.
+#' @param grazInput Via grazing parameter, you can tell the modell where are the data files, which contains the grazing informations. As default it reads this from the iniFiles.
+#' @param harvInput Via harvesting parameter, you can tell the modell where are the data files, which contains the harvesting informations. As default it reads this from the iniFiles.
+#' @param plougInput Via ploughing parameter, you can tell the modell where are the data files, which contains the ploughing informations. As default it reads this from the iniFiles.
+#' @param fertInput Via fertilizing parameter, you can tell the modell where are the fertilizing data files, which contains the fertilizing informations. As default it reads this from the iniFiles.
+#' @param irrInput Via irrigation parameter, you can tell the modell where are the data files, which contains the irrigation informations. As default it reads this from the iniFiles.
+#' @param nitInput Via this parameter, you can tell the modell where are the NO2 data files. As default it reads this from the iniFiles.
+#' @param iniInput Via this parameter, you can tell the modell where are the ini files. As default it reads this from the iniFiles.
+#' @param epcInput Via this parameter, you can tell the modell where are the epc data files. As default it reads this from the iniFiles.
+#' @usage setupMuso(executable=NULL, parallel = F, calibrationPar =c(1),
+#' outputLoc=NULL, inputLoc=NULL,
+#' metInput=NULL, CO2Input=NULL,
+#' plantInput=NULL, thinInput=NULL,
+#' mowInput=NULL, grazInput=NULL,
+#' harvInput=NULL, plougInput=NULL,
+#' fertInput=NULL, irrInput=NULL,
+#' nitInput=NULL, iniInput=NULL, epcInput=NULL)
 #' @return The output is a the modell setting list wich contains the following elements:
-#' executable, calibrationpar, outputloc, outputname, inputloc, ininput, metinput, epcinput,thininput,CO2input, mowinput, grazinput, harvinput, plouginput, fertinput, irrinput, nitinput, inputfiles, numdata, startyear, numyears, outputvars
+#' executable, calibrationPar, outputLoc, outputName, inputLoc, iniInput, metInput, epcInput,thinInput,CO2Input, mowInput, grazInput, harvInput, plougInput, fertInput, irrInput, nitInput, inputFiles, numData, startyear, numYears, outputVars
 #' @export
 setupMuso <- function(executable=NULL,
                       parallel = F,
-                      calibrationpar =c(1),
-                      outputloc=NULL,
-                      inputloc=NULL,
-                      metinput=NULL,
-                      CO2input=NULL,
-                      plantinput=NULL,
-                      thininput=NULL,
-                      mowinput=NULL,
-                      grazinput=NULL,
-                      harvinput=NULL,
-                      plouginput=NULL,
-                      fertinput=NULL,
-                      irrinput=NULL,
-                      nitinput=NULL,
-                      ininput=NULL,
-                      epcinput=NULL,
-                      mapData=NULL
+                      calibrationPar =c(1),
+                      outputLoc=NULL,
+                      inputLoc=NULL,
+                      metInput=NULL,
+                      CO2Input=NULL,
+                      plantInput=NULL,
+                      thinInput=NULL,
+                      mowInput=NULL,
+                      grazInput=NULL,
+                      harvInput=NULL,
+                      plougInput=NULL,
+                      fertInput=NULL,
+                      irrInput=NULL,
+                      nitInput=NULL,
+                      iniInput=NULL,
+                      epcInput=NULL,
+                      mapData=NULL,
+                      leapYear=FALSE,
+                      version=5
                       ){
 
     Linuxp <-(Sys.info()[1]=="Linux")
+    writep <- 0
 
+    if(is.null(mapData)&version==4){
+        mData <- mMapping4
+    }
+    
     inputParser <- function(string,fileName,counter,value=TRUE){
         unlist(strsplit(grep(string,fileName,value=TRUE),"[\ \t]"))[counter]
     }
 
-    
-    if(is.null(inputloc)){
-        inputloc<- "./"
-    } else {
-        inp <- unlist(strsplit(inputloc,"")) #This is the charactervector of the given imput location
+    outMaker <- function(inputVar,grepString,filep){
+        tempVar <- eval(parse(text=inputVar))
+        if(is.null(tempVar)){
+            writep <<- writep+1
+            if(filep)
+            {
+                tempVar["spinup"] <- paste0(inputLoc,inputParser(string=grepString,fileName=iniFiles$spinup,counter=1,value=TRUE))
+                tempVar["normal"] <- paste0(inputLoc,inputParser(string=grepString,fileName=iniFiles$normal,counter=1,value=TRUE))
+            } else {
+                tempVar["spinup"] <- inputParser(string=grepString,fileName=iniFiles$spinup,counter=1,value=TRUE)
+                tempVar["normal"] <- inputParser(string=grepString,fileName=iniFiles$normal,counter=1,value=TRUE)
+                
+            }
 
