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Initial commit, copying files from bitbicket

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hollorol 2017-02-13 11:05:00 +01:00
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\relax
\catcode \string ``=12
\@writefile{toc}{\select@language{magyar} \contentsline {section}{\numberline {1}A csomag alapf\IeC {\"u}ggv\IeC {\'e}nyei}{1}}
\@writefile{toc}{\select@language{magyar} \contentsline {section}{\numberline {2}Tartalmazott f\IeC {\"u}ggv\IeC {\'e}ny-csoportok \IeC {\'a}ttekint\IeC {\'e}se}{1}}
\@writefile{toc}{\select@language{magyar} \contentsline {section}{\numberline {3}Haszn\IeC {\'a}lat}{2}}

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\documentclass[12pt,a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage[magyar]{babel}
\usepackage[T1]{fontenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage[left=2cm,right=2cm,top=2cm,bottom=2cm]{geometry}
\frenchspacing
\title{Az RMuso csomag használata}
%\author{Hollós Roland}
\begin{document}
\maketitle
\section{A csomag alapfüggvényei}
Az R-muso csomag az alábbi fő függvényeket használja:
\begin{itemize}
\item muso.R
\item changecontent.R
\item setup.R
\item other\_usefull\_functions.R
\item getOutput.R
\end{itemize}
\section{Tartalmazott függvény-csoportok áttekintése}
\subsubsection*{setup.R}
Ebben az R fileban találhatjuk a \textit{setup()} függvényt, amelyben beállíthatjuk a fő paramétereket, mint például a végrehajtható fájl(muso.exe) neve/elérési útvonala, az outputfile-ok elérési helye.
\subsubsection*{muso.R}
Itt olyan fügvények találhatók, mint a \textit{rungetMuso()}, valamint a \textit{spinupMuso()} és a \textit{normalMuso()}. Az előbbi bekéri a bemeneti paramétereket.
\subsubsection*{chagecontent.R}
Itt definiáltuk azt a függvényt( \textit{changemulline()}), ami alkalmas arra, hogy adott fájlnak, adott sorait, adott tartalmakra cserélje.
\subsubsection*{other\_usefull\_functions.R}
Két függvényt tartalmaz: \textit{getyearlycum()} és \textit{getyearlymax()} Az előbbi éves összegzést végez a megfelelő változóra vonatkozóan, az utóbbi pedig meghatározza az éves maximumértéket.
\subsubsection*{getOutput.R}
Ez a file felelős az output adadok beolvasásáért, a \textit{getdailyout()}, a \textit{getmonthlyout()} és a \textit{getyearlyout()} függvények nevüknek megfelelő formátum szerint adják vissza a kimeneti értékeket.
\section{Használat}
\subsubsection*{setup()}
A függvény, mely beállítja a környezetet a MuSo számára összesen 8 paramétert fogad el, ezek sorban: executable, parallel, calibrationpar, outputloc, inputloc, metinput, ininput, epcinput. Ezekből 11 elemű lista képződik, amit a rungetMuso igényel. Részletesebben:
\begin{itemize}
\item \textbf{executable}: A muso/muso.exe file helye és neve.
\item \textbf{calibrationpar}: A kalibráláshoz kiválasztott változók sorszáma az epc file-ban.
\item \textbf{inputloc}: Az .ini file-ok helye.
\item \textbf{metinput}: A met. file-ok helye.
\item \textbf{epcinput}: Az epc file-ok helye.
\end{itemize}
Alapértelmezés szerint a végrehatjható fájl az ini, a met, és az epc fájlokkal megegyező helyen található.\\
\newline \newline
\textbf{Példa:}\\
settings=setup(executable = "executable", calibrationpar = c(,,,), inputloc = "inputloc", metimput = "metinput", ininput = "ininput", epcinput = "epcinput")
\subsubsection*{rungetMuso}
A rungetMuso az RMuso fő függvénye. 3 dolgot csinál: a felhasználó igényei alapján megváltoztatja a bemeneti paramétereket, futtatja spinup és normal módban a MuSo-t, kiírja a kimeneti fájlokat igény szerint. Elsődlegesen a képernyőre, de az könnyen átirányítható egy változóba. \par
Mindehhez az alábbi 3 bemenetre van szüksége:
\begin{itemize}
\item \textbf{settings}: ez egy 11 elemű lista, amit akár a setup() függvénnyel is legenerálhatunk.
\item \textbf{parameters}: ez a változó tartalmazza az új értékeket.
\item \textbf{timee}: A változó tartalmazza, hogy az output milyen felbontásban érkezzen. 3 értéke lehet: "d"(napi) ,"m" (havi),"y" (évi). Az évi az alapértelmezett.
\end{itemize}
\newline \newline
\textbf{Példa:}\newline \newline
I. mód:\newline
settings<-setup(...)\\
rungetMuso(settings,parameters,timee="y")\\
II.mód:\newline
rungetMuso(setup(..),parameters,timee="y")
\end{document}

