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fix the output problems

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hollorol 2017-05-16 10:00:11 +02:00
parent 214d1540e1
commit 2a694681b5
9 changed files with 47 additions and 26 deletions
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4
.Rhistory
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@ -1 +1,5 @@
install.packages("RBBGCMuso_0.1.8.tar.gz") install.packages("RBBGCMuso_0.1.8.tar.gz")
install.packages("RBBGCMuso_0.1.8.tar.gz")
install.packages("RBBGCMuso_0.1.8.tar.gz")
install.packages("RBBGCMuso_0.1.8.tar.gz")
install.packages("RBBGCMuso_0.1.8.tar.gz")

2
RBBGCMuso/DESCRIPTION
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@ -1,6 +1,6 @@
Package: RBBGCMuso Package: RBBGCMuso
Title: What the Package Does (one line, title case) Title: What the Package Does (one line, title case)
Version: 0.1.8 Version: 0.1.9.0-1
Authors@R: person("Roland", "Hollos", , "hollorol@gmail.com", role = c("aut", "cre")) Authors@R: person("Roland", "Hollos", , "hollorol@gmail.com", role = c("aut", "cre"))
Description: What the package does (one paragraph) Description: What the package does (one paragraph)
License: GPL-2 License: GPL-2

13
RBBGCMuso/R/calibMuso.R
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@ -14,6 +14,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
##Copy the variables from settings ##Copy the variables from settings
inputloc <- settings$inputloc inputloc <- settings$inputloc
outputloc <- settings$outputloc
executable <- settings$executable executable <- settings$executable
ininput <- settings$ininput ininput <- settings$ininput
epc <- settings$epcinput epc <- settings$epcinput
@ -32,7 +33,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
} }
if(aggressive==TRUE){ if(aggressive==TRUE){
cleanupMuso() cleanupMuso(location=outputloc)
} }
##change the epc file if and only if there are given parameters ##change the epc file if and only if there are given parameters
@ -64,12 +65,12 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
if(length(logspinup)==0){ if(length(logspinup)==0){
return("Modell Failure")#in that case the modell did not create even a logfile return("Modell Failure")#in that case the modell did not create even a logfile
} }
spincrash<-tail(readLines(paste(inputloc,logspinup,sep=""),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
if(!spincrash){##If spinup did not crashed, run the normal run. if(!spincrash){##If spinup did not crashed, run the normal run.
@ -102,13 +103,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
} }
logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
############################################### ###############################################
#############LOG SECTION####################### #############LOG SECTION#######################
############################################### ###############################################
perror<-as.numeric(as.vector(lapply(paste(inputloc,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((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
#If log or ERROR directory does not exists create it! #If log or ERROR directory does not exists create it!
@ -186,7 +187,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
}} }}
cleanupMuso() cleanupMuso(location=outputloc)
if(errorsign==1){ if(errorsign==1){
return("Modell Failure") return("Modell Failure")
} }

14
RBBGCMuso/R/cleanup.R
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@ -1,4 +1,4 @@
cleanupMuso <- function(location=NULL,deep=FALSE){ cleanupMuso <- function(location=NULL, simplicity=TRUE,deep=FALSE){
whereAmI <- getwd() whereAmI <- getwd()
if(!is.null(location)){ if(!is.null(location)){
@ -44,11 +44,13 @@ cleanupMuso <- function(location=NULL,deep=FALSE){
) )
} }
if(!simplicity){
file.remove( file.remove(
grep("(out$)|(endpoint$)|(log$)", grep("(out$)|(endpoint$)|(log$)",
list.files(), value = T) list.files(), value = T)
) )} else {
file.remove(grep("log$",list.files(),value = T))
}
setwd(whereAmI) setwd(whereAmI)

2
RBBGCMuso/R/getOutput.R
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@ -12,7 +12,7 @@ getthespecdata<-function(settings,colnumbers){
} }
getdailyout<-function(settings){ getdailyout<-function(settings){
binaryname<-paste(settings$inputloc,settings$outputname,".dayout",sep="") binaryname<-paste(settings$inputloc,settings$outputnames,".dayout",sep="")
d<-file(binaryname,"rb") d<-file(binaryname,"rb")
dayoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE) dayoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE)
close(d) close(d)