-        if(inp[length(inp)]!="/"){
-            inp<-c(inp,"/")
-            inputloc <- paste(inp,collapse = "")
-            rm(inp)
-        }# If inp not ends in / paste one at the end, then make a string, that will be the new inputloc
-
-        ##Example: "a/b/c ==> a/b/c/"
+        } else {
+            iniFiles$spinup[grep(grepString,iniFiles$spinup)] <<- paste0(tempVar[1],"\t ",grepString)
+            
+            if(length(tempVar)==2){
+                iniFiles$normal[grep(" grepString",iniFiles$normal)] <<- paste0(tempVar[2],"\t ",grepString)
+            }
+        }
+        return(tempVar)
     }
-    inichangedp <- FALSE
 
-    if(is.null(ininput)){
-        spinups<-grep("s.ini$",list.files(inputloc),value=TRUE)
-        normals<-grep("n.ini$",list.files(inputloc),value=TRUE)
+    if(is.null(inputLoc)){
+           inputLoc<- "./"}
+    
+    #iniChangedp <- FALSE
+
+    if(is.null(iniInput)){
+        spinups<-grep("s.ini$",list.files(inputLoc),value=TRUE)
+        normals<-grep("n.ini$",list.files(inputLoc),value=TRUE)
 
         if(length(spinups)==1){
-            ininput[1]<-paste(inputloc,spinups,sep="")
-        } else {return(print("There are multiple or no spinup files, please choose"))}
+            iniInput[1]<-file.path(inputLoc,spinups)
+        } else {stop("There are multiple or no spinup ini files, please choose")}
         
 
         if(length(normals)==1){
-            ininput[2]<-paste(inputloc,normals,sep="")
-        } else {return(print("There are multiple or no normal files, please choose"))}
+            iniInput[2]<-file.path(inputLoc,normals)
+        } else {stop("There are multiple or no normal ini files, please choose")}
 
     }
 
     ##read the ini files for the further changes
 
-    inifiles<-lapply(ininput, function (x) readLines(x,-1))
-    inifiles[[1]] <- gsub("\\","/", inifiles[[1]],fixed=TRUE) #replacing \ to /
-    inifiles[[2]] <- gsub("\\","/", inifiles[[2]],fixed=TRUE) #replacing \ to /
+    iniFiles<-lapply(iniInput, function (x) readLines(x,-1))
+    iniFiles[[1]] <- gsub("\\","/", iniFiles[[1]],fixed=TRUE) #replacing \ to /
+    iniFiles[[2]] <- gsub("\\","/", iniFiles[[2]],fixed=TRUE) #replacing \ to /
+    names(iniFiles) <- c("spinup","normal")
+
+
+
     
-    if(is.null(epcinput)){
-        epcflag=TRUE
-        epcinput[1] <-  paste0(inputloc,inputParser(string=" EPC file name",fileName=inifiles[[1]],counter=1,value=TRUE))
-        epcinput[2] <-  paste0(inputloc,inputParser(string=" EPC file name",fileName=inifiles[[2]],counter=1,value=TRUE))
-    } else {
-        inifiles[[1]][grep(" EPC file name",inifiles[[1]])]<-paste(epcinput[1],"\t EPC file name",sep="")
+    inputs <- lapply(1:nrow(grepHelper), function (x) {
 
-        if(length(epcinput)==2){
-            inifiles[[2]][grep(" EPC file name",inifiles[[2]])]<-paste(epcinput[2],"\t EPC file name",sep="")
-        }
-    }
+        outMaker(grepHelper[x,1],grepHelper[x,2],grepHelper[x,3])
+        
+    })   
+    names(inputs) <- grepHelper$inputVar   
+    ## grepHelper is in sysdata.rda it is a table like this:
+    ##
+    ## inputVar         string      isFile  
+    ## 1    epcInput  EPC file name TRUE 
+    ## 2    metInput  met file name TRUE
+    ## 3    CO2Input       CO2 file TRUE
+    ## 4    nitInput     N-dep file TRUE
+    ## 5   thinInput    do THINNING FALSE
+    ## 6  plantInput    do PLANTING FALSE
+    ## 7    mowInput      do MOWING FALSE
+    ## 8   grazInput     do GRAZING FALSE
+    ## 9   harvInput  do HARVESTING FALSE
+    ## 10 plougInput   do PLOUGHING FALSE
+    ## 11  fertInput do FERTILIZING FALSE
+    ## 12   irrInput  do IRRIGATION FALSE
+   # return(inputs) debug element 
 
