solve the old file(con,"r") problem, and many more

RBBGCMuso/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RBBGCMuso
 Title: An R package for BiomeBGC-MuSo ecosystem modelling
-Version: 0.3.1.0-1
+Version: 0.3.2.0-0
 Authors@R: person("Roland", "Hollo's", , "hollorol@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 Depends: R (>= 2.10)
@@ -15,5 +15,5 @@ Imports:
 Maintainer: Roland Hollo's <hollorol@gmail.com>
 RoxygenNote: 6.0.1
 Suggests: knitr,
-    rmarkdown
+    rmarkdown,
 VignetteBuilder: knitr

RBBGCMuso/R/calibMuso.R

@@ -1,4 +1,4 @@
-#' calibMuso
+t#' calibMuso
 #'
 #' This function changes the epc file and after that  runs the BBGC-MuSo model and reads in its outputfile in a very structured way.
 #' 
@@ -92,7 +92,17 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
 
-    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
+    if(length(logspinup)>1){
+        spincrash<-TRUE
+    } else {
+        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)
+        }
+    }
+    
+                                        #If the last line in the logfile is 0 There are mistakes so the spinup crashes
     
     if(!spincrash){##If spinup did not crashed, run the normal run.
         
@@ -151,11 +161,16 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
 
     ##if errorsign is 1 there is error, if it is 0 everything ok
+    perror[is.na(perror)]<-0
     if(length(perror)>sum(perror)){
         errorsign <- 1
+    } else {
+        if(spincrash){
+            errorsign <- 1
         } else {
             errorsign <- 0
         } 
+    }
 
 
     if(keepEpc){#if keepepc option tured on

RBBGCMuso/R/otherUsefullFunctions.R

@@ -133,3 +133,39 @@ file.path2<-function(str1, str2){
         return(file.path(str1,str2))
     }
 } 
+
+numFactors <- function(x,type="pos"){
+    x <- as.integer(abs(x))
+    div <- seq_len(x)
+    posdiv <- div[x%%div==0L]
+    negdiv <- posdiv*-1
+    alldiv <- c(negdiv,posdiv)
+    switch(type,"pos"=return(posdiv),"neg"=return(negdiv),"all"=return(alldiv))
+}
+
+niceMatrixLayoutForPlots <- function(n){
+    if(n==0){
+        return(cat("Ther is nothing to do with 0 graph"))
+    }
+    n <- as.integer(n)
+    factors <- numFactors(n)
+    if(length(factors)==2){
+        return(n)}
+    sqrtn <- round(sqrt(n))
+    num1 <- factors[which(min(abs(factors-sqrtn))==abs(factors-sqrtn))[1]]
+    num2 <- n/num1
+    return(c(num1,num2))
+}
+
+truncNorm<-function(N,mean, sd, min, max){
+n=0
+randomNorm<-rep(NA,N)
+while(n<=N){
+  transNorm<-rnorm(1,mean,sd)
+  if((transNorm>min)&(transNorm<max)){
+    randomNorm[n]<-transNorm
+    n<-n+1
+  }
+}
+return(randomNorm)
+}

RBBGCMuso/R/plotMuso.R

@@ -2,7 +2,7 @@
 #'
 #' This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way, and after that plot the results automaticly 
 #' 
-#' @author Roland Hollos
+#' @author Roland Hollos, Dora Hidy
 #' @param settings You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment
 #' @param timee The required timesteps in the modell output. It can be "d", if it is daily, "m", if it's monthly, "y", it it is yearly
 #' @param debugging If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles
@@ -57,16 +57,18 @@ plotMuso <- function(settings,
      } else {
          if(variable=="all"){
             
-            musoData  <- rbind((1:ncol(musoData)),musoData) #creating the column indexes
+             musoData  <- rbind(1:numVari,musoData) #creating the column indexes
-            par(mfrow = c(2,numVari/2))
+             par(mfrow = niceMatrixLayoutForPlots(numVari))
 
              apply(musoData, 2, function(x) plot(x[2:length(x)],pch=20,col="dark blue",xlab=xlab_muso,ylab = colnames(musoData)[x[1]]))
+             par(mfrow=c(1,1))
              return(print("Everything was Ok. ;)"))
          } else {
              return(print("The variable option is the coloumn number of the output data-matrix, so it must be numeric, of if you want to plot the whole data matrix set it \"all\""))
          }
 
             
+        
      }
 
     

RBBGCMuso/R/rungetMuso.R

@@ -87,7 +87,18 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
     
-    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
+    
+    if(length(logspinup)>1){
+        spincrash<-TRUE
+    } else {
+        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)
+        }
+    }
+    
+    
     
     if(!spincrash){##If spinup did not crashed, run the normal run.
         