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\documentclass[12pt,a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage[magyar]{babel}
\usepackage[T1]{fontenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage[left=2cm,right=2cm,top=2cm,bottom=2cm]{geometry}
\frenchspacing
\title{Az RBBGCMuso csomag használata}
%\author{Hollós Roland}
\begin{document}
\maketitle
\section{A csomag alapfüggvényei}
Az R-muso csomag az alábbi fő függvényeket használja:
\begin{itemize}
\item muso.R
\item changecontent.R
\item setup.R
\item other\_usefull\_functions.R
\item getOutput.R
\end{itemize}
\section{Tartalmazott függvény-csoportok áttekintése}
\subsubsection*{setup.R}
Ebben az R fileban találhatjuk a \textit{setup()} függvényt, amelyben beállíthatjuk a fő paramétereket, mint például a végrehajtható fájl(muso.exe) neve/elérési útvonala, az outputfile-ok elérési helye.
\subsubsection*{muso.R}
Itt olyan fügvények találhatók, mint a \textit{rungetMuso()}, valamint a \textit{spinupMuso()} és a \textit{normalMuso()}. Az előbbi bekéri a bemeneti paramétereket.
\subsubsection*{chagecontent.R}
Itt definiáltuk azt a függvényt( \textit{changemulline()}), ami alkalmas arra, hogy adott fájlnak, adott sorait, adott tartalmakra cserélje.
\subsubsection*{other\_usefull\_functions.R}
Két függvényt tartalmaz: \textit{getyearlycum()} és \textit{getyearlymax()} Az előbbi éves összegzést végez a megfelelő változóra vonatkozóan, az utóbbi pedig meghatározza az éves maximumértéket.
\subsubsection*{getOutput.R}
Ez a file felelős az output adadok beolvasásáért, a \textit{getdailyout()}, a \textit{getmonthlyout()} és a \textit{getyearlyout()} függvények nevüknek megfelelő formátum szerint adják vissza a kimeneti értékeket.
\section{Használat}
\subsubsection*{setup()}
A függvény, mely beállítja a környezetet a MuSo számára összesen 8 paramétert fogad el, ezek sorban: executable, parallel, calibrationpar, outputloc, inputloc, metinput, ininput, epcinput. Ezekből 11 elemű lista képződik, amit a rungetMuso igényel. Részletesebben:
\begin{itemize}
\item \textbf{executable}: A muso/muso.exe file helye és neve.
\item \textbf{calibrationpar}: A kalibráláshoz kiválasztott változók sorszáma az epc file-ban.
\item \textbf{inputloc}: Az .ini file-ok helye.
\item \textbf{metinput}: A met. file-ok helye.
\item \textbf{epcinput}: Az epc file-ok helye.
\end{itemize}
Alapértelmezés szerint a végrehatjható fájl az ini, a met, és az epc fájlokkal megegyező helyen található.\\
\newline \newline
\textbf{Példa:}\\
settings=setup(executable = "executable", calibrationpar = c(,,,), inputloc = "inputloc", metimput = "metinput", ininput = "ininput", epcinput = "epcinput")
\subsubsection*{rungetMuso}
A rungetMuso az RMuso fő függvénye. 3 dolgot csinál: a felhasználó igényei alapján megváltoztatja a bemeneti paramétereket, futtatja spinup és normal módban a MuSo-t, kiírja a kimeneti fájlokat igény szerint. Elsődlegesen a képernyőre, de az könnyen átirányítható egy változóba. \par
Mindehhez az alábbi 3 bemenetre van szüksége:
\begin{itemize}
\item \textbf{settings}: ez egy 11 elemű lista, amit akár a setup() függvénnyel is legenerálhatunk.
\item \textbf{parameters}: ez a változó tartalmazza az új értékeket.
\item \textbf{timee}: A változó tartalmazza, hogy az output milyen felbontásban érkezzen. 3 értéke lehet: "d"(napi) ,"m" (havi),"y" (évi). Az évi az alapértelmezett.
\end{itemize}
\textbf{Példa:}\newline \newline
I. mód:\newline
settings<-setup(...)\\
rungetMuso(settings,parameters,timee="y")\\
II.mód:\newline
rungetMuso(setup(..),parameters,timee="y")
\end{document}

