Major update, big improvement.
This commit is contained in:
hollorol
parent
900e97397d
commit
957bb9055d
@ -1,6 +1,6 @@
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Package: RBBGCMuso
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Title: An R package for BiomeBGC-MuSo ecosystem modelling
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Version: 0.3.3.0-0
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Version: 0.4.0.0-0
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Authors@R: person("Roland", "Hollo's", , "hollorol@gmail.com", role = c("aut", "cre"))
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Description: What the package does (one paragraph).
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Depends: R (>= 2.10)
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@ -20,7 +20,7 @@
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#' @export
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calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE){
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calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE,keepBinary=FALSE, binayPlace="./"){
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##########################################################################
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@ -29,12 +29,12 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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Linuxp <-(Sys.info()[1]=="Linux")
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##Copy the variables from settings
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inputloc <- settings$inputloc
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outputloc <- settings$outputloc
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inputLoc <- settings$inputLoc
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outputLoc <- settings$outputLoc
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executable <- settings$executable
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ininput <- settings$ininput
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epc <- settings$epcinput
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calibrationpar <- settings$calibrationpar
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iniInput <- settings$iniInput
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epc <- settings$epcInput
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calibrationPar <- settings$calibrationPar
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whereAmI<-getwd()
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@ -57,7 +57,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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##alma
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if(silent!=TRUE){
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if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){
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if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){
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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")
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}
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@ -65,19 +65,19 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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}
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if(aggressive==TRUE){
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cleanupMuso(location=outputloc,deep = TRUE)
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cleanupMuso(location=outputLoc,deep = TRUE)
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}
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##change the epc file if and only if there are given parameters
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if(!is.null(parameters)){
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changemulline(filename=epc[2],calibrationpar,parameters)
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changemulline(filename=epc[2],calibrationPar,parameters)
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}
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##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.
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## Set the working directory to the inputloc temporary.
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setwd(inputloc)
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## Set the working directory to the inputLoc temporary.
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setwd(inputLoc)
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##Run the model for the spinup run.
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@ -85,19 +85,19 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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if(silent){#silenc mode
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if(Linuxp){
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#In this case, in linux machines
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system(paste(executable,ininput[1],"> /dev/null",sep=" "))
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system(paste(executable,iniInput[1],"> /dev/null",sep=" "))
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} else {
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#In windows machines there is a show.output.on.console option
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system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
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system(paste(executable,iniInput[1],sep=" "),show.output.on.console = FALSE)
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}
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} else {
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system(paste(executable,ininput[1],sep=" "))
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system(paste(executable,iniInput[1],sep=" "))
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}
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logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
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logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
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if(length(logspinup)==0){
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return("Modell Failure")#in that case the modell did not create even a logfile
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}
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@ -105,10 +105,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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if(length(logspinup)>1){
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spincrash<-TRUE
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} else {
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if(identical(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1),character(0))){
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if(identical(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1),character(0))){
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spincrash<-TRUE
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} else {
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spincrash<-(tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)!=1)
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spincrash<-(tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1)!=1)
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}
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}
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@ -121,17 +121,17 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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#################################################################
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##for the sake of safe we set the location again
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setwd(inputloc)
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setwd(inputLoc)
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if(silent){
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if(Linuxp){
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system(paste(executable,ininput[2],"> /dev/null",sep=" "))
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system(paste(executable,iniInput[2],"> /dev/null",sep=" "))
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} else {
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system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
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system(paste(executable,iniInput[2],sep=" "),show.output.on.console = FALSE)
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}
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} else {
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system(paste(executable,ininput[2],sep=" "))
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system(paste(executable,iniInput[2],sep=" "))
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}
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@ -142,10 +142,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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"m"=(Reva<-getmonthlyout(settings)),
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"y"=(Reva<-getyearlyout(settings))
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)
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if(keepBinary){
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file.copy(grep("out$",list.files(outputLoc),value=TRUE)
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,file.path(binaryPlace,paste0(stamp(binaryPlace),"-",grep("out$",list.files(outputLoc),value=TRUE))))
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}
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}
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logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
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logfiles <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]#creating a vector for logfilenames
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###############################################
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#############LOG SECTION#######################
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@ -153,13 +156,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
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perror<-as.numeric(as.vector(lapply(paste(outputLoc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
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if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
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#If log or ERROR directory does not exists create it!
