Complete the documentations, and repar the namespaces

RBBGCMuso/DESCRIPTION

@@ -1,12 +1,18 @@
 Package: RBBGCMuso
-Title: What the Package Does (one line, title case)
-Version: 0.2.0.0-1
-Authors@R: person("Roland", "Hollos", , "hollorol@gmail.com", role = c("aut", "cre"))
-Description: What the package does (one paragraph)
+Title: An R package for BiomeBGC-MuSo ecosystem modelling
+Version: 0.3.0.0-1
+Authors@R: person("Roland", "Hollo's", , "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>
+Packaged: 2017-07-19 14:00:04 UTC; hollorol
+Author: Roland Hollo's [aut, cre]
+Imports:
+	utils,
+	graphics
+Maintainer: Roland Hollo's <hollorol@gmail.com>
 RoxygenNote: 6.0.1
+Suggests: knitr,
+    rmarkdown
+VignetteBuilder: knitr

RBBGCMuso/NAMESPACE

@@ -1 +1,13 @@
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
+
+export(calibMuso)
+export(corrigMuso)
+export(getyearlycum)
+export(getyearlymax)
+export(musoDate)
+export(plotMuso)
+export(rungetMuso)
+export(spinupMuso)
+export(supportedMuso)
+import(graphics)
+import(utils)

RBBGCMuso/R/calibMuso.R

@@ -2,18 +2,21 @@
 #'
 #' This function changes the epc file and after that  runs the BBGC-MuSo model and reads in its outputfile in a very structured way.
 #' 
-#' @author Roland Hollós
-#' @param settings You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment
+#' @author Roland Hollos
+#' @param settings You have to run the setupMuso function before calibMuso. It is its output which contains all of the necessary system variables. It sets the whole running environment
 #' @param timee The required timesteps in the modell output. It can be "d", if it is daily, "m", if it's monthly, "y", it it is yearly
 #' @param debugging If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles
 #' @param keepEpc If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.
 #' @param export if it is yes or you give a filename here, it converts the output to the specific extension. For example, if you set export to "example.csv", it converts the output to "csv", if you set it to "example.xls" it converts to example.xls with the xlsx package. If it is not installed it gives back a warning message and converts it to csv.
 #' @param silent If you set it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.
 #' @param aggressive It deletes every possible modell-outputs from the previous modell runs.
-#' @param leapyear future feature.
 #' @param parameters In the settings variable you have set the row indexes of the variables, you wish to change. In this parameter you can give an exact value for them in a vector like: c(1,2,3,4)
+#' @param logfilename If you want to set a specific name for your logfiles you can set this via logfile parameter
+#' @param leapYear  Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled. 
 #' @return No return, outputs are written to file 
-#' @usage calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+#' @usage calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL,
+#' keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+#' @import utils
 #' @export
 
 
@@ -33,44 +36,6 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     epc <- settings$epcinput
     calibrationpar <- settings$calibrationpar
     whereAmI<-getwd()
-    ########################################################
-###############################Preparational functions###############
-#####################################################
-
-    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))}
-}
-
-
-    
-    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.
-         ##From now changespecline is in the forarcheologist file, because its no longer needed
-        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)
-    }
     
 #############################################################
 ############################spinup run############################

RBBGCMuso/R/changeMuso.R

@@ -0,0 +1,23 @@
+
+#' This is the function which is capable change multiple specific lines to other using their row numbers.
+#'
+#' he function uses the previous changspecline function to operate.
+         ##From now changespecline is in the forarcheologist file, because its no longer needed
+#' 
+#' @author Roland Hollos
+#' @keywords internal
+
+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.
+         ##From now changespecline is in the forarcheologist file, because its no longer needed
+        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)
+    }

RBBGCMuso/R/musoTime.R

@@ -4,12 +4,8 @@
 #'
 #'@param year a year
 #'@usage isLeapyear(year)
-#'@examples
-#' isLeapyear(2004)
-#' isLeapyear(2000)
-#' isLeapyear(2100)
 #'@return TRUE, if leapyear, FALSE if dont.
-
+#' @keywords internal
 isLeapyear <- function(year){
     ##This Boolean function tells us whether the given year is leapyear or not
 