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^\.Rproj\.user$

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Package: RBBGCMuso
Title: What the Package Does (one line, title case)
Version: 0.1.7
Authors@R: person("Roland", "Hollos", , "hollorol@gmail.com", role = c("aut", "cre"))
Description: What the package does (one paragraph)
License: GPL-2
LazyData: true
NeedsCompilation: no
Packaged: 2016-11-15 13:58:04 UTC; hollorol
Author: First Last [aut, cre]
Maintainer: First Last <first.last@example.com>

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#' This runs the BBGC-MuSo model
#' @author Roland Hollós
#' @param filename Name of the initialisation files
#' @return No return, outputs are written to file
#' @usage The function works only, if ...
Linuxp <-(Sys.info()[1]=="Linux")
rungetMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE){
#############################################################
############################spinup run############################
##########################################################
##Copy the variables from settings
inputloc <- settings$inputloc
executable <- settings$executable
ininput <- settings$ininput
epc <- settings$epcinput
calibrationpar <- settings$calibrationpar
##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
if(silent!=TRUE){
if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){
cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
}
}
if(aggressive==TRUE){
cleanupMuso()
}
##change the epc file if and only if there are given parameters
if(!is.null(parameters)){
changemulline(filename=epc[2],calibrationpar,parameters)
}
##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
whereAmI<-getwd()
## Set the working directory to the inputloc temporary.
setwd(inputloc)
##Run the model for the spinup run.
if(silent){#silenc mode
if(Linuxp){
#In this case, in linux machines
system(paste(executable,ininput[1],"> /dev/null",sep=" "))
} else {
#In windows machines there is a show.output.on.console option
system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
}
} else {
system(paste(executable,ininput[1],sep=" "))
}
logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles
if(length(logspinup)==0){
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
if(!spincrash){##If spinup did not crashed, run the normal run.
#####################################################################
###########################normal run#########################
#################################################################
##for the sake of safe we set the location again
setwd(inputloc)
if(silent){
if(Linuxp){
system(paste(executable,ininput[2],"> /dev/null",sep=" "))
} else {
system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
}
} else {
system(paste(executable,ininput[2],sep=" "))
}
##read the output
switch(timee,
"d"=(Reva<-getdailyout(settings)),
"m"=(Reva<-getmonthlyout(settings)),
"y"=(Reva<-getyearlyout(settings))
)
}
logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames
###############################################
#############LOG SECTION#######################
###############################################
perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
#If log or ERROR directory does not exists create it!
dirName<-paste(inputloc,"LOG",sep="")
dirERROR<-paste(inputloc,"ERROR",sep="")
if(!dir.exists(dirName)){
dir.create(dirName)
}
if(!dir.exists(dirERROR)){
dir.create(dirERROR)
}
}
##if errorsign is 1 there is error, if it is 0 everything ok
if(length(perror)>sum(perror)){
errorsign <- 1
} else {
errorsign <- 0
}
if(keepEpc){#if keepepc option tured on
if(length(unique(dirname(epc)))>1){
print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
} else {
epcdir <- dirname(epc[1])
WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
EPCS<-paste(inputloc,"EPCS",sep="")
if(!dir.exists(WRONGEPC)){
dir.create(WRONGEPC)
}
if(!dir.exists(EPCS)){
dir.create(EPCS)
}
epcfiles <- list.files(epcdir)[grep("epc$",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)
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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)){
lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
if(errorsign==1){
lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
}
} else {
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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()
if(errorsign==1){
return("Modell Failure")
}
if(timee=="d"){
colnames(Reva) <- unlist(settings$outputvars[[1]])
} else {
if(timee=="y")
colnames(Reva) <- unlist(settings$outputvars[[2]])
}
if(export!=FALSE){
setwd(whereAmI)
## switch(fextension(export),
## "csv"=(write.csv(Reva,export)),
## "xlsx"=(),
## "odt"=
## )
} else{
setwd(whereAmI)
return(Reva)}
}

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list.files()

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#' This function calls the UNIX(-like) sed program to change specific line to other, using the row numbers.
#' @author Roland
#' @param The name of the file which is needed to be changed in some lines, the numbers of this lines(vector), and
#' the contents(vector).
#' @return void
changeSpecLine<-function(lineNumber,content,file){
TOT=readLines(file,-1)
TOT[lineNumber]<-content
writeLines(TOT,file)
}
changemulline <- function(filename,calibrationpar,contents){
#This is the function which is capable change multiple specific lines to other using their row numbers.
#The function uses the previous changspecline function to operate.
varnum <- length(calibrationpar)
if(length(contents)!=varnum)
{
cat("Error: number of the values is not the same as the number of the changed parameters")
}
TOT=readLines(filename,-1)
TOT[calibrationpar]<-contents
writeLines(TOT,filename)
}

