forarcheologists is obsolate by design...
This commit is contained in:
Roland Hollós
parent
6e2094453a
commit
6b1dd9af9f
446
forarcheologists
446
forarcheologists
@ -1,446 +0,0 @@
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<TRASH FROM MUSO.R>
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## runMuso <- function(settings, parameters=c(" ECOPHYS")){
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## #changing section
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## # for(i in changeinput){
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## # changemulline(settings, parameters[[i]])
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## # }
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## changemulline(settings,parameters)
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## #spinup run
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## # changemulline(type=1,setup(), parameters[[2]])
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## setwd(settings$inputloc)
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## system(paste(settings$executable,settings$ininput[1],sep=" "))
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## #normal run
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## setwd(settings$inputloc)
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## system(paste(settings$executable,settings$ininput[2],sep=" "))
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## }
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## rungetMusowc <- function(settings,parameters=c(" ECOPHYS"),timee="y",logfile=FALSE,logfilename=NULL){
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## #spinup run
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## # changemulline(type=1,setup(), parameters[[2]])
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## changemulline(settings,parameters)
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## setwd(settings$inputloc)
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## system(paste(settings$executable,settings$ininput[1],sep=" "))
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## #normal run
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## setwd(settings$inputloc)
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## system(paste(settings$executable,settings$ininput[2],sep=" "))
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## switch(timee,
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## "d"=(Reva<-getdailyout(settings)),
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## "m"=(Reva<-getmonthlyout(settings)),
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## "y"=(Reva<-getyearlyout(settings))
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## )
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## return(Reva)
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## }
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<TRASH FROM OTHER_USEFULL_FUNCTIONS.R>
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##For this functions there is a built in dirname function in R, which do the same.
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## splitstr <- function(string, sep){
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## return(unlist(strsplit(string,sep)))
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## }
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## containerdir<-function(string){
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## return(paste(splitstr(string,"/")[1:(length(splitstr(string,"/"))-1)],collapse = "/"))
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##}
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<TRASH FROM CHANGECONTENT.R>
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## changspecline <- function(filename, line_number,content){
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## #This function calls the UNIX(-like) sed program to change specific line to other, using the row numbers.
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## for_command_line <- paste("sed -i '",line_number,"s/.*/",content,"/'"," ",filename, sep="")
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## system(for_command_line)
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## }
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## changespecline<- function(filename,line_number,content){
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## TOT=readLines(filename,-1)
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## TOT[line_number]<-content
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## writeLines(TOT,filename)
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## }
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## changemulline <- function(settings,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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## varnum <- length(settings$calibrationpar)
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## if(length(contents)!=varnum)
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## {
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## cat("Error: number of the values is not the same as the number of the changed parameters")
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## }
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## for(i in 1:varnum){
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## changspecline(settings$epcinput,settings$calibrationpar[i], contents[i] )
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## }
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## }
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## changmulline2 <- function(settings,contents){
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## #This is the function which is capable change multiple specific lines to other using their row numbers.
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## #The function uses the previous changspecline function to operate.
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## varnum <- length(settings$calibrationpar)
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## if(length(contents)!=varnum)
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## {
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## cat("Error: number of the values is not the same as the number of the changed parameters")
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## }
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## for(i in 1:varnum){
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## changespecline(settings$epcinput,settings$calibrationpar[i], contents[i] )
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## }
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## }
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## changeSpecLine<-function(lineNumber,content,file){
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## TOT=readLines(file,-1)
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## TOT[lineNumber]<-content
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## writeLines(TOT,file)
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## }
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###Old solution for path joins, now I use file.path() function
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## if(is.null(inputLoc)){
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## inputLoc<- "./"
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## } else {
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## file.path(inputLoc,"")
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## }
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## inp <- unlist(strsplit(inputLoc,"")) #This is the charactervector of the given imput location
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## if(inp[length(inp)]!="/"){
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## inp<-c(inp,"/")
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## inputLoc <- paste(inp,collapse = "")
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## rm(inp)
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## }# If inp not ends in / paste one at the end, then make a string, that will be the new inputLoc
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## ##Example: "a/b/c ==> a/b/c/"
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if(is.null(epcInput)){
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epcflag=TRUE
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epcInput[1] <- paste0(inputLoc,inputParser(string=" EPC file name",fileName=iniFiles[[1]],counter=1,value=TRUE))
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epcInput[2] <- paste0(inputLoc,inputParser(string=" EPC file name",fileName=iniFiles[[2]],counter=1,value=TRUE))
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} else {