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dirName<-paste(inputloc,"LOG",sep="")
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dirERROR<-paste(inputloc,"ERROR",sep="")
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dirName<-paste(inputLoc,"LOG",sep="")
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dirERROR<-paste(inputLoc,"ERROR",sep="")
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if(!dir.exists(dirName)){
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dir.create(dirName)
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@ -190,8 +193,8 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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} else {
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epcdir <- dirname(epc[1])
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WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
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EPCS<-paste(inputloc,"EPCS",sep="")
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WRONGEPC<-paste(inputLoc,"WRONGEPC",sep="")
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EPCS<-paste(inputLoc,"EPCS",sep="")
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if(!dir.exists(WRONGEPC)){
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dir.create(WRONGEPC)
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@ -216,11 +219,11 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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if(debugging=="stamplog"){
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stampnum<-stamp(dirName)
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if(inputloc==outputloc){
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
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if(inputLoc==outputLoc){
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
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} else {
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",(stampnum+1),"-",x,sep="")))
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}
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if(errorsign==1){
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@ -229,10 +232,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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} else { if(debugging){
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if(is.null(logfilename)){
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if(inputloc==outputloc){
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
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if(inputLoc==outputLoc){
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName,"/", x, sep="")))
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} else {
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName,"/", x, sep="")))
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName,"/", x, sep="")))
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}
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if(errorsign==1){
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@ -241,10 +244,10 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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} else {
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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)
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))
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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)
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep=""), to=paste(dirName, "/",logfilename,"-",x,sep="")))
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} else {
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lapply( logfiles, function (x) file.rename(from=paste(outputloc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))
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lapply( logfiles, function (x) file.rename(from=paste(outputLoc,x, sep="/"), to=paste(dirName, "/",logfilename,"-",x,sep="")))
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}
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if(errorsign==1){
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@ -254,16 +257,16 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
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}}
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cleanupMuso(location=outputloc,deep = TRUE)
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cleanupMuso(location=outputLoc,deep = TRUE)
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if(errorsign==1){
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return("Modell Failure")
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}
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if(timee=="d"){
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colnames(Reva) <- unlist(settings$outputvars[[1]])
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colnames(Reva) <- unlist(settings$outputVars[[1]])
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} else {
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if(timee=="y")
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colnames(Reva) <- unlist(settings$outputvars[[2]])
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colnames(Reva) <- unlist(settings$outputVars[[2]])
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}
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@ -6,11 +6,11 @@
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#' @author Roland Hollos
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#' @keywords internal
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changemulline <- function(filename,calibrationpar,contents){
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changemulline <- function(filename,calibrationPar,contents){
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##This is the function which is capable change multiple specific lines to other using their row numbers.
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##The function uses the previous changspecline function to operate.
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##From now changespecline is in the forarcheologist file, because its no longer needed
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varnum <- length(calibrationpar)
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varnum <- length(calibrationPar)
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contents <- as.list(contents)
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if(length(contents)!=varnum)
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{
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@ -20,7 +20,7 @@ changemulline <- function(filename,calibrationpar,contents){
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readedFile = readLines(filename,-1)
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for(i in 1:varnum){
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readedFile[calibrationpar[i]] <- paste(contents[[i]],collapse = " ")
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readedFile[calibrationPar[i]] <- paste(contents[[i]],collapse = " ")
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}
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writeLines(unlist(readedFile),filename)
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@ -12,9 +12,9 @@ getthespecdata<-function(settings,colnumbers){
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}
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getdailyout<-function(settings){
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binaryname<-paste(settings$inputloc,settings$outputnames,".dayout",sep="")
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binaryname<-paste(settings$inputLoc,settings$outputNames,".dayout",sep="")
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d<-file(binaryname,"rb")
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dayoutput<-matrix(readBin(d,"double",size=8,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE)
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dayoutput<-matrix(readBin(d,"double",size=8,n=(settings$numData[1])),(settings$numYears*365),byrow=TRUE)
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close(d)
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return(dayoutput)
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}
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@ -86,6 +86,7 @@ sumDaysOfPeriod <- function(year, periodlen, corrigated=TRUE){
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return(days)
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} else {
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days <- periodlen*365