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cleanupMuso <- function(location=NULL,deep=FALSE){
whereAmI <- getwd()
if(!is.null(location)){
setwd(location)
}
if(deep){
if(dir.exists("LOG")){
setwd("LOG")
file.remove(
grep("(out$)|(endpoint$)|(log$)",
list.files(), value = T)
)}
if(dir.exists("../ERROR")){
setwd("../ERROR")
file.remove(
grep("(out$)|(endpoint$)|(log$)",
list.files(), value = T)
)}
if(dir.exists("../EPCS")){
setwd("../EPCS")
file.remove(
grep("(out$)|(endpoint$)|(log$)|(epc$)",
list.files(), value = T)
)}
if(dir.exists("../WRONGEPC")){
setwd("../WRONGEPC")
file.remove(
grep("(out$)|(endpoint$)|(log$)|(epc$)",
list.files(), value = T)
)}
setwd("..")
file.remove(
grep("(out$)|(endpoint$)|(log$)",
list.files(), value = T)
)
}
file.remove(
grep("(out$)|(endpoint$)|(log$)",
list.files(), value = T)
)
setwd(whereAmI)
}

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getthewholedata<-function(settings){
f1<-settings$ininput[2]
filename = paste(settings$inputloc,settings$outputname,"_ann.txt",sep="")
alloutput<-read.table(filename,skip=22, header = FALSE)
return(alloutput)
}
getthespecdata<-function(settings,colnumbers){
filename<-paste(settings$inputloc,settings$outputname,"_ann.txt",sep="")
specoutput<-read.table(filename,skip=22, header = FALSE)[,colnumbers]
return(specoutput)
}
getdailyout<-function(settings){
binaryname<-paste(settings$inputloc,settings$outputname,".dayout",sep="")
d<-file(binaryname,"rb")
dayoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE)
close(d)
return(dayoutput)
}
getmonthlyout<-function(settings){
binaryname<-paste(settings$inputloc,settings$outputname,".monavgout",sep="")
d<-file(binaryname,"rb")
monoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[2])),(settings$numyears*12),byrow=TRUE)
close(d)
return(monoutput)
}
getyearlyout<-function(settings){
binaryname<-paste(settings$inputloc,settings$outputname,".annout",sep="")
d<-file(binaryname,"rb")
yearoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[3])),(settings$numyears),byrow=TRUE)
close(d)
return(yearoutput)
}

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isLeapyear <- function(year){
if(((year%%4==0)&(year%%100!=0))|(year%%400==0)){
return(TRUE)
} else {
return(FALSE)
}
}
dayOfMonths <- function(year){
dayMonths <- c(31,28,31,30,31,30,31,31,30,31,30,31)
if(isLeapyear(year)==TRUE){
dayMonths[2] <-29
}
return(dayMonths)
}
dayOfYears <- function(year){
if(isLeapyear(year)==TRUE){
return(366)
} else {
return(365)
}
}
sumDaysOfPeriod <- function(year, periodlen){
years <- year:(year+periodlen)
years100 <-length(which(years%%100==0))
years400 <-length(which(years%%400==0))
years4 <- length(which(years%%4==0))
numberOfLeapdays <- years4-years100+years400
days <- periodlen*365+numberOfLeapdays
return(days)
}
musoDate <- function(settings,timestep="d",combined=TRUE, corrigate=TRUE){
days <- sumDaysOfPeriod(settings$startyear,settings$numyears)
dates <- matrix(rep(NA,days*3),ncol=3)
dates[1,] <- c(settings$startyear,1,1)
for(i in 2:days){
dates[i,]<-dates[(i-1),]
if((dates[i-1,2]==12)&(dates[i-1,3]==31)){
dates[i,] <-c((dates[(i-1),1]+1),1,1)
} else {
if(dates[i-1,3]==(dayOfMonths(dates[(i-1),1])[dates[(i-1),2]] )){
dates[i,]<-c(dates[(i-1),1],(dates[(i-1),2]+1),1)
} else {
dates[i,3]<-dates[(i-1),3]+1
}
}
}
if(corrigate==TRUE){
if(comined==TRUE){
dates <- apply(dates,1,function(x) paste(x,collapse="."))[1:(settings$numyears*365)]
return(dates)
}
dates<-dates[(1:(settings$numyears*365)),]
}
if(comined==TRUE){
dates <- apply(dates,1,function(x) paste(x,collapse="."))
return(dates)
}
return(dates)
}