@@ -145,9 +156,14 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     ##if errorsign is 1 there is error, if it is 0 everything ok
     if(length(perror)>sum(perror)){
         errorsign <- 1
+
+    } else {
+        if(spincrash){
+            errorsign <- 1
         } else {
             errorsign <- 0
         } 
+    }
 
 
     if(keepEpc){#if keepepc option tured on

RBBGCMuso/R/rungettanul.R

@@ -1,240 +1,240 @@
-rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE){
+## rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE){
     
 
 
 
+## ##########################################################################
+## ###########################Set local variables########################
 ## ########################################################################
-###########################Set local variables########################
-########################################################################
     
-    Linuxp <-(Sys.info()[1]=="Linux")
+##     Linuxp <-(Sys.info()[1]=="Linux")
-    ##Copy the variables from settings
+##     ##Copy the variables from settings
-    inputloc <- settings$inputloc
+##     inputloc <- settings$inputloc
-    outputloc <- settings$outputloc
+##     outputloc <- settings$outputloc
-    executable <- settings$executable
+##     executable <- settings$executable
-    ininput <- settings$ininput
+##     ininput <- settings$ininput
-    epc <- settings$epcinput
+##     epc <- settings$epcinput
-    calibrationpar <- settings$calibrationpar
+##     calibrationpar <- settings$calibrationpar
-    whereAmI<-getwd()
+##     whereAmI<-getwd()
         
-#############################################################
+## #############################################################
-############################spinup run############################
+## ############################spinup run############################
-########################################################## 
+## ########################################################## 
 
     
-    ##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
+##     ##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
     
 
-    if(silent!=TRUE){
+##     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")
+##             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")
 
-        }
+##         }
       
-    }
+##     }
     
-    if(aggressive==TRUE){
+##     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc)
+##         cleanupMuso(location=outputloc)
-    }
+##     }
 
-    ##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.
+##     ##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.
+##     ## Set the working directory to the inputloc temporary.
-    setwd(inputloc)
+##     setwd(inputloc)
 
 
-    ##Run the model for the spinup run.
+##     ##Run the model for the spinup run.
 
-    if(silent){#silenc mode
+##     if(silent){#silenc mode
-        if(Linuxp){
+##         if(Linuxp){
-                                        #In this case, in linux machines
+##                                         #In this case, in linux machines
-            system(paste(executable,ininput[1],"> /dev/null",sep=" "))
+##             system(paste(executable,ininput[1],"> /dev/null",sep=" "))
-        } else {
+##         } else {
-                                        #In windows machines there is a show.output.on.console option
+##                                         #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,ininput[1],sep=" "),show.output.on.console = FALSE)
-        }
+##         }
         
-    } else {
+##     } else {
-        system(paste(executable,ininput[1],sep=" "))
+##         system(paste(executable,ininput[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){
+##     if(length(logspinup)==0){
-        return("Modell Failure")#in that case the modell did not create even a logfile
+##         return("Modell Failure")#in that case the modell did not create even a logfile
-    }
+##     }
     
-    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
+##     spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
     
-    if(!spincrash){##If spinup did not crashed, run the normal run.
+##     if(!spincrash){##If spinup did not crashed, run the normal run.
         
-##################################################################### 
+## ##################################################################### 
-###########################normal run#########################
+## ###########################normal run#########################
-#################################################################
+## #################################################################
 
-        ##for the sake of safe we set the location again
+##         ##for the sake of safe we set the location again
-        setwd(inputloc)
+##         setwd(inputloc)
 
-        if(silent){
+##         if(silent){
-            if(Linuxp){
+##             if(Linuxp){
-                system(paste(executable,ininput[2],"> /dev/null",sep=" "))
+##                 system(paste(executable,ininput[2],"> /dev/null",sep=" "))
-            } else {
+##             } else {
-                system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
+##                 system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
-            }
+##             }
             