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iniFiles[[1]][grep(" EPC file name",iniFiles[[1]])]<-paste(epcInput[1],"\t EPC file name",sep="")
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if(length(epcInput)==2){
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iniFiles[[2]][grep(" EPC file name",iniFiles[[2]])]<-paste(epcInput[2],"\t EPC file name",sep="")
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}
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}
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if(is.null(metInput)){
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metflag=TRUE
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metInput[1] <- unlist(strsplit(grep(" met file name",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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metInput[2] <- unlist(strsplit(grep(" met file name",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep(" met file name",iniFiles[[1]])]<-paste(metInput[1],"\t met file name",sep="")
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if(length(metInput)==2){
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iniFiles[[2]][grep(" met file name",iniFiles[[2]])]<-paste(metInput[2],"\t met file name",sep="")
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}}
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if(is.null(CO2Input)){
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CO2flag=TRUE
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CO2Input[1] <- unlist(strsplit(grep(" CO2 file",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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CO2Input[2] <- unlist(strsplit(grep(" CO2 file",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep(" CO2 file",iniFiles[[1]])]<-paste(CO2Input[1],"\t CO2 file",sep="")
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if(length(CO2Input)==2){
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iniFiles[[2]][grep(" CO2 file",iniFiles[[2]])]<-paste(CO2Input[2],"\t CO2 file",sep="")
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}}
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if(is.null(nitInput)){
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nitflag=TRUE
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nitInput[1] <- unlist(strsplit(grep("N-dep file",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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nitInput[2] <- unlist(strsplit(grep("N-dep file",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("N-dep file",iniFiles[[1]])]<-paste(nitInput[1],"N-dep file",sep="N-dep file")
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if(length(epcInput)==2){
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iniFiles[[2]][grep("N-dep file",iniFiles[[2]])]<-paste(nitInput[2],"N-dep file",sep="")
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}}
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if(is.null(thinInput)){
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thinflag=TRUE
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thinInput[1] <- unlist(strsplit(grep("do THINNING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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thinInput[2] <- unlist(strsplit(grep("do THINNING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do THINNING",iniFiles[[1]])]<-paste(thinInput[1],"do THINNING",sep="")
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if(length(thinInput)==2){
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iniFiles[[2]][grep("do THINNING",iniFiles[[2]])]<-paste(thinInput[2],"do THINNING",sep="")
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}}
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if(is.null(plantInput)){
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plantflag=TRUE
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plantInput[1] <- unlist(strsplit(grep("do PLANTING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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plantInput[2] <- unlist(strsplit(grep("do PLANTING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do PLANTING",iniFiles[[1]])]<-paste(plantInput[1],"do PLANTING",sep="")
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if(length(plantInput)==2){
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iniFiles[[2]][grep("do PLANTING",iniFiles[[2]])]<-paste(plantInput[2],"do PLANTING",sep="")
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}}
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if(is.null(mowInput)){
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mowflag=TRUE
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mowInput[1] <- unlist(strsplit(grep("do MOWING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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mowInput[2] <- unlist(strsplit(grep("do MOWING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do MOWING",iniFiles[[1]])]<-paste(mowInput[1],"do MOWING",sep="")
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if(length(mowInput)==2){
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iniFiles[[2]][grep("do MOWING",iniFiles[[2]])]<-paste(mowInput[2],"do MOWING",sep="")
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}}
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if(is.null(grazInput)){
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grazflag=TRUE
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grazInput[1] <- unlist(strsplit(grep("do GRAZING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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grazInput[2] <- unlist(strsplit(grep("do GRAZING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do GRAZING",iniFiles[[1]])]<-paste(grazInput[1],"do GRAZING",sep="")
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if(length(grazInput)==2){
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iniFiles[[2]][grep("do GRAZING",iniFiles[[2]])]<-paste(grazInput[2],"do GRAZING",sep="")
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}}
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if(is.null(harvInput)){
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harvflag=TRUE
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harvInput[1] <- unlist(strsplit(grep("do HARVESTING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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harvInput[2] <- unlist(strsplit(grep("do HARVESTING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do HARVESTING",iniFiles[[1]])]<-paste(harvInput[1],"do HARVESTING",sep="")
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if(length(harvInput)==2){
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iniFiles[[2]][grep("do HARVESTING",iniFiles[[2]])]<-paste(harvInput[2],"do HARVESTING",sep="")
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}}
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if(is.null(plougInput)){
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plougflag=TRUE
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plougInput[1] <- unlist(strsplit(grep("do PLOUGHING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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plougInput[2] <- unlist(strsplit(grep("do PLOUGHING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do PLOUGHING",iniFiles[[1]])]<-paste(plougInput[1],"do PLOUGHING",sep="")
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if(length(plougInput)==2){
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iniFiles[[2]][grep("do PLOUGHING",iniFiles[[2]])]<-paste(plougInput[2],"do PLOUGHING",sep="")
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}}
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if(is.null(fertInput)){
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fertflag=TRUE
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fertInput[1] <- unlist(strsplit(grep("do FERTILIZING",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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fertInput[2] <- unlist(strsplit(grep("do FERTILIZING",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do FERTILIZING",iniFiles[[1]])]<-paste(fertInput[1],"do FERTILIZING",sep="")
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if(length(fertInput)==2){
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iniFiles[[2]][grep("do FERTILIZING",iniFiles[[2]])]<-paste(fertInput[2],"do FERTILIZING",sep="")
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}}
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if(is.null(irrInput)){
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irrflag=TRUE
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irrInput[1] <- unlist(strsplit(grep("do IRRIGATION",iniFiles[[1]],value=TRUE),"[\ \t]"))[1]
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irrInput[2] <- unlist(strsplit(grep("do IRRIGATION",iniFiles[[2]],value=TRUE),"[\ \t]"))[1]