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normalMuso<- function(settings,parameters=c(" ECOPHYS"),timee="d",debugging=FALSE,logfilename=NULL){
changemulline(settings,parameters)
inputloc<-settings$inputloc
executable<-settings$executable
ininput<-settings$ininput
setwd(inputloc)
#normal run
system(paste(executable,ininput[2],sep=" "))
switch(timee,
"d"=(Reva<-getdailyout(settings)),
"m"=(Reva<-getmonthlyout(settings)),
"y"=(Reva<-getyearlyout(settings))
)
logfiles<-list.files(inputloc)[grep("log$",list.files(inputloc))]
#############LOG SECTION#######################
perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1))))
dirName<-paste(inputloc,"/LOG",sep="")
dirERROR<-paste(inputloc,"/ERROR",sep="")
ERROR_EPC<-paste(inputloc,"/ERROR_EPC",sep="")
if(!dir.exists(dirName)){
dir.create(dirName)
}
if(!dir.exists(dirERROR)){
dir.create(dirERROR)
}
if(length(perror)>sum(perror)){
errorsign <- 1
} else {
errorsign <- 0
}
if(debugging=="stamplog"){
stampnum<-stamp(dirName)
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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)){
lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
if(errorsign==1){
lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
}
} else {
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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()
if(errorsign==1){
return("Modell Failure")
}
return(Reva)
}

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#' 'Funtion for getting cumulative yearly data from observations
#' @author Roland Hollós
#' @param A vector of the daily observations.
#' @return A vector of yearly data
getyearlycum<-function(daily_observations){
number_of_years<-length(daily_observations)/365
# daily_observations[is.na(daily_observations)]<-0 # 3+NA=NA
fr<-1
yearlycum<-rep(NA,number_of_years)
for(i in 1:number_of_years){
to<-i*365
yearlycum[i]<-sum(daily_observations[fr:to],na.rm = TRUE)
fr<-i*365+1
}
return(yearlycum)
}
#' 'Function for getting the maximum values of the years, from daily data
#' @author Roland Hollós
#' @param A vector of the daily observations
#' @return A vector of yearly data
getyearlymax<-function(daily_observations){
number_of_years<-length(daily_observations)/365
# daily_observations[is.na(daily_observations)]<-0 # 3+NA=NA
fr<-1
yearlycum<-rep(NA,number_of_years)
for(i in 1:number_of_years){
to<-i*365
yearlymax[i]<-max(daily_observations[fr:to],na.rm=TRUE)
fr<-i*365+1
}
return(yearlymax)
}
fextension <- function(x){
#this function gives back the given filenames extension
fextension <- tail(unlist(strsplit(x,"\\.")),1)
}
supportedMuso <- function(x="outputs"){
supportedFormats <- c("xls","xlsx","odt","csv","txt")
if(x=="outputs"){
#If you add new format supports, please expand the lists
return(supportedFormats)
}
if(x=="message"){
return(cat("Supported formats are ",supportedFormats,"If your fileformat is something else, we automaticle coerced it to csv.\n"))
}
}

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plotMuso <- function(settings,
variable,
##compare,
##plotname,
parameters="ECOPHYS",
timee="d",
silent=TRUE,
debugging=FALSE,
keepEpc=FALSE,
logfilename=NULL,
export=FALSE){
musoData <- rungetMuso(settings=settings,
silent=silent,
timee=timee,
parameters=parameters,
debugging=debugging,
keepEpc=keepEpc,
logfilename=logfilename,
export=export)
xlab_muso<- switch(timee, "d"="days","y"="years","m"=months)
numVari <- ncol(musoData)
if(is.numeric(variable)){
if((variable>numVari)|(variable<1)){
return(print(paste("The variable parameter must be between 1 and ",numVari)))
}
plot(musoData[,variable],pch=20,col = "dark blue",xlab=xlab_muso,ylab=colnames(musoData)[variable])
} else {
if(variable=="all"){
musoData <- rbind((1:ncol(musoData)),musoData) #creating the column indexes
par(mfrow = c(2,numVari/2))
apply(musoData, 2, function(x) plot(x[2:length(x)],pch=20,col="dark blue",xlab=xlab_muso,ylab = colnames(musoData)[x[1]]))
return(print("Everything was Ok. ;)"))
} else {
return(print("The variable option is the coloumn number of the output data-matrix, so it must be numeric, of if you want to plot the whole data matrix set it \"all\""))
}
}
}