-    if(is.null(metinput)){
-        metflag=TRUE
-        metinput[1] <-  unlist(strsplit(grep(" met file name",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        metinput[2] <-  unlist(strsplit(grep(" met file name",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep(" met file name",inifiles[[1]])]<-paste(metinput[1],"\t met file name",sep="")
-
-        if(length(metinput)==2){
-            inifiles[[2]][grep(" met file name",inifiles[[2]])]<-paste(metinput[2],"\t EPC file name",sep="")
-        }}
     
-    if(is.null(CO2input)){
-        CO2flag=TRUE
-        CO2input[1] <-  unlist(strsplit(grep(" CO2 file",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        CO2input[2] <-  unlist(strsplit(grep(" CO2 file",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep(" CO2 file",inifiles[[1]])]<-paste(CO2input[1],"\t CO2 file",sep="")
-
-        if(length(CO2input)==2){
-            inifiles[[2]][grep(" CO2 file",inifiles[[2]])]<-paste(CO2input[2],"\t CO2 file",sep="")
-        }}
-    
-    if(is.null(nitinput)){
-        nitflag=TRUE
-        nitinput[1] <-  unlist(strsplit(grep("N-dep file",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        nitinput[2] <-  unlist(strsplit(grep("N-dep file",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("N-dep file",inifiles[[1]])]<-paste(nitinput[1],"N-dep file",sep="N-dep file")
-
-        if(length(epcinput)==2){
-            inifiles[[2]][grep("N-dep file",inifiles[[2]])]<-paste(nitinput[2],"N-dep file",sep="")
-        }}
-
-    if(is.null(thininput)){
-        thinflag=TRUE
-        thininput[1] <-  unlist(strsplit(grep("do THINNING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        thininput[2] <-  unlist(strsplit(grep("do THINNING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do THINNING",inifiles[[1]])]<-paste(thininput[1],"do THINNING",sep="")
-
-        if(length(thininput)==2){
-            inifiles[[2]][grep("do THINNING",inifiles[[2]])]<-paste(thininput[2],"do THINNING",sep="")
-        }}
-    
-    if(is.null(plantinput)){
-        plantflag=TRUE
-        plantinput[1] <-  unlist(strsplit(grep("do PLANTING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        plantinput[2] <-  unlist(strsplit(grep("do PLANTING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do PLANTING",inifiles[[1]])]<-paste(plantinput[1],"do PLANTING",sep="")
-
-        if(length(plantinput)==2){
-            inifiles[[2]][grep("do PLANTING",inifiles[[2]])]<-paste(plantinput[2],"do PLANTING",sep="")
-        }}
-
-    if(is.null(mowinput)){
-        mowflag=TRUE
-        mowinput[1] <-  unlist(strsplit(grep("do MOWING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        mowinput[2] <-  unlist(strsplit(grep("do MOWING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do MOWING",inifiles[[1]])]<-paste(mowinput[1],"do MOWING",sep="")
-
-        if(length(mowinput)==2){
-            inifiles[[2]][grep("do MOWING",inifiles[[2]])]<-paste(mowinput[2],"do MOWING",sep="")
-        }}
-
-    if(is.null(grazinput)){
-        grazflag=TRUE
-        grazinput[1] <-  unlist(strsplit(grep("do GRAZING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        grazinput[2] <-  unlist(strsplit(grep("do GRAZING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do GRAZING",inifiles[[1]])]<-paste(grazinput[1],"do GRAZING",sep="")
-
-        if(length(grazinput)==2){
-            inifiles[[2]][grep("do GRAZING",inifiles[[2]])]<-paste(grazinput[2],"do GRAZING",sep="")
-        }}
-    
-    if(is.null(harvinput)){
-        harvflag=TRUE
-        harvinput[1] <-  unlist(strsplit(grep("do HARVESTING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        harvinput[2] <-  unlist(strsplit(grep("do HARVESTING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do HARVESTING",inifiles[[1]])]<-paste(harvinput[1],"do HARVESTING",sep="")
-
-        if(length(harvinput)==2){
-            inifiles[[2]][grep("do HARVESTING",inifiles[[2]])]<-paste(harvinput[2],"do HARVESTING",sep="")
-        }}
-    
-    if(is.null(plouginput)){
-        plougflag=TRUE
-        plouginput[1] <-  unlist(strsplit(grep("do PLOUGHING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        plouginput[2] <-  unlist(strsplit(grep("do PLOUGHING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do PLOUGHING",inifiles[[1]])]<-paste(plouginput[1],"do PLOUGHING",sep="")
-
-        if(length(plouginput)==2){
-            inifiles[[2]][grep("do PLOUGHING",inifiles[[2]])]<-paste(plouginput[2],"do PLOUGHING",sep="")
-        }}
-    
-    if(is.null(fertinput)){
-        fertflag=TRUE
-        fertinput[1] <-  unlist(strsplit(grep("do FERTILIZING",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        fertinput[2] <-  unlist(strsplit(grep("do FERTILIZING",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do FERTILIZING",inifiles[[1]])]<-paste(fertinput[1],"do FERTILIZING",sep="")
-
-        if(length(fertinput)==2){
-            inifiles[[2]][grep("do FERTILIZING",inifiles[[2]])]<-paste(fertinput[2],"do FERTILIZING",sep="")
-        }}
-    
-    if(is.null(irrinput)){
-        irrflag=TRUE
-        irrinput[1] <-  unlist(strsplit(grep("do IRRIGATION",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
-        irrinput[2] <-  unlist(strsplit(grep("do IRRIGATION",inifiles[[2]],value=TRUE),"[\ \t]"))[1] 
-    } else {
-        inifiles[[1]][grep("do IRRIGATION",inifiles[[1]])]<-paste(irrinput[1],"do IRRIGATION",sep="")
-
-        if(length(irrinput)==2){
-            inifiles[[2]][grep("do IRRIGATION",inifiles[[2]])]<-paste(irrinput[2],"do IRRIGATION",sep="")
-        }}
-
     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)]
+        c<-grep("DAILY_OUTPUT",iniFiles[[2]])+1
+        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
+        dailyVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
         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)]
+        c<-grep("ANNUAL_OUTPUT",iniFiles[[2]])+1
+        numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
+        annualVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
         annualVarnames<-lapply(annualVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1]))
-        outputvars<-list(dailyVarnames,annualVarnames)} else {
+        outputVars<-list(dailyVarnames,annualVarnames)} else {
 
