daily output list

RBBGCMuso/NAMESPACE

@@ -7,6 +7,7 @@ export(cleanupMuso)
 export(compareMuso)
 export(copyMusoExampleTo)
 export(corrigMuso)
+export(getDailyOutputList)
 export(getMeteoData1BGC)
 export(getyearlycum)
 export(getyearlymax)

RBBGCMuso/R/calibMuso.R

@@ -142,6 +142,13 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
         settings$numData <- round(settings$numData*outputVarChanges[[2]])
     }
 
+    # if(modifyOriginal){
+    #     suppressWarnings(dir.create())
+    #     sapply(c(iniInput,epc),)
+    #
+    # }
+
+    
    if(!skipSpinup) {
 
     ##Run the model for the spinup run.

RBBGCMuso/R/getOutPutList.R

@@ -0,0 +1,27 @@
+#' getDailyOutputList
+#'
+#' bla bla
+#' @param settings bla
+#' @export
+
+
+getDailyOutputList <- function(settings=NULL){
+    if(is.null(settings)){
+        settings<- setupMuso()
+    }
+    settings$dailyOutputTable
+}
+
+#' getAnnualOutputList
+#'
+#' bla bla
+#' @param settings bla
+#' @export
+
+
+getDailyOutputList <- function(settings=NULL){
+    if(is.null(settings)){
+        settings<- setupMuso()
+    }
+    settings$annualOutputTable
+}

RBBGCMuso/R/outputMapping.R

@@ -32,7 +32,11 @@ updateMusoMapping<-function(output_map_init="output_map_init.c"){
 musoMapping <- function(code,
                         mapData=getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]]){
     if(is.null(mapData)){
-        return(unlist(mMapping[which(mMapping[,1]==code),2])) #mMapping is package-scoped system variable generated by udateMusoMapping
+        return(unlist(tryCatch(mMapping[which(mMapping[,1]==code),2],error = function(e){
+                                   
+        stop(sprintf("The code %s in inifile is not valid muso output variable code",code))                                   
+                                   
+}))) #mMapping is package-scoped system variable generated by udateMusoMapping
     } else {
         return(unlist(mapData[which(mapData[,1]==code),2]))
     }

RBBGCMuso/R/setupMuso.R

@@ -159,6 +159,8 @@ setupMuso <- function(executable=NULL,
                                 error = function(e){
         stop("Cannot read indexes of output variables from the normal ini file, please make sure you have not skiped a line after the flag: \"DAILY_OUTPUT\"")    
         })
+
+        dailyVarCodes<-unlist(lapply(dailyVarCodes, function(x) unlist(strsplit(x,"[\ \t]"))[1]))
         dailyVarnames<-unlist(lapply(dailyVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1])))
 
         outIndex<-grep("ANNUAL_OUTPUT",iniFiles[[2]])+1
@@ -268,6 +270,10 @@ setupMuso <- function(executable=NULL,
     }
     epcFiles <- tryCatch(sapply(iniFiles,function(x){(searchBellow(x,"EPC_FILE"))}),error = function(e){""}) 
     metInput <- tryCatch(sapply(iniFiles,function(x){(searchBellow(x,"MET_INPUT"))}),error = function(e){""})
+    dailyOutputTable <- cbind.data.frame(seq_along(dailyVarCodes),dailyVarCodes,outputVars[[1]])
+    colnames(dailyOutputTable) <- c("index","code","name")
+    annualOutputTable <- cbind.data.frame(seq_along(annualVarCodes),annualVarCodes,outputVars[[2]])
+    colnames(dailyOutputTable) <- c("index","code","name")
     
     settings = list(executable = executable,
                     calibrationPar = calibrationPar,
@@ -293,7 +299,9 @@ setupMuso <- function(executable=NULL,
                     outputVars=outputVars,
                     soilFile=soilFiles,
                     dailyVarCodes= gsub("\\s.*","",dailyVarCodes),
-                    annualVarCodes = gsub("\\s.*","",annualVarCodes)
+                    annualVarCodes = gsub("\\s.*","",annualVarCodes),
+                    dailyOutputTable=dailyOutputTable,
+                    annualOutputTable=annualOutputTable
                     )
 
     # if(getOption("RMuso_version")==6){
@@ -324,6 +332,9 @@ setupMuso <- function(executable=NULL,
     #         writeLines(iniFiles[[2]],iniInput[[2]])      
     #     }
     # }
+
+    suppressWarnings(dir.create(file.path(inputLoc,"bck")))
+    # sapply(iniFiles,epc)
     return(settings)
 
 }

RBBGCMuso/getOutPutList.R

@@ -0,0 +1,27 @@
+#' getDailyOutputList
+#'
+#' bla bla
+#' @param settings bla
+#' @export
+
+
+getDailyOutputList <- function(settings=NULL){
+    if(is.null(settings)){
+        settings<- setupMuso()
+    }
+    settings$dailyOutputTable
+}
+
+#' getAnnualOutputList
+#'
+#' bla bla
+#' @param settings bla
+#' @export
+
+
+getDailyOutputList <- function(settings=NULL){
+    if(is.null(settings)){
+        settings<- setupMuso()
+    }
+    settings$annualOutputTable
+}

RBBGCMuso/man/getDailyOutputList.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getOutPutList.R
+\name{getDailyOutputList}
+\alias{getDailyOutputList}
+\title{getDailyOutputList}
+\usage{
+getDailyOutputList(settings = NULL)
+
+getDailyOutputList(settings = NULL)
+}
+\arguments{
+\item{settings}{bla}
+}
+\description{
+bla bla
+
+bla bla
+}