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return(days)
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}
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}
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@ -121,7 +122,7 @@ musoDate <- function(settings,timestep="d",combined=TRUE, corrigated=TRUE, forma
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days <- sumDaysOfPeriod(settings$startyear,settings$numyears, corrigated=corrigated)
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days <- sumDaysOfPeriod(settings$startyear,settings$numYears, corrigated=corrigated)
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dates <- matrix(rep(NA,days*3),ncol=3)
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dates[1,] <- c(1,1,settings$startyear)
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@ -9,7 +9,7 @@
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updateMusoMapping<-function(output_map_init="output_map_init.c"){
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outputRaw<-grep("\\[",readLines("output_map_init",-1),value=TRUE)
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outputRaw<-grep("\\[",readLines(output_map_init,-1),value=TRUE)
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codes <- as.vector(lapply(outputRaw, function (x) as.numeric(unlist(strsplit(unlist(strsplit(x,"\\["))[2],"\\]"))[1])))
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names <- unlist(lapply(outputRaw, function (x) unlist(strsplit(unlist(strsplit(x,">"))[2],";"))[1]))
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@ -31,9 +31,9 @@ updateMusoMapping<-function(output_map_init="output_map_init.c"){
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musoMapping <- function(code, mapData=NULL){
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if(is.null(mapData)){
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return(unlist(mMapping[which(mMapping[,1]==code),2])) #mMapping is package-scoped system variable generated by uudateMusoMapping
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return(unlist(mMapping[which(mMapping[,1]==code),2])) #mMapping is package-scoped system variable generated by udateMusoMapping
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} else {
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return(unlist(mapData[which(mapData[,1]==650),2]))
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return(unlist(mapData[which(mapData[,1]==code),2]))
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}
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}
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@ -31,12 +31,12 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
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Linuxp <-(Sys.info()[1]=="Linux")
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##Copy the variables from settings
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inputloc <- settings$inputloc
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outputloc <- settings$outputloc
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inputLoc <- settings$inputLoc
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outputLoc <- settings$outputLoc
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executable <- settings$executable
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ininput <- settings$ininput
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epc <- settings$epcinput
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calibrationpar <- settings$calibrationpar
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iniInput <- settings$iniInput
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epc <- settings$epcInput
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calibrationPar <- settings$calibrationPar
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whereAmI<-getwd()
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#############################################################
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@ -48,7 +48,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
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if(silent!=TRUE){
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if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){
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if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){
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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")
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}
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@ -56,13 +56,13 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
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}
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if(aggressive==TRUE){
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cleanupMuso(location=outputloc, deep=TRUE)
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cleanupMuso(location=outputLoc, deep=TRUE)
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}
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##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.
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## Set the working directory to the inputloc temporary.
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setwd(inputloc)
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## Set the working directory to the inputLoc temporary.
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setwd(inputLoc)
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##Run the model for the spinup run.
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@ -70,19 +70,19 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
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if(silent){#silenc mode
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if(Linuxp){
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#In this case, in linux machines
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system(paste(executable,ininput[1],"> /dev/null",sep=" "))
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system(paste(executable,iniInput[1],"> /dev/null",sep=" "))
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} else {
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#In windows machines there is a show.output.on.console option
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system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
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system(paste(executable,iniInput[1],sep=" "),show.output.on.console = FALSE)
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}
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} else {
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system(paste(executable,ininput[1],sep=" "))
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system(paste(executable,iniInput[1],sep=" "))
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}
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logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
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logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
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if(length(logspinup)==0){
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return("Modell Failure")#in that case the modell did not create even a logfile
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}
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@ -91,10 +91,10 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
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if(length(logspinup)>1){
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spincrash<-TRUE
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||||
} 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$outputVars[[2]])
|
||||
}
|
||||
|
||||
if(leapYear){
|
||||
|
||||
@ -14,7 +14,7 @@
|
||||
## executable <- settings$executable
|
||||
## ininput <- settings$ininput
|
||||
## epc <- settings$epcinput
|
||||
## calibrationpar <- settings$calibrationpar
|
||||
## calibrationPar <- settings$calibrationPar
|
||||
## whereAmI<-getwd()
|
||||
|
||||
## #############################################################
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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){
|
||||
|
||||
Binary file not shown.
Binary file not shown.
BIN
RBBGCMuso_0.4.0.0-0.tar.gz
Normal file
BIN
RBBGCMuso_0.4.0.0-0.tar.gz
Normal file
Binary file not shown.
154
forarcheologists
154
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="")
|
||||
}}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user