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#' This runs the BBGC-MuSo model
#' @author Roland Hollós
#' @param filename Name of the initialisation files
#' @return No return, outputs are written to file
#' @usage The function works only, if ...
Linuxp <-(Sys.info()[1]=="Linux")
rungetMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE){
#############################################################
############################spinup run############################
##########################################################
##Copy the variables from settings
inputloc <- settings$inputloc
executable <- settings$executable
ininput <- settings$ininput
epc <- settings$epcinput
calibrationpar <- settings$calibrationpar
##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
##alma
if(silent!=TRUE){
if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){
cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
}
}
if(aggressive==TRUE){
cleanupMuso()
}
##change the epc file if and only if there are given parameters
if(!is.null(parameters)){
changemulline(filename=epc[2],calibrationpar,parameters)
}
##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
whereAmI<-getwd()
## Set the working directory to the inputloc temporary.
setwd(inputloc)
##Run the model for the spinup run.
if(silent){#silenc mode
if(Linuxp){
#In this case, in linux machines
system(paste(executable,ininput[1],"> /dev/null",sep=" "))
} else {
#In windows machines there is a show.output.on.console option
system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)
}
} else {
system(paste(executable,ininput[1],sep=" "))
}
logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles
if(length(logspinup)==0){
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
if(!spincrash){##If spinup did not crashed, run the normal run.
#####################################################################
###########################normal run#########################
#################################################################
##for the sake of safe we set the location again
setwd(inputloc)
if(silent){
if(Linuxp){
system(paste(executable,ininput[2],"> /dev/null",sep=" "))
} else {
system(paste(executable,ininput[2],sep=" "),show.output.on.console = FALSE)
}
} else {
system(paste(executable,ininput[2],sep=" "))
}
##read the output
switch(timee,
"d"=(Reva<-getdailyout(settings)),
"m"=(Reva<-getmonthlyout(settings)),
"y"=(Reva<-getyearlyout(settings))
)
}
logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames
###############################################
#############LOG SECTION#######################
###############################################
perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
#If log or ERROR directory does not exists create it!
dirName<-paste(inputloc,"LOG",sep="")
dirERROR<-paste(inputloc,"ERROR",sep="")
if(!dir.exists(dirName)){
dir.create(dirName)
}
if(!dir.exists(dirERROR)){
dir.create(dirERROR)
}
}
##if errorsign is 1 there is error, if it is 0 everything ok
if(length(perror)>sum(perror)){
errorsign <- 1
} else {
errorsign <- 0
}
if(keepEpc){#if keepepc option tured on
if(length(unique(dirname(epc)))>1){
print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
} else {
epcdir <- dirname(epc[1])
WRONGEPC<-paste(inputloc,"WRONGEPC",sep="")
EPCS<-paste(inputloc,"EPCS",sep="")
if(!dir.exists(WRONGEPC)){
dir.create(WRONGEPC)
}
if(!dir.exists(EPCS)){
dir.create(EPCS)
}
epcfiles <- list.files(epcdir)[grep("epc$",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)
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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)){
lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
if(errorsign==1){
lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
}
} else {
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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()
if(errorsign==1){
return("Modell Failure")
}
if(timee=="d"){
colnames(Reva) <- unlist(settings$outputvars[[1]])
} else {
if(timee=="y")
colnames(Reva) <- unlist(settings$outputvars[[2]])
}
if(export!=FALSE){
setwd(whereAmI)
## switch(fextension(export),
## "csv"=(write.csv(Reva,export)),
## "xlsx"=(),
## "odt"=
## )
} else{
setwd(whereAmI)
return(Reva)}
}

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#' This runs the BBGC-MuSo model
#' @author Roland Hollós
#' @param calibrationpar vector with line numbers
#' @return No return, outputs are written to file
setup <- 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
){
Linuxp <-(Sys.info()[1]=="Linux")
if(is.null(inputloc)){
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(outputloc)){
outputloc<-inputloc
}
if(is.null(ininput)){
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"))}
if(length(normals)==1){
ininput[2]<-paste(inputloc,normals,sep="")
} else {return(print("There are multiple or no normal files, please choose"))}
}
##read the ini files for the further changes
inifiles<-lapply(ininput, function (x) readLines(x,-1))
if(is.null(epcinput)){
epcflag=TRUE
epcinput[1] <- unlist(strsplit(grep(" EPC file name",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
epcinput[2] <- unlist(strsplit(grep(" EPC file name",inifiles[[2]],value=TRUE),"[\ \t]"))[1]
} 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 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="")
}}
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)]
annualVarnames<-lapply(annualVarCodes, function(x) musoMapping(unlist(strsplit(x,"[\ \t]"))[1]))
outputvars<-list(dailyVarnames,annualVarnames)
if(is.null(executable)){
if(Linuxp){
executable<-paste(inputloc,"muso",sep="")
} else {
executable<-paste(inputloc,"muso.exe",sep="")
}
} else {
file.copy(executable,inputloc)
if(Linuxp){
executable<-paste(inputloc,"muso",sep="")
} else {
executable<-paste(inputloc,"muso.exe",sep="")
}
}
5+4
outputname <- unlist(strsplit(grep("prefix for output files",inifiles[[2]],value=TRUE),"[\ \t]"))[1]
## outputname<-unlist(read.table(ininput[2],skip=93,nrows = 1))[1]
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
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,
startyear=startyear,
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]])
}
}
return(settings)
}

