Merge branch 'Devel' into feature/glue
This commit is contained in:
Roland Hollós
commit
f131dbc49a
@ -11,6 +11,7 @@ Packaged: 2017-07-19 14:00:04 UTCs; hollorol
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Author: Roland Hollo's [aut, cre]
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Imports:
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grDevices,
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lubridate,
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limSolve,
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stats,
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utils,
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@ -29,7 +29,7 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
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debugging=FALSE, logfilename=NULL,
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keepEpc=FALSE, export=FALSE,
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silent=FALSE, aggressive=FALSE,
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leapYear=FALSE,keepBinary=FALSE,
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keepBinary=FALSE,
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binaryPlace="./", fileToChange="epc",
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skipSpinup = TRUE, modifyOriginal =FALSE, prettyOut = FALSE){
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########################################################################
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@ -325,14 +325,10 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
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if(!prettyOut){
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colnames(Reva) <- unlist(settings$outputVars[[1]])
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} else{
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dates <- as.Date(musoDate(startYear = settings$startYear,
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numYears = settings$numYears,
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timestep="d",combined = TRUE,corrigated = FALSE),
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"%d.%m.%Y")
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Reva <- cbind.data.frame(dates,
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Reva <- cbind.data.frame(
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musoDate(startYear = settings$startYear,
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numYears = settings$numYears,
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timestep = "d", combined = FALSE, corrigated = FALSE),
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combined = FALSE, prettyOut = TRUE),
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Reva)
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colnames(Reva) <- as.character(c("date","day","month","year",unlist(settings$outputVars[[1]])) )
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@ -344,20 +340,23 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
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if(leapYear){
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Reva <- corrigMuso(settings,Reva)
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## if(leapYear){
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## Reva <- corrigMuso(settings,Reva)
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## if(!prettyOut){
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## rownames(Reva) <- musoDate(settings$startYear,settings$numYears)
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## }
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## } else {
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## if(!prettyOut){
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## rownames(Reva) <- musoDate(settings$startYear, settings$numYears)
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## }
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## }
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if(!prettyOut){
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rownames(Reva) <- musoDate(settings$startYear,settings$numYears)
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rownames(Reva) <- musoDate(settings$startYear, numYears = settings$numYears)
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}
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} else {
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if(!prettyOut){
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rownames(Reva) <- musoDate(settings$startYear, settings$numYears, corrigated=FALSE)
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}
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}
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if(export!=FALSE){
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setwd(whereAmI)
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@ -1,160 +1,76 @@
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#' isLeapyear
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#' musoDate
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#'
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#'This function tells us if its argument a leapyear or not.
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#'
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#'@param year a year
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#'@usage isLeapyear(year)
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#'@return TRUE, if leapyear, FALSE if dont.
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#' @keywords internal
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isLeapyear <- function(year){
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##This Boolean function tells us whether the given year is leapyear or not
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if(((year%%4==0)&(year%%100!=0))|(year%%400==0)){
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return(TRUE)
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} else {
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return(FALSE)
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}
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}
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#' dayOfMonths
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#'
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#'This function gives as a vector which contains the number of the days per each month
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#'
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#'@param year a year
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#'@param corrigated Do you want to handle the leapyears, if yes choose TRUE
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#'@usage dayOfMonths(year, corrigated=TRUE)
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#'@return vector with 12 element. First is January, the last is December. All of the vector element represents the number of the days in that specific month
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#'@keywords internal
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dayOfMonths <- function(year,corrigated=TRUE){
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##This function tells us how many days are in the months in the choosen year.
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dayMonths <- c(31,28,31,30,31,30,31,31,30,31,30,31)
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if(corrigated){
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if(isLeapyear(year)==TRUE){
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dayMonths[2] <-29
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}
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}
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return(dayMonths)
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}
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#' This function tells us how many days are in the given year.
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#'
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#' This function tells us how many days are in the given year.
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#' @author Roland Hollos
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#' @keywords internal
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dayOfYears <- function(year, corrigated=TRUE){
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##This function tells us how many days are in the given year.
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if(corrigated){
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if(isLeapyear(year)==TRUE){
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return(366)
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} else {
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return(365)
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}
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} else {
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return(365)
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}
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}
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#' How many days are from the given date and given period length(periodlen)?
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#'
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#'How many days are from the given date and given period length(periodlen)?
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#' @author Roland Hollos
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#' @keywords internal
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sumDaysOfPeriod <- function(year, periodlen, corrigated=TRUE){
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##How many days are from the given date and given period length(periodlen)?
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years <- year:(year+periodlen)
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if(corrigated){
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years100 <-length(which(years%%100==0))
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years400 <-length(which(years%%400==0))
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years4 <- length(which(years%%4==0))
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numberOfLeapdays <- years4-years100+years400
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days <- periodlen*365+numberOfLeapdays
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return(days)
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} else {
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days <- periodlen*365
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return(days)
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}
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}
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#' Musoleapyear
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#'
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#' How many days are from the given date and given period length(periodlen)?
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#' @author Roland Hollos
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#' @keywords internal
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musoLeapYears <- function(settings){
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days <- 365*settings$numyears
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years <- settings$startyear:(settings$startyear+settings$numyears-1)
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Leapyears <-unlist(lapply(years,isLeapyear))
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return(Leapyears)
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}
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#' It generates BiomeBGC-MuSo dates
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#'
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#' It generates all of the day-dates which are between the start and endyear of BiomeBGC-MuSo run.
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#' How many days are from the given date and given period length(periodlen)?