-        } else {
+##         } else {
-            system(paste(executable,ininput[2],sep=" "))
+##             system(paste(executable,ininput[2],sep=" "))
-        }
+##         }
 
 
-        ##read the output
+##         ##read the output
-        
-        switch(timee,
-               "d"=(Reva<-getdailyout(settings)),
-               "m"=(Reva<-getmonthlyout(settings)),
-               "y"=(Reva<-getyearlyout(settings))
-               )
-    }
-
-    
-    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
-
-###############################################    
-#############LOG SECTION#######################
-###############################################
-    
-    perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
-    
-    if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
-                                        ##If log or ERROR directory does not exists create it!
-        dirName<-paste(inputloc,"LOG",sep="") 
-        dirERROR<-paste(inputloc,"ERROR",sep="")
-        
-        if(!dir.exists(dirName)){
-            dir.create(dirName)
-        }
-
-        if(!dir.exists(dirERROR)){
-            dir.create(dirERROR)
-        }
-    }
-
-    ##if errorsign is 1 there is error, if it is 0 everything ok
-    if(length(perror)>sum(perror)){
-        errorsign <- 1
-    } else {
-        errorsign <- 0
-    }
-
-
-    if(keepEpc){#if keepepc option tured on
-        
-        if(length(unique(dirname(epc)))>1){
-            print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
-        } else {
-            epcdir <- dirname(epc[1])
-            
-            WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
-            EPCS<-paste(inputloc,"EPCS",sep="")
-            
-            if(!dir.exists(WRONGEPC)){
-                dir.create(WRONGEPC)
-            }
-
-            if(!dir.exists(EPCS)){
-                dir.create(EPCS)
-            }
-            
-            epcfiles <- list.files(epcdir)[grep("epc$",list.files(epcdir))]
-            stampnum<-stamp(EPCS)
-            lapply(epcfiles,function (x) file.copy(from = paste(epcdir,"/",x,sep=""),to=paste(EPCS,"/",(stampnum+1),"-",x,sep="")))
-            if(errorsign==1){
-                lapply(epcfiles,function (x) file.copy(from = paste(EPCS,"/",(stampnum+1),"-",x,sep=""), to=WRONGEPC))
-            }
-
-        }
-    }
-    
-
-
-
-
-    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="")))
-            
-        } else {
-            lapply( logfiles, function (x) file.rename(from=paste(outputloc,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)){
-
-                     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="")))     
-                     }
-
-                     if(errorsign==1){
-                         lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
-                     }
-
-                 } 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="")))                        
-                     } else {
-                         lapply( logfiles, function (x) file.rename(from=paste(outputloc,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))
-                     }
-                 }    
-                 
-             }}
-    
-    cleanupMuso(location=outputloc)
-    if(errorsign==1){
-        return("Modell Failure")
-    }
-
-    if(timee=="d"){
-        colnames(Reva) <- unlist(settings$outputvars[[1]])
-    } else {
-        if(timee=="y")
-            colnames(Reva) <- unlist(settings$outputvars[[2]])
-    }
-
-    if(leapYear){
-        Reva <- corrigMuso(settings,Reva)
-        rownames(Reva) <- musoDate(settings)
-    } else { 
-        rownames(Reva) <- musoDate(settings, corrigated=FALSE)
-    }
-
-    if(export!=FALSE){
-        setwd(whereAmI)
-
-        ## switch(fextension(export),
-        ##        "csv"=(write.csv(Reva,export)),
-        ##        "xlsx"=(),
-        ##        "odt"=
-        
         
+##         switch(timee,
+##                "d"=(Reva<-getdailyout(settings)),
+##                "m"=(Reva<-getmonthlyout(settings)),
+##                "y"=(Reva<-getyearlyout(settings))
 ##                )
-        write.csv(Reva,export)
+##     }
 