-                                                          c<-grep("DAILY_OUTPUT",inifiles[[2]])+1
-                                                          numVar<-as.numeric(unlist(strsplit(inifiles[[2]][c],"[\ \t]"))[1])
-                                                          dailyVarCodes<-inifiles[[2]][(c+1):(c+numVar)]
+                                                          c<-grep("DAILY_OUTPUT",iniFiles[[2]])+1
+                                                          numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
+                                                          dailyVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
                                                           dailyVarnames<-lapply(dailyVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1],mapData))
 
-                                                          c<-grep("ANNUAL_OUTPUT",inifiles[[2]])+1
-                                                          numVar<-as.numeric(unlist(strsplit(inifiles[[2]][c],"[\ \t]"))[1])
-                                                          annualVarCodes<-inifiles[[2]][(c+1):(c+numVar)]
+                                                          c<-grep("ANNUAL_OUTPUT",iniFiles[[2]])+1
+                                                          numVar<-as.numeric(unlist(strsplit(iniFiles[[2]][c],"[\ \t]"))[1])
+                                                          annualVarCodes<-iniFiles[[2]][(c+1):(c+numVar)]
                                                           annualVarnames<-lapply(annualVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1],mapData))
-                                                          outputvars<-list(dailyVarnames,annualVarnames)
+                                                          outputVars<-list(dailyVarnames,annualVarnames)
 
 
                                                           
@@ -261,76 +176,78 @@ setupMuso <- function(executable=NULL,
     
     if(is.null(executable)){
         if(Linuxp){
-            executable<-paste(inputloc,"muso",sep="")
+            executable<-file.path(inputLoc,"muso")
         } else {
-            executable<-paste(inputloc,"muso.exe",sep="")
+            executable<-file.path(inputLoc,"muso.exe")
         }
     } else {        
-        file.copy(executable,inputloc)
+        file.copy(executable,inputLoc)
     }
 
-    outputname <- unlist(strsplit(inifiles[[2]][grep("OUTPUT_CONTROL",inifiles[[2]])+1],"[\ \t]"))[1]
-    ##  outputname <- unlist(strsplit(grep("output",grep("prefix",inifiles[[2]],value=TRUE),value=TRUE),"[\ \t]"))[1]
+    outputName <- unlist(strsplit(iniFiles[[2]][grep("OUTPUT_CONTROL",iniFiles[[2]])+1],"[\ \t]"))[1]
+    ##  outputName <- unlist(strsplit(grep("output",grep("prefix",iniFiles[[2]],value=TRUE),value=TRUE),"[\ \t]"))[1]
     ##THIS IS AN UGLY SOLUTION, WHICH NEEDS AN UPGRADE!!! FiXED (2017.09.11)
-    ## outputname <- unlist(strsplit(grep("prefix for output files",inifiles[[2]],value=TRUE),"[\ \t]"))[1]
-    if(is.null(outputname)){
-        cat("I cannot find outputname, in your default ini file \n Please make sure that the line wich contains the name alse contains the prefix and the outmut keywords!")
+    ## outputName <- unlist(strsplit(grep("prefix for output files",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
+    if(is.null(outputName)){
+        stop("I cannot find outputName in your default ini file \n Please make sure that the line wich contains the name also contains the prefix and the outmut keywords!")
         