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} else {
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iniFiles[[1]][grep("do IRRIGATION",iniFiles[[1]])]<-paste(irrInput[1],"do IRRIGATION",sep="")
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if(length(irrInput)==2){
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iniFiles[[2]][grep("do IRRIGATION",iniFiles[[2]])]<-paste(irrInput[2],"do IRRIGATION",sep="")
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}}
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getthewholedata<-function(settings){
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f1<-settings$ininput[2]
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filename = paste(settings$inputloc,settings$outputname,"_ann.txt",sep="")
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alloutput<-read.table(filename,skip=22, header = FALSE)
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return(alloutput)
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}
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getthespecdata<-function(settings,colnumbers){
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filename<-paste(settings$inputloc,settings$outputname,"_ann.txt",sep="")
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specoutput<-read.table(filename,skip=22, header = FALSE)[,colnumbers]
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return(specoutput)
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}
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getdailyout<-function(settings){
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binaryname<-paste(settings$inputLoc,settings$outputNames,".dayout",sep="")
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d<-file(binaryname,"rb")
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dayoutput<-matrix(readBin(d,"double",size=8,n=(settings$numData[1])),(settings$numYears*365),byrow=TRUE)
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close(d)
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return(dayoutput)
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}
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getmonthlyout<-function(settings){
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binaryname<-paste(settings$inputloc,settings$outputname,".monavgout",sep="")
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d<-file(binaryname,"rb")
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monoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[2])),(settings$numyears*12),byrow=TRUE)
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close(d)
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return(monoutput)
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}
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getyearlyout<-function(settings){
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binaryname<-paste(settings$inputloc,settings$outputname,".annout",sep="")
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d<-file(binaryname,"rb")
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yearoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[3])),(settings$numyears),byrow=TRUE)
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close(d)
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return(yearoutput)
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}
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##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
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##alma
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## if(silent!=TRUE){
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## if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){
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## warning("there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
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## }
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## }
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## file.copy(file.path(outputLoc,possibleNames)
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## ,file.path(binaryPlace,paste0((stamp(binaryPlace)+1),"-",possibleNames)))
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## epcfiles <- list.files(epcdir)[grep("epc$",list.files(
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## stampnum<-stamp(EPCS)
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## lapply(epc,function (x) file.copy(from = x ,to=paste(EPCS,"/",(stampnum+1),"-", basename(x),sep="")))
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## if(errorsign==1){
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## lapply(epc, function (x) file.copy(from = paste(EPCS,"/",(stampnum+1),"-",basename(x),sep=""), to=WRONGEPC))
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## }
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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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## } 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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## }
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## if(errorsign==1){
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## lapply( logfiles, function (x) file.copy(from=paste(dirName, "/",(stampnum+1),"-",x,sep=""), to=dirERROR ))}
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if(debugging=="stamplog"){
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logfiles <- file.path(outputLoc,logfiles)
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stampAndDir(stampDir=dirName, wrongDir=dirERROR, names=logfiles, type="general",errorsign=errorsign,logfiles=logfiles)
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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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} 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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}
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if(errorsign==1){
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lapply( logfiles, function (x) file.copy(from=paste(dirName,"/", x, sep=""), to=dirERROR))
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}
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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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} 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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}
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if(errorsign==1){
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lapply( logfiles, function (x) file.copy(from=paste(dirName, "/",logfilename,"-",x,sep=""), to=dirERROR))
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}
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}
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}}
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##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory- NOT ANYMORE! :)
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## if(silent!=TRUE){
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## if(length(grep("(dayout$)|(log$)",list.files(inputLoc)))>0){
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## warning(" \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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##With the aggressive option every unneeded file will deleted
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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[1], calibrationPar, parameters)}
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## logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]
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## spincrash<-tail(readLines(paste(outputLoc,logspinup,sep="/"),-1),1)==0
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# logspinup<-list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
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|
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## logfiles <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]
|
||||
|
||||
## if(keepEpc){#if keepepc option tured on
|
||||
|
||||
## if(length(unique(dirname(epc)))>1){
|
||||
## print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
|
||||
## } else {
|
||||
## epcdir <- dirname(epc[1])
|
||||
|
||||
## WRONGEPC<-paste(inputLoc,"WRONGEPC",sep="")
|
||||
## EPCS<-paste(inputLoc,"EPCS",sep="")
|
||||
|
||||
## if(!dir.exists(WRONGEPC)){
|
||||
## dir.create(WRONGEPC)
|
||||
## }
|
||||
|
||||
## if(!dir.exists(EPCS)){
|
||||
## dir.create(EPCS)
|
||||
## }
|
||||
|
||||
## epcfiles <- list.files(epcdir)[grep("epc$",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)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user