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soilMatrix <- function(numberOfLayers=)

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spinupMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, silent=FALSE, aggressive=FALSE){
##Copy the variables from settings
inputloc <- settings$inputloc
executable <- settings$executable
ininput <- settings$ininput
epc <- settings$epcinput
calibrationpar <- settings$calibrationpar
##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
if(silent!=TRUE){
if(length(grep("(dayout$)|(log$)",list.files(inputloc)))>0){
cat(" \n \n WARMING: there is a log or dayout file nearby the ini files, that may cause problemes. \n \n If you want to avoid that possible problemes, please copy the log or dayout files into a save place, and after do a cleanupMuso(), or delete these manually, or run the rungetMuso(), with the agressive=TRUE parameter \n \n")
}
}
##With the aggressive option every unneeded file will deleted
if(aggressive==TRUE){
cleanupMuso()
}
##change the epc file if and only if there are given parameters
if(!is.null(parameters)){
changemulline(settings, parameters)
}
##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
whereAmI<-getwd()
## Set the working directory to the inputloc temporary.
setwd(inputloc)
##Run the spinup
system(paste(executable,ininput[1],sep=" "))
logfiles<-list.files(inputloc)[grep("log$",list.files(inputloc))]
perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1))))
dirName<-paste(inputloc,"/LOG",sep="")
dirERROR<-paste(inputloc,"/ERROR",sep="")
ERROR_EPC<-paste(inputloc,"/ERROR_EPC",sep="")
if(!dir.exists(dirName)){
dir.create(dirName)
}
if(!dir.exists(dirERROR)){
dir.create(dirERROR)
}
if(length(perror)>sum(perror)){
errorsign <- 1
} else {
errorsign <- 0
}
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)
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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)){
lapply( logfiles, function (x) file.rename(from=paste(inputloc,x, sep=""), to=paste(dirName,"/", x, sep="")))
if(errorsign==1){
lapply( logfiles, function (x) file.rename(from=paste(dirName,"/", x, sep=""), to=dirERROR))
}
} else {
lapply( logfiles, function (x) file.rename(from=paste(inputloc,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()
if(errorsign==1){
return("Modell Failure")
}
}

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numcut<-function(string){
#This function returns only the starting numbers of a string
unlist(strsplit(grep("^[0-9]",string,value = TRUE),"[aAzZ-]"))[1]
}
numcutall<-function(vector){
#numcall apply numcut for all elements of a string vector
as.numeric(unlist(apply(as.matrix(vector),1,numcut)))
}
stamp<-function(path="./"){
#It gives back a stamp wich is the maximum number of the output numcall
numbers<-numcutall(list.files(path))
if(length(numbers)==0){
return (0)} else {
return(max(numbers))}
}

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Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
BuildType: Package
PackageInstallArgs: --no-multiarch --with-keep.source