     }
-    ##    outputname<-unlist(read.table(ininput[2],skip=93,nrows = 1))[1]
+    ##    outputName<-unlist(read.table(iniInput[2],skip=93,nrows = 1))[1]
 
 
-    if(is.null(outputloc)){
-        ##  outputloc<-paste((rev(rev(unlist(strsplit(outputname,"/")))[-1])),collapse="/")
-        outputloc <- dirname(outputname)
+    if(is.null(outputLoc)){
+        ##  outputLoc<-paste((rev(rev(unlist(strsplit(outputName,"/")))[-1])),collapse="/")
+        outputLoc <- dirname(outputName)
     }
 
     
     
-    inputfiles<-c(ininput,epcinput,metinput)
-    numdata<-rep(NA,3)
-    numyears <-  as.numeric(unlist(strsplit(grep("simulation years",inifiles[[2]],value=TRUE),"[\ \t]"))[1])
-    ##    numyears<-unlist(read.table(ininput[2],skip = 14,nrows = 1)[1])
-    numvalues <-  as.numeric(unlist(strsplit(grep("number of daily output variables",inifiles[[2]],value=TRUE),"[\ \t]"))[1])
-    ## numvalues<-unlist(read.table(ininput[2],skip=102,nrows = 1)[1])
-    startyear <- as.numeric(unlist(strsplit(grep("first simulation year",inifiles[[2]],value=TRUE),"[\ \t]"))[1])
-    numdata[1]<-numyears*numvalues*365
-    numdata[2]<-numyears*numvalues*12
-    numdata[3]<-numyears*numvalues
+    inputFiles<-c(iniInput,epcInput,metInput)
+    numData<-rep(NA,3)
+    numYears <-  as.numeric(unlist(strsplit(grep("simulation years",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])
+    ##    numYears<-unlist(read.table(iniInput[2],skip = 14,nrows = 1)[1])
+    numValues <-  as.numeric(unlist(strsplit(grep("number of daily output variables",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])
+    ## numValues will be replaced to numVar
+    ## numValues<-unlist(read.table(iniInput[2],skip=102,nrows = 1)[1])
+    startyear <- as.numeric(unlist(strsplit(grep("first simulation year",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])
+    numData[1] <- numValues * sumDaysOfPeriod(startyear,numYears,corrigated=leapYear)
+        
+    numData[2] <- numYears * numValues*12
+    numData[3] <- numYears * numValues
 
     ##Writing out changed ini-file
 
-    writeLines(inifiles[[1]],ininput[1])
-    writeLines(inifiles[[2]],ininput[2])
+    writeLines(iniFiles[[1]],iniInput[1])
+    writeLines(iniFiles[[2]],iniInput[2])
     
     settings = list(executable = executable,
-                    calibrationpar = calibrationpar,
-                    outputloc=outputloc,
-                    outputnames=outputname,
-                    inputloc=inputloc,
-                    ininput=ininput,
-                    metinput=metinput,
-                    epcinput=epcinput,
-                    thininput=thininput,
-                    CO2input=CO2input,
-                    mowinput=mowinput,
-                    grazinput=grazinput,
-                    harvinput=harvinput,
-                    plouginput=plouginput,
-                    fertinput=fertinput,
-                    irrinput=irrinput,
-                    nitinput=nitinput,
-                    inputfiles=inputfiles,
-                    numdata=numdata,
+                    calibrationPar = calibrationPar,
+                    outputLoc=outputLoc,
+                    outputNames=outputName,
+                    inputLoc=inputLoc,
+                    iniInput=iniInput,
+                    metInput=metInput,
+                    epcInput=epcInput,
+                    thinInput=thinInput,
+                    CO2Input=CO2Input,
+                    mowInput=mowInput,
+                    grazInput=grazInput,
+                    harvInput=harvInput,
+                    plougInput=plougInput,
+                    fertInput=fertInput,
+                    irrInput=irrInput,
+                    nitInput=nitInput,
+                    inputFiles=inputFiles,
+                    numData=numData,
                     startyear=startyear,
-                    numyears=numyears,
-                    outputvars=outputvars
+                    numYears=numYears,
+                    outputVars=outputVars
                     )
     
