add updateMusoMapping function and fix musoMapping function

RBBGCMuso/DESCRIPTION

@@ -3,6 +3,7 @@ Title: An R package for BiomeBGC-MuSo ecosystem modelling
 Version: 0.3.1.0-1
 Authors@R: person("Roland", "Hollo's", , "hollorol@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
+Depends: R (>= 2.10)
 License: GPL-2
 LazyData: true
 NeedsCompilation: no

RBBGCMuso/NAMESPACE

@@ -6,10 +6,12 @@ export(corrigMuso)
 export(getyearlycum)
 export(getyearlymax)
 export(musoDate)
+export(musoMapping)
 export(plotMuso)
 export(rungetMuso)
 export(setupMuso)
 export(spinupMuso)
 export(supportedMuso)
+export(updateMusoMapping)
 import(graphics)
 import(utils)

RBBGCMuso/R/calibMuso.R

@@ -55,7 +55,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
     
     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc)
+        cleanupMuso(location=outputloc,deep = TRUE)
     }
     
     ##change the epc file if and only if there are given parameters
@@ -229,7 +229,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
                  
              }}
     
-    cleanupMuso(location=outputloc)
+    cleanupMuso(location=outputloc,deep = TRUE)
     if(errorsign==1){
         return("Modell Failure")
     }

RBBGCMuso/R/cleanup.R

@@ -26,6 +26,7 @@ cleanupMuso <- function(location=NULL, simplicity=TRUE,deep=FALSE){
             areThereAnyFolders <- TRUE
         }
         
+        
         if(dir.exists("../ERROR")){
             setwd("../ERROR")
 

RBBGCMuso/R/otherUsefullFunctions.R

@@ -113,20 +113,3 @@ corrigMuso <- function(settings, data){
     }
     return(data)
 }
-
-#' genMusoMapping
-#'
-#' This function leapyear-corrigate the output of the modell
-#' @author Roland Hollos
-#' @param settings This is the output of the setupMuso() function. It contains all of the RBBGCMuso settings
-#' @param data the models outputdata
-#' @return It returns the modells leapyear-corrigated output data.
-#' @export
-#' @usage corrigMuso(settings, data)
-
-genMusoMapping<-function(output_map_init="output_map_init.c"){
-    
-    outputRaw<-grep("\\[",readLines("output_map_init",-1),value=TRUE)
-    
-    
-}

RBBGCMuso/R/rungetMuso.R

@@ -56,7 +56,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     }
     
     if(aggressive==TRUE){
-        cleanupMuso(location=outputloc)
+        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.

RBBGCMuso/man/musoMapping.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputMapping.R
+\name{musoMapping}
+\alias{musoMapping}
+\title{musoMapping}
+\usage{
+musoMapping(code, mapData=NULL)
+}
+\arguments{
+\item{code}{the MuSo outputcode}
+
+\item{mapData}{updateMusomapping generated matrix}
+}
+\value{
+The name of the MuSo outputcode
+}
+\description{
+musoMapping can give us the name of a muso outputcode
+}
+\author{
+Roland Hollos
+}

RBBGCMuso/man/updateMusoMapping.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputMapping.R
+\name{updateMusoMapping}
+\alias{updateMusoMapping}
+\title{updateMusoMapping}
+\usage{
+updateMusoMapping(output_map_init="output_map_init.c")
+}
+\arguments{
+\item{output_map_init}{The outputcode-variable bindings is described in output_map_init.c file, via this parameter, you can give it the the function}
+}
+\value{
+The outputcode-variable matrix, and also change the global variable
+}
+\description{
+This function update the the muso outputcode-variable matrix
+}
+\author{
+Roland Hollos
+}