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#' @author Roland Hollos
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#' @param timestep timestep, which can be daily ("d"), monthly ("m"), yearly("y")
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#' @param settings You have to run the setupMuso function before musoDate. It is its output which contains all of the necessary system variables. It sets the whole environment.
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#' @param combined If FALSE the output is a vector of 3 string: day, month year, if true, these strings will be concatenated.
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#' @param corrigated If True it counts with leapyears, else dont.
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#' @param format This is the format of the date. It can be "en" (dd.mm.yyyy), or "hu" (yyyy.mm.dd)
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#' @return The exact date-vectors for the BioBGC-MuSo output. You can use this for labelling purpose for example.
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#' This function generates MuSo compatibla dates for the data
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#' @author Roland HOLLOS
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#' @param startYear
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#' @param numYears
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#' @param timestep
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#' @param combined
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#' @param corrigated
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#' @param format
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#' @importFrom lubridate leap_year
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#' @export
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musoDate <- function(startYear, numYears, timestep="d", combined=TRUE, corrigated=TRUE, format="en"){
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##purpose: generate date label for muso
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musoDate <- function(startYear, endYears = NULL, numYears, combined = TRUE, leapYearHandling = FALSE, prettyOut = FALSE){
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if(is.null(endYears) & is.null(numYears)){
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stop("You should provide endYears or numYears")
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}
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if(is.null(endYears)){
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endYear <- startYear + numYears -1
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}
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days <- sumDaysOfPeriod(startYear, numYears, corrigated=corrigated)
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dates <- matrix(rep(NA,days*3),ncol=3)
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dates <- seq(from = as.Date(paste0(startYear,"01","01"),format = "%Y%m%d"), to = as.Date(paste0(endYear,"12","31"),format = "%Y%m%d"), by = "day")
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if(leapYearHandling){
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if(prettyOut){
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return(cbind(format(dates,"%d.%m.%Y"),as.numeric(format(dates,"%d")),as.numeric(format(dates,"%m")),as.numeric(format(dates,"%Y"))) )
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}
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dates[1,] <- c(1,1,startYear)
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for(i in 2:days){
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dates[i,]<-dates[(i-1),]
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if((dates[i-1,2]==12)&(dates[i-1,1]==31)){
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dates[i,] <-c(1,1,(dates[(i-1),3]+1))
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if(combined == FALSE){
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return(cbind(format(dates,"%d"),format(dates,"%m"),format(dates,"%Y")))
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} else {
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if(dates[i-1,1]==(dayOfMonths(dates[(i-1),3],corrigated=corrigated)[dates[(i-1),2]] )){
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dates[i,]<-c(1,(dates[(i-1),2]+1),dates[(i-1),3])
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} else {
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dates[i,1]<-dates[(i-1),1]+1
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return(format(dates,"%d.%m.%Y"))
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}
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}
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}
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if(format=="en"){
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} else {
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if(format=="hu"){
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dates<-dates[,c(3,2,1)]
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if(prettyOut){
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return(cbind(format(dates,"%d.%m.%Y"),as.numeric(format(dates,"%d")),as.numeric(format(dates,"%m")),as.numeric(format(dates,"%Y"))) )
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}
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dates <- dates[format(dates,"%m%d")!="0229"]
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if(combined == FALSE){
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return(cbind(format(dates,"%d"),format(dates,"%m"),format(dates,"%Y")))
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} else {
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cat("format is coerced to english, because I don't know what do you mean by:",format)
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return(format(dates,"%d.%m.%Y"))
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}
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}
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if(combined==TRUE){
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dates <- apply(dates,1,function(x) paste(x,collapse="."))
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return(dates)
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}
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return(dates)
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corrigLeapYear <- function(data, dataCol, modellSettings = NULL, startYear, fromDate = NULL,toDate = NULL,formatString = "%Y-%m-%d"){
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data <- as.data.frame(data)
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numDays <- nrow(data)
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dates <- seq(as.Date(paste0(startYear,"01","01"),format = "%Y%m%d"), by= "day", length = numDays)
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goodInd <- which(!(leap_year(dates)&
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(format(date,"%m") == "12")&
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(format(date,"%d") == "31")))
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realDate <- musoDate(startYear = startYear, numYears = numYears)
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data <- cbind.data.frame(real,data[goodInd])
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modellDates <- musoDate(startYear = settings$startYear,numYears = settings$numYears)
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if(is.null(modellSettings)){
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modellSettings <- setupMuso()
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}
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}
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alignDataWithModelIndex <- function(){
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}
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@ -229,7 +229,7 @@ setupMuso <- function(executable=NULL,
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## numValues will be replaced to numVar
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## numValues<-unlist(read.table(iniInput[2],skip=102,nrows = 1)[1])
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startYear <- as.numeric(unlist(strsplit(iniFiles[[2]][grep("TIME_DEFINE",iniFiles[[2]])+3],"[\ \t]"))[1])
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numData[1] <- numValues * sumDaysOfPeriod(startYear,numYears,corrigated=leapYear)
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numData[1] <- numValues * numYears*365 #LEAPYEAR CORRECTION NEEDED
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numData[2] <- numYears * numValues*12
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numData[3] <- numYears * numValues
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@ -241,7 +241,7 @@ setupMuso <- function(executable=NULL,
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if(!is.null(modelOutputs)){
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outVarChanges <- putOutVars(iniFile = iniInput[2],outputVars = modelOutputs, modifyOriginal = TRUE)
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numData <- round(numDate*outVarChanges[[2]])
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numData <- round(numData*outVarChanges[[2]])
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outputVars[[1]] <-outVarChanges[[1]]
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}
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