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<TRASH FROM MUSO.R>
## runMuso <- function(settings, parameters=c(" ECOPHYS")){
## #changing section
## # for(i in changeinput){
## # changemulline(settings, parameters[[i]])
## # }
## changemulline(settings,parameters)
## #spinup run
## # changemulline(type=1,setup(), parameters[[2]])
## setwd(settings$inputloc)
## system(paste(settings$executable,settings$ininput[1],sep=" "))
## #normal run
## setwd(settings$inputloc)
## system(paste(settings$executable,settings$ininput[2],sep=" "))
## }
## rungetMusowc <- function(settings,parameters=c(" ECOPHYS"),timee="y",logfile=FALSE,logfilename=NULL){
## #spinup run
## # changemulline(type=1,setup(), parameters[[2]])
## changemulline(settings,parameters)
## setwd(settings$inputloc)
## system(paste(settings$executable,settings$ininput[1],sep=" "))
## #normal run
## setwd(settings$inputloc)
## system(paste(settings$executable,settings$ininput[2],sep=" "))
## switch(timee,
## "d"=(Reva<-getdailyout(settings)),
## "m"=(Reva<-getmonthlyout(settings)),
## "y"=(Reva<-getyearlyout(settings))
## )
## return(Reva)
## }
<TRASH FROM OTHER_USEFULL_FUNCTIONS.R>
##For this functions there is a built in dirname function in R, which do the same.
## splitstr <- function(string, sep){
## return(unlist(strsplit(string,sep)))
## }
## containerdir<-function(string){
## return(paste(splitstr(string,"/")[1:(length(splitstr(string,"/"))-1)],collapse = "/"))
##}
<TRASH FROM CHANGECONTENT.R>
## changspecline <- function(filename, line_number,content){
## #This function calls the UNIX(-like) sed program to change specific line to other, using the row numbers.
## for_command_line <- paste("sed -i '",line_number,"s/.*/",content,"/'"," ",filename, sep="")
## system(for_command_line)
## }
## changespecline<- function(filename,line_number,content){
## TOT=readLines(filename,-1)
## TOT[line_number]<-content
## writeLines(TOT,filename)
## }
## changemulline <- function(settings,contents){
## #This is the function which is capable change multiple specific lines to other using their row numbers.
## #The function uses the previous changspecline function to operate.
## varnum <- length(settings$calibrationpar)
## if(length(contents)!=varnum)
## {
## cat("Error: number of the values is not the same as the number of the changed parameters")
## }
## for(i in 1:varnum){
## changspecline(settings$epcinput,settings$calibrationpar[i], contents[i] )
## }
## }
## changmulline2 <- function(settings,contents){
## #This is the function which is capable change multiple specific lines to other using their row numbers.
## #The function uses the previous changspecline function to operate.
## varnum <- length(settings$calibrationpar)
## if(length(contents)!=varnum)
## {
## cat("Error: number of the values is not the same as the number of the changed parameters")
## }
## for(i in 1:varnum){
## changespecline(settings$epcinput,settings$calibrationpar[i], contents[i] )
## }
## }

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/setup.r
\name{setup}
\alias{setup}
\title{This runs the Muso model}
\usage{
setup(executable = NULL, parallel = F, calibrationpar = c(1),
outputloc = NULL, inputloc = NULL, metinput = NULL, ininput = NULL,
epcinput = NULL)
}
\arguments{
\item{calibrationpar}{vector with line numbers}
}
\value{
No return, outputs are written to file
}
\description{
This runs the Muso model
}
\author{
Roland
}

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/changcontent.R
\name{changspecline}
\alias{changspecline}
\title{This function calls the UNIX(-like) sed program to change specific line to other, using the row numbers.}
\usage{
changspecline(filename, line_number, content)
}
\arguments{
\item{The}{name of the file which is needed to be changed in some lines, the numbers of this lines(vector), and
the contents(vector).}
}
\value{
void
}
\description{
This function calls the UNIX(-like) sed program to change specific line to other, using the row numbers.
}
\author{
Roland
}

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/other_usefull_functions.R
\name{getyearlycum}
\alias{getyearlycum}
\title{'Funtion for getting cumulative yearly data from observations}
\usage{
getyearlycum(daily_observations)
}
\arguments{
\item{A}{vector of the daily observations.}
}
\value{
A vector of yearly data
}
\description{
'Funtion for getting cumulative yearly data from observations
}
\author{
Roland Hollós
}

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/other_usefull_functions.R
\name{getyearlymax}
\alias{getyearlymax}
\title{'Function for getting the maximum values of the years, from daily data}
\usage{
getyearlymax(daily_observations)
}
\arguments{
\item{A}{vector of the daily observations}
}
\value{
A vector of yearly data
}
\description{
'Function for getting the maximum values of the years, from daily data
}
\author{
Roland Hollós
}

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/muso.R
\name{runMuso}
\alias{runMuso}
\title{This runs the Muso model}
\usage{
The function works only, if ...
}
\arguments{
\item{filename}{Name of the initialisation files}
}
\value{
No return, outputs are written to file
}
\description{
This runs the Muso model
}
\author{
Roland
}

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% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/setup.r
\name{setup}
\alias{setup}
\title{This runs the Muso model}
\usage{
setup(executable = NULL, parallel = F, calibrationpar = c(1),
outputloc = NULL, inputloc = NULL, metinput = NULL, ininput = NULL,
epcinput = NULL)
}
\arguments{
\item{calibrationpar}{vector with line numbers}
}
\value{
No return, outputs are written to file
}
\description{
This runs the Muso model
}
\author{
Roland
}

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README
This is one of the most important part of the package

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RECOMENDATIONS
-
-
-
-
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