-    } else{
+    
-        setwd(whereAmI)
+##     logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
-        return(Reva)}
+
-}
+## ###############################################    
+## #############LOG SECTION#######################
+## ###############################################
+    
+##     perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
+    
+##     if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
+##                                         ##If log or ERROR directory does not exists create it!
+##         dirName<-paste(inputloc,"LOG",sep="") 
+##         dirERROR<-paste(inputloc,"ERROR",sep="")
+        
+##         if(!dir.exists(dirName)){
+##             dir.create(dirName)
+##         }
+
+##         if(!dir.exists(dirERROR)){
+##             dir.create(dirERROR)
+##         }
+##     }
+
+##     ##if errorsign is 1 there is error, if it is 0 everything ok
+##     if(length(perror)>sum(perror)){
+##         errorsign <- 1
+##     } else {
+##         errorsign <- 0
+##     }
+
+
+##     if(keepEpc){#if keepepc option tured on
+        
+##         if(length(unique(dirname(epc)))>1){
+##             print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
+##         } else {
+##             epcdir <- dirname(epc[1])
+            
+##             WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
+##             EPCS<-paste(inputloc,"EPCS",sep="")
+            
+##             if(!dir.exists(WRONGEPC)){
+##                 dir.create(WRONGEPC)
+##             }
+
+##             if(!dir.exists(EPCS)){
+##                 dir.create(EPCS)
+##             }
+            
+##             epcfiles <- list.files(epcdir)[grep("epc$",list.files(epcdir))]
+##             stampnum<-stamp(EPCS)
+##             lapply(epcfiles,function (x) file.copy(from = paste(epcdir,"/",x,sep=""),to=paste(EPCS,"/",(stampnum+1),"-",x,sep="")))
+##             if(errorsign==1){
+##                 lapply(epcfiles,function (x) file.copy(from = paste(EPCS,"/",(stampnum+1),"-",x,sep=""), to=WRONGEPC))
+##             }
+
+##         }
+##     }
+    
+
+
+
+
+##     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="")))
+            
+##         } else {
+##             lapply( logfiles, function (x) file.rename(from=paste(outputloc,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)){
+
+##                      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="")))     
+##                      }
+
+##                      if(errorsign==1){
+##                          lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
+##                      }
+
+##                  } 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="")))                        
+##                      } else {
+##                          lapply( logfiles, function (x) file.rename(from=paste(outputloc,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))
+##                      }
+##                  }    
+                 
+##              }}
+    
+##     cleanupMuso(location=outputloc)
+##     if(errorsign==1){
+##         return("Modell Failure")
+##     }
+
+##     if(timee=="d"){
+##         colnames(Reva) <- unlist(settings$outputvars[[1]])
+##     } else {
+##         if(timee=="y")
+##             colnames(Reva) <- unlist(settings$outputvars[[2]])
+##     }
+
+##     if(leapYear){
+##         Reva <- corrigMuso(settings,Reva)
+##         rownames(Reva) <- musoDate(settings)
+##     } else { 
+##         rownames(Reva) <- musoDate(settings, corrigated=FALSE)
+##     }
+
+##     if(export!=FALSE){
+##         setwd(whereAmI)
+
+##         ## switch(fextension(export),
+##         ##        "csv"=(write.csv(Reva,export)),
+##         ##        "xlsx"=(),
+##         ##        "odt"=
+        
+        
+##         ## )
+##         write.csv(Reva,export)
+        
+##     } else{
+##         setwd(whereAmI)
+##         return(Reva)}
+## }
 
 
 

RBBGCMuso/R/setupMuso.R

@@ -49,7 +49,8 @@ setupMuso <- function(executable=NULL,
                       irrinput=NULL,
                       nitinput=NULL,
                       ininput=NULL,
-                  epcinput=NULL
+                      epcinput=NULL,
+                      mapData=NULL
                       ){
 
     Linuxp <-(Sys.info()[1]=="Linux")
@@ -223,6 +224,8 @@ setupMuso <- function(executable=NULL,
             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)]
@@ -232,9 +235,25 @@ setupMuso <- function(executable=NULL,
         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 {
+
+                                                          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)]
+                                                          annualVarnames<-lapply(annualVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1],mapData))
                                                           outputvars<-list(dailyVarnames,annualVarnames)
 
 
+                                                          
+                                                      }
+    
+    
+    
     if(is.null(executable)){
         if(Linuxp){
             executable<-paste(inputloc,"muso",sep="")

RBBGCMuso/man/plotMuso.Rd

@@ -38,5 +38,5 @@ It depends on the export parameter. The function returns with a matrix with the
 This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way, and after that plot the results automaticly
 }
 \author{
-Roland Hollos
+Roland Hollos, Dora Hidy
 }