13
RBBGCMuso/R/rungetMuso.R
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@ -14,6 +14,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
##Copy the variables from settings ##Copy the variables from settings
inputloc <- settings$inputloc inputloc <- settings$inputloc
outputloc <- settings$outputloc
executable <- settings$executable executable <- settings$executable
ininput <- settings$ininput ininput <- settings$ininput
epc <- settings$epcinput epc <- settings$epcinput
@ -32,7 +33,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
} }
if(aggressive==TRUE){ if(aggressive==TRUE){
cleanupMuso() cleanupMuso(location=outputloc)
} }
##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it. ##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
@ -59,12 +60,12 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
if(length(logspinup)==0){ if(length(logspinup)==0){
return("Modell Failure")#in that case the modell did not create even a logfile return("Modell Failure")#in that case the modell did not create even a logfile
} }
spincrash<-tail(readLines(paste(inputloc,logspinup,sep=""),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
if(!spincrash){##If spinup did not crashed, run the normal run. if(!spincrash){##If spinup did not crashed, run the normal run.
@ -97,13 +98,13 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
} }
logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
############################################### ###############################################
#############LOG SECTION####################### #############LOG SECTION#######################
############################################### ###############################################
perror<-as.numeric(as.vector(lapply(paste(inputloc,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((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
#If log or ERROR directory does not exists create it! #If log or ERROR directory does not exists create it!
@ -181,7 +182,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
}} }}
cleanupMuso() cleanupMuso(location=outputloc)
if(errorsign==1){ if(errorsign==1){
return("Modell Failure") return("Modell Failure")
} }

23
RBBGCMuso/R/setupMuso.R
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@ -26,8 +26,7 @@ setupMuso <- function(executable=NULL,
if(is.null(inputloc)){ if(is.null(inputloc)){
inputloc<- "./" inputloc<- "./"
} } else {
inp <- unlist(strsplit(inputloc,"")) #This is the charactervector of the given imput location inp <- unlist(strsplit(inputloc,"")) #This is the charactervector of the given imput location
if(inp[length(inp)]!="/"){ if(inp[length(inp)]!="/"){
@ -37,10 +36,8 @@ setupMuso <- function(executable=NULL,
}# If inp not ends in / paste one at the end, then make a string, that will be the new inputloc }# 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/" ##Example: "a/b/c ==> a/b/c/"
if(is.null(outputloc)){
outputloc<-inputloc
} }
inichangedp <- FALSE
if(is.null(ininput)){ if(is.null(ininput)){
spinups<-grep("s.ini$",list.files(inputloc),value=TRUE) spinups<-grep("s.ini$",list.files(inputloc),value=TRUE)
@ -60,6 +57,8 @@ setupMuso <- function(executable=NULL,
##read the ini files for the further changes ##read the ini files for the further changes
inifiles<-lapply(ininput, function (x) readLines(x,-1)) 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 /
if(is.null(epcinput)){ if(is.null(epcinput)){
epcflag=TRUE epcflag=TRUE
@ -230,6 +229,15 @@ setupMuso <- function(executable=NULL,
} }
## outputname<-unlist(read.table(ininput[2],skip=93,nrows = 1))[1] ## outputname<-unlist(read.table(ininput[2],skip=93,nrows = 1))[1]
if(is.null(outputloc)){
## outputloc<-paste((rev(rev(unlist(strsplit(outputname,"/")))[-1])),collapse="/")
outputloc <- dirname(outputname)
}
inputfiles<-c(ininput,epcinput,metinput) inputfiles<-c(ininput,epcinput,metinput)
numdata<-rep(NA,3) numdata<-rep(NA,3)
numyears <- as.numeric(unlist(strsplit(grep("simulation years",inifiles[[2]],value=TRUE),"[\ \t]"))[1]) numyears <- as.numeric(unlist(strsplit(grep("simulation years",inifiles[[2]],value=TRUE),"[\ \t]"))[1])
@ -241,6 +249,11 @@ setupMuso <- function(executable=NULL,
numdata[2]<-numyears*numvalues*12 numdata[2]<-numyears*numvalues*12
numdata[3]<-numyears*numvalues numdata[3]<-numyears*numvalues
##Writing out changed ini-file
writeLines(inifiles[[1]],ininput[1])
writeLines(inifiles[[2]],ininput[2])
settings = list(executable = executable, settings = list(executable = executable,
calibrationpar = calibrationpar, calibrationpar = calibrationpar,
outputloc=outputloc, outputloc=outputloc,

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RBBGCMuso_0.1.8.tar.gz
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RBBGCMuso_0.1.9.0-1.tar.gz Normal file
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