-    if(!(epcflag&CO2flag&nitflag&thinflag&plantflag&mowflag&grazflag&harvflag&plougflag&fertflag&irrflag)){
-        writeLines(inifiles[[1]],ininput[[1]])
-        if(epcinput[1]!=epcinput[2]){
-            writeLines(inifiles[[2]],ininput[[2]])      
+    if(writep!=nrow(grepHelper)){
+        writeLines(iniFiles[[1]],iniInput[[1]])
+        if(epcInput[1]!=epcInput[2]){ #Change need here
+            writeLines(iniFiles[[2]],iniInput[[2]])      
         }
     }
     return(settings)
diff --git a/RBBGCMuso/R/spinupMuso.R b/RBBGCMuso/R/spinupMuso.R
index 4cba8b1..60e5c58 100644
--- a/RBBGCMuso/R/spinupMuso.R
+++ b/RBBGCMuso/R/spinupMuso.R
@@ -23,12 +23,12 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
     
     Linuxp <-(Sys.info()[1]=="Linux")
     ##Copy the variables from settings
-    inputloc <- settings$inputloc
-    outputloc <- settings$outputloc
+    inputLoc <- settings$inputLoc
+    outputLoc <- settings$outputLoc
     executable <- settings$executable
-    ininput <- settings$ininput
-    epc <- settings$epcinput
-    calibrationpar <- settings$calibrationpar
+    iniInput <- settings$iniInput
+    epc <- settings$epcInput
+    calibrationPar <- settings$calibrationPar
     whereAmI<-getwd()
 
 
@@ -39,22 +39,22 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
 ##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
     
     if(silent!=TRUE){
-        if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){    
+        if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){    
             cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")}}
     
     ##With the aggressive option every unneeded file will deleted
     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc)}
+        cleanupMuso(location=outputLoc)}
 
     
     ##change the epc file if and only if there are given parameters
     if(!is.null(parameters)){
-        changemulline(filename=epc[1], calibrationpar, parameters)}
+        changemulline(filename=epc[1], calibrationPar, parameters)}
 
     ##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)
+    ## Set the working directory to the inputLoc temporary.
+    setwd(inputLoc)
     ##Run the spinup
 
 
@@ -62,22 +62,22 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
     if(silent){#silenc mode
         if(Linuxp){
             #In this case, in linux machines
-            system(paste(executable,ininput[1],"> /dev/null",sep=" "))
+            system(paste(executable,iniInput[1],"> /dev/null",sep=" "))
         } else {
             #In windows machines there is a show.output.on.console option
-            system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)}        
+            system(paste(executable,iniInput[1],sep=" "),show.output.on.console = FALSE)}        
     } else {
-        system(paste(executable,ininput[1],sep=" "))}
+        system(paste(executable,iniInput[1],sep=" "))}
 
 ###############################################
 #############LOG SECTION#######################
 ###############################################
-    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]
-    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0
-    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]
+    logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]
+    spincrash<-tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1)==0
+    logfiles <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]
 
-    dirName<-paste(inputloc,"/LOG",sep="")
-    dirERROR<-paste(inputloc,"/ERROR",sep="")
+    dirName<-paste(inputLoc,"/LOG",sep="")
+    dirERROR<-paste(inputLoc,"/ERROR",sep="")
     
     if(!dir.exists(dirName)){
         dir.create(dirName)}
@@ -99,8 +99,8 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
         } else {
             epcdir <- dirname(epc[1])
             
-            WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
-            EPCS<-paste(inputloc,"EPCS",sep="")
+            WRONGEPC<-paste(inputLoc,"WRONGEPC",sep="")
+            EPCS<-paste(inputLoc,"EPCS",sep="")
             
             if(!dir.exists(WRONGEPC)){
                 dir.create(WRONGEPC)
@@ -126,11 +126,11 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
 
     if(debugging=="stamplog"){
         stampnum<-stamp(dirName)
-        if(inputloc==outputloc){
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+        if(inputLoc==outputLoc){
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
             
         } else {
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
+            lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
         }
         
         if(errorsign==1){
@@ -139,10 +139,10 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
     } else { if(debugging){
                  if(is.null(logfilename)){
 
-                     if(inputloc==outputloc){
-                          lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
+                     if(inputLoc==outputLoc){
+                          lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName,"/", x, sep="")))
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName,"/", x, sep="")))     
                      }
 
                      if(errorsign==1){
@@ -151,10 +151,10 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
 