@@ -27,12 +23,8 @@ isLeapyear <- function(year){
 #'@param year a year
 #'@param corrigated Do you want to handle the leapyears, if yes choose TRUE
 #'@usage dayOfMonths(year, corrigated=TRUE)
-#'@examples
-#' dayOfMonths(2004, corrigated=TRUE)
-#' 
-#' dayOfMonths(2004, corrigated=FALSE)
-#'
 #'@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
+#' @keywords internal
 
 
 
@@ -53,6 +45,12 @@ dayOfMonths <- function(year,corrigated=TRUE){
 
 
 
+#' This function tells us how many days are in the given year.
+#' 
+#' This function tells us how many days are in the given year.
+#' @author Roland Hollos
+#' @keywords internal
+
 dayOfYears <- function(year, corrigated=TRUE){
     ##This function tells us how many days are in the given year.
 
@@ -68,6 +66,12 @@ dayOfYears <- function(year, corrigated=TRUE){
 
 }
 
+#' How many days are from the given date and given period length(periodlen)? 
+#' 
+#'How many days are from the given date and given period length(periodlen)? 
+#' @author Roland Hollos
+#' @keywords internal
+
 sumDaysOfPeriod <- function(year, periodlen, corrigated=TRUE){
     ##How many days are from the given date and given period length(periodlen)?    
 
@@ -85,6 +89,12 @@ sumDaysOfPeriod <- function(year, periodlen, corrigated=TRUE){
     }
 }
 
+#' Musoleapyear
+#' 
+#' How many days are from the given date and given period length(periodlen)? 
+#' @author Roland Hollos
+#' @keywords internal
+
 musoLeapYears <- function(settings){
     days <- 365*settings$numyears
     years <- settings$startyear:(settings$startyear+settings$numyears-1)
@@ -92,6 +102,19 @@ musoLeapYears <- function(settings){
     return(Leapyears)
 }
 
+#' It generates BiomeBGC-MuSo dates
+#' 
+#' It generates all of the day-dates which are between the start and endyear of BiomeBGC-MuSo run.
+#' How many days are from the given date and given period length(periodlen)? 
+#' @author Roland Hollos
+#' @param timestep timestep, which can be daily ("d"), monthly ("m"), yearly("y") 
+#' @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.
+#' @param combined If FALSE the output is a vector of 3 string: day, month year, if true, these strings will be concatenated.
+#' @param corrigated If True it counts with leapyears, else dont. 
+#' @param format This is the format of the date. It can be "en" (dd.mm.yyyy), or "hu" (yyyy.mm.dd)
+#' @return The exact date-vectors for the BioBGC-MuSo output. You can use this for labelling purpose for example. 
+#' @export
+
 musoDate <- function(settings,timestep="d",combined=TRUE, corrigated=TRUE, format="en"){
     ##purpose: generate date label for muso
 
@@ -122,7 +145,7 @@ musoDate <- function(settings,timestep="d",combined=TRUE, corrigated=TRUE, forma
         if(format=="hu"){
          dates<-dates[,c(3,2,1)]   
         } else {
-            cat("format is coerced to english, because I don't know",format)
+            cat("format is coerced to english, because I don't know what do you mean by:",format)
         }
     }
 

RBBGCMuso/R/otherUsefullFunctions.R

@@ -1,9 +1,10 @@
 #' getyearlycum
 #'
 #' Funtion for getting cumulative yearly data from observations
-#' @author Roland Hollós
-#' @param A vector of the daily observations.
+#' @author Roland Hollos
+#' @param daily_observations vector of the daily observations.
 #' @return A vector of yearly data
+#' @export
 
 
 getyearlycum<-function(daily_observations){
@@ -22,10 +23,11 @@ getyearlycum<-function(daily_observations){
 #' getyearlymax
 #'
 #' Function for getting the maximum values of the years, from daily data
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param daily_observations vector of the daily observations
 #' @return A vector of yearly data
 #' @usage getyearlymax(daily_observations)
+#' @export
 
 getyearlymax<-function(daily_observations){
   number_of_years<-length(daily_observations)/365
@@ -43,36 +45,34 @@ getyearlymax<-function(daily_observations){
 #' fextension
 #'
 #' A function for extracting the extension name from the filename string
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param filename The string of the filenam
 #' @return the extension of the given file
 #' @usage fextension(filename)
-#' @example
-#' fextension(filename="file.csv")
 
 fextension <- function(filename){
     #this function gives back the given filenames extension
     fextension <- tail(unlist(strsplit(filename,"\\.")),1)
+    return(fextension)
 }
 