                  } else {
 
-                     if(inputloc==outputloc){#These are very ugly solutions for a string problem: inputloc: "./", if outputloc equalent of inputloc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
+                     if(inputLoc==outputLoc){#These are very ugly solutions for a string problem: inputLoc: "./", if outputLoc equalent of inputLoc, it ends with "/", the string manipulation can not handle this. The better solution is easy, but I dont have enough time(Roland Hollo's) 
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))                        
                      } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
+                         lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))    
                      }
                      
                      if(errorsign==1){
@@ -164,7 +164,7 @@ spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=N
                  
              }}
     
-    cleanupMuso(location=outputloc)
+    cleanupMuso(location=outputLoc)
 
     
     if(errorsign==1){
diff --git a/RBBGCMuso/R/sysdata.rda b/RBBGCMuso/R/sysdata.rda
index 0c15c68..1136e26 100644
Binary files a/RBBGCMuso/R/sysdata.rda and b/RBBGCMuso/R/sysdata.rda differ
diff --git a/RBBGCMuso_0.3.2.0-0.tar.gz b/RBBGCMuso_0.3.2.0-0.tar.gz
deleted file mode 100644
index a281e78..0000000
Binary files a/RBBGCMuso_0.3.2.0-0.tar.gz and /dev/null differ
diff --git a/RBBGCMuso_0.4.0.0-0.tar.gz b/RBBGCMuso_0.4.0.0-0.tar.gz
new file mode 100644
index 0000000..2a5b07a
Binary files /dev/null and b/RBBGCMuso_0.4.0.0-0.tar.gz differ
diff --git a/forarcheologists b/forarcheologists
index a7def2d..9905a78 100644
--- a/forarcheologists
+++ b/forarcheologists
@@ -94,3 +94,157 @@
 ##    TOT[lineNumber]<-content
 ##    writeLines(TOT,file)
 ##    }
+
+  
+      ###Old solution for path joins, now I use file.path() function 
+        ## if(is.null(inputLoc)){
+        ##     inputLoc<- "./"
+        ## } else {
+        ##     file.path(inputLoc,"")
+        ##     }
+        ## inp <- unlist(strsplit(inputLoc,"")) #This is the charactervector of the given imput location
+
+        ## if(inp[length(inp)]!="/"){
+        ##     inp<-c(inp,"/")
+        ##     inputLoc <- paste(inp,collapse = "")
+        ##     rm(inp)
+        ## }# If inp not ends in / paste one at the end, then make a string, that will be the new inputLoc
+
+        ## ##Example: "a/b/c ==> a/b/c/"
+
+
+
+
+ 
+    if(is.null(epcInput)){
+        epcflag=TRUE
+        epcInput[1] <-  paste0(inputLoc,inputParser(string=" EPC file name",fileName=iniFiles[[1]],counter=1,value=TRUE))
+        epcInput[2] <-  paste0(inputLoc,inputParser(string=" EPC file name",fileName=iniFiles[[2]],counter=1,value=TRUE))
+    } else {
+        iniFiles[[1]][grep(" EPC file name",iniFiles[[1]])]<-paste(epcInput[1],"\t EPC file name",sep="")
+
+        if(length(epcInput)==2){
+            iniFiles[[2]][grep(" EPC file name",iniFiles[[2]])]<-paste(epcInput[2],"\t EPC file name",sep="")
+        }
+    }
+
+    if(is.null(metInput)){
+        metflag=TRUE
+        metInput[1] <-  unlist(strsplit(grep(" met file name",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        metInput[2] <-  unlist(strsplit(grep(" met file name",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep(" met file name",iniFiles[[1]])]<-paste(metInput[1],"\t met file name",sep="")
+
+        if(length(metInput)==2){
+            iniFiles[[2]][grep(" met file name",iniFiles[[2]])]<-paste(metInput[2],"\t met file name",sep="")
+        }}
+    
+    if(is.null(CO2Input)){
+        CO2flag=TRUE
+        CO2Input[1] <-  unlist(strsplit(grep(" CO2 file",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        CO2Input[2] <-  unlist(strsplit(grep(" CO2 file",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep(" CO2 file",iniFiles[[1]])]<-paste(CO2Input[1],"\t CO2 file",sep="")
+
+        if(length(CO2Input)==2){
+            iniFiles[[2]][grep(" CO2 file",iniFiles[[2]])]<-paste(CO2Input[2],"\t CO2 file",sep="")
+        }}
+    
+    if(is.null(nitInput)){
+        nitflag=TRUE
+        nitInput[1] <-  unlist(strsplit(grep("N-dep file",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        nitInput[2] <-  unlist(strsplit(grep("N-dep file",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("N-dep file",iniFiles[[1]])]<-paste(nitInput[1],"N-dep file",sep="N-dep file")