 #'supportedMuso
 #'
 #' A function for getting the list of the output formats which is supported by RBBGCMuso
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param type "outputs" or "message", if you choose "outputs", it gives you a simple vector of the formats, if you choose "message", it gives you a full sentence which contains the same information. 
 #' @return if you choose "outputs", it gives you a simple vector of the formats, if you choose "message", it gives you a full sentence which contains the same information.
 #' @usage supportedMuso(type="outputs")
-#' @example
-#'  supportedMuso(type="outputs")
+#' @export
 
 supportedMuso <- function(type="outputs"){
     supportedFormats <- c("xls","xlsx","odt","csv","txt")
     
-    if(x=="outputs"){
+    if(type=="outputs"){
         #If you add new format supports, please expand the lists
         return(supportedFormats)
     }
-    if(x=="message"){
+    if(type=="message"){
         return(cat("Supported formats are ",supportedFormats,"If your fileformat is something else, we automaticle coerced it to csv.\n"))
     }
 }
@@ -80,10 +80,11 @@ supportedMuso <- function(type="outputs"){
 #' corrigMuso
 #'
 #' This function leapyear-corrigate the output of the modell
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param settings This is the output of the setupMuso() function. It contains all of the RBBGCMuso settings
 #' @param data the models outputdata
 #' @return It returns the modells leapyear-corrigated output data.
+#' @export
 #' @usage corrigMuso(settings, data)
 
 corrigMuso <- function(settings, data){

RBBGCMuso/R/plotMuso.R

@@ -2,7 +2,7 @@
 #'
 #' This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way, and after that plot the results automaticly 
 #' 
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param settings You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment
 #' @param timee The required timesteps in the modell output. It can be "d", if it is daily, "m", if it's monthly, "y", it it is yearly
 #' @param debugging If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles
@@ -11,31 +11,34 @@
 #' @param silent If you set it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.
 #' @param aggressive It deletes every possible modell-outputs from the previous modell runs.
 #' @param variable column number of the variable which should be plottedor "all" if you have less than 10 variables. In this case it will plot everything in a matrix layout 
-#' @param leapyear Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled. 
+#' @param leapYear Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.
+#' @param logfilename If you want to set a specific name for your logfiles you can set this via logfile parameter
 #' @return It depends on the export parameter. The function returns with a matrix with the modell output, or writes this in a file, which is given previously
-#' @usage rungetMuso(settings, timee="d", debugging=FALSE, logfilename=NULL,
-#' keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+#' @usage plotMuso(settings, variable,
+#' timee="d", silent=TRUE,
+#' debugging=FALSE, keepEpc=FALSE,
+#' logfilename=NULL, aggressive=FALSE,
+#' leapYear=FALSE, export=FALSE)
+#' @import graphics
 #' @export
 
 plotMuso <- function(settings,
                      variable,
                      ##compare,
                      ##plotname,
-                     parameters="ECOPHYS",
                      timee="d",
                      silent=TRUE,
                      debugging=FALSE,
                      keepEpc=FALSE,
                      logfilename=NULL,
                      aggressive=FALSE,
-                     leapyear=FALSE,
+                     leapYear=FALSE,
                      export=FALSE){
 
     
     musoData <- rungetMuso(settings=settings,
                            silent=silent,
                            timee=timee,
-                           parameters=parameters,
                            debugging=debugging,
                            keepEpc=keepEpc,
                            logfilename=logfilename,