+
+        if(length(epcInput)==2){
+            iniFiles[[2]][grep("N-dep file",iniFiles[[2]])]<-paste(nitInput[2],"N-dep file",sep="")
+        }}
+
+    if(is.null(thinInput)){
+        thinflag=TRUE
+        thinInput[1] <-  unlist(strsplit(grep("do THINNING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        thinInput[2] <-  unlist(strsplit(grep("do THINNING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do THINNING",iniFiles[[1]])]<-paste(thinInput[1],"do THINNING",sep="")
+
+        if(length(thinInput)==2){
+            iniFiles[[2]][grep("do THINNING",iniFiles[[2]])]<-paste(thinInput[2],"do THINNING",sep="")
+        }}
+    
+    if(is.null(plantInput)){
+        plantflag=TRUE
+        plantInput[1] <-  unlist(strsplit(grep("do PLANTING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        plantInput[2] <-  unlist(strsplit(grep("do PLANTING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do PLANTING",iniFiles[[1]])]<-paste(plantInput[1],"do PLANTING",sep="")
+
+        if(length(plantInput)==2){
+            iniFiles[[2]][grep("do PLANTING",iniFiles[[2]])]<-paste(plantInput[2],"do PLANTING",sep="")
+        }}
+
+    if(is.null(mowInput)){
+        mowflag=TRUE
+        mowInput[1] <-  unlist(strsplit(grep("do MOWING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        mowInput[2] <-  unlist(strsplit(grep("do MOWING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do MOWING",iniFiles[[1]])]<-paste(mowInput[1],"do MOWING",sep="")
+
+        if(length(mowInput)==2){
+            iniFiles[[2]][grep("do MOWING",iniFiles[[2]])]<-paste(mowInput[2],"do MOWING",sep="")
+        }}
+
+    if(is.null(grazInput)){
+        grazflag=TRUE
+        grazInput[1] <-  unlist(strsplit(grep("do GRAZING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        grazInput[2] <-  unlist(strsplit(grep("do GRAZING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do GRAZING",iniFiles[[1]])]<-paste(grazInput[1],"do GRAZING",sep="")
+
+        if(length(grazInput)==2){
+            iniFiles[[2]][grep("do GRAZING",iniFiles[[2]])]<-paste(grazInput[2],"do GRAZING",sep="")
+        }}
+    
+    if(is.null(harvInput)){
+        harvflag=TRUE
+        harvInput[1] <-  unlist(strsplit(grep("do HARVESTING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        harvInput[2] <-  unlist(strsplit(grep("do HARVESTING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do HARVESTING",iniFiles[[1]])]<-paste(harvInput[1],"do HARVESTING",sep="")
+
+        if(length(harvInput)==2){
+            iniFiles[[2]][grep("do HARVESTING",iniFiles[[2]])]<-paste(harvInput[2],"do HARVESTING",sep="")
+        }}
+    
+    if(is.null(plougInput)){
+        plougflag=TRUE
+        plougInput[1] <-  unlist(strsplit(grep("do PLOUGHING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        plougInput[2] <-  unlist(strsplit(grep("do PLOUGHING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do PLOUGHING",iniFiles[[1]])]<-paste(plougInput[1],"do PLOUGHING",sep="")
+
+        if(length(plougInput)==2){
+            iniFiles[[2]][grep("do PLOUGHING",iniFiles[[2]])]<-paste(plougInput[2],"do PLOUGHING",sep="")
+        }}
+    
+    if(is.null(fertInput)){
+        fertflag=TRUE
+        fertInput[1] <-  unlist(strsplit(grep("do FERTILIZING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        fertInput[2] <-  unlist(strsplit(grep("do FERTILIZING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do FERTILIZING",iniFiles[[1]])]<-paste(fertInput[1],"do FERTILIZING",sep="")
+
+        if(length(fertInput)==2){
+            iniFiles[[2]][grep("do FERTILIZING",iniFiles[[2]])]<-paste(fertInput[2],"do FERTILIZING",sep="")
+        }}
+    
+    if(is.null(irrInput)){
+        irrflag=TRUE
+        irrInput[1] <-  unlist(strsplit(grep("do IRRIGATION",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
+        irrInput[2] <-  unlist(strsplit(grep("do IRRIGATION",iniFiles[[2]],value=TRUE),"[\ \t]"))[1] 
+    } else {
+        iniFiles[[1]][grep("do IRRIGATION",iniFiles[[1]])]<-paste(irrInput[1],"do IRRIGATION",sep="")
+
+        if(length(irrInput)==2){
+            iniFiles[[2]][grep("do IRRIGATION",iniFiles[[2]])]<-paste(irrInput[2],"do IRRIGATION",sep="")
+        }}