RBBGCMuso/R/rungetMuso.R

@@ -2,7 +2,7 @@
 #'
 #' This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way.
 #' 
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param settings You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment
 #' @param timee The required timesteps in the modell output. It can be "d", if it is daily, "m", if it's monthly, "y", it it is yearly
 #' @param debugging If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles
@@ -10,10 +10,12 @@
 #' @param export if it is yes or you give a filename here, it converts the output to the specific extension. For example, if you set export to "example.csv", it converts the output to "csv", if you set it to "example.xls" it converts to example.xls with the xlsx package. If it is not installed it gives back a warning message and converts it to csv.
 #' @param silent If you set it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.
 #' @param aggressive It deletes every possible modell-outputs from the previous modell runs.
-#' @param leapyear Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled. 
+#' @param leapYear Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.
+#' @param logfilename If you want to set a specific name for your logfiles you can set this via logfile parameter
 #' @return It depends on the export parameter. The function returns with a matrix with the modell output, or writes this in a file, which is given previously
 #' @usage rungetMuso(settings, timee="d", debugging=FALSE, logfilename=NULL,
 #' keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+#' @import utils
 #' @export
 
 
@@ -36,29 +38,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     epc <- settings$epcinput
     calibrationpar <- settings$calibrationpar
     whereAmI<-getwd()
-    
-    ########################################################
-###############################Preparational functions###############
-#####################################################
-
-    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))}
-}
-    
+        
 #############################################################
 ############################spinup run############################
 ########################################################## 

RBBGCMuso/R/setupMuso.R

@@ -2,7 +2,7 @@
 #'
 #' This funcion is fundamental for the BiomBGC-MuSo modell related functions like spinupMuso, normalMuso, rungetMuso, because it sets the modells environment.
 #'
-#' @author Roland Hollós
+#' @author Roland Hollos
 #' @param parallel Do you want to run multiple modell paralelly, if yes, set this variable to TRUE
 #' @param executable This parameter stores the place of the modell-executable file. In normal usage, you don't have to be set this, because a RBBgcmuso package contains allways the latest modell executable. In spite of this, if you would like to use this package for modell development or just want to use different models (for example for comparison), you will find it useful
 #' @param calibrationpar You may want to change some parameters in your epc file, before you run the modell. You have to select the appropirate modell parameters. You can refence to these with the number of the line in the epc file where the variables are. It indexes from one. You should use a vector for this, like: c(1,5,8)
@@ -21,10 +21,14 @@
 #' @param nitinput Via this parameter, you can tell the modell where are the NO2 data files. As default it reads this from the inifiles.
 #' @param ininput Via this parameter, you can tell the modell where are the ini files. As default it reads this from the inifiles.
 #' @param epcinput Via this parameter, you can tell the modell where are the epc data files. As default it reads this from the inifiles.
-#' @usage setupMuso(executable=NULL, parallel = F, calibrationpar =c(1), outputloc=NULL, inputloc=NULL,
-#' metinput=NULL, CO2input=NULL, plantinput=NULL, thininput=NULL,
-#' mowinput=NULL, grazinput=NULL, harvinput=NULL, plouginput=NULL, fertinput=NULL,
-#' irrinput=NULL, nitinput=NULL, ininput=NULL, epcinput=NULL)
+#' @usage setupMuso(executable=NULL, parallel = F, calibrationpar =c(1),
+#' outputloc=NULL, inputloc=NULL,
+#' metinput=NULL, CO2input=NULL,
+#' plantinput=NULL, thininput=NULL,
+#' mowinput=NULL, grazinput=NULL,
+#' harvinput=NULL, plouginput=NULL,
+#' fertinput=NULL, irrinput=NULL,
+#' nitinput=NULL, ininput=NULL, epcinput=NULL)
 #' @return The output is a the modell setting list wich contains the following elements:
 #' executable, calibrationpar, outputloc, outputname, inputloc, ininput, metinput, epcinput,thininput,CO2input, mowinput, grazinput, harvinput, plouginput, fertinput, irrinput, nitinput, inputfiles, numdata, startyear, numyears, outputvars
 setupMuso <- function(executable=NULL,

RBBGCMuso/R/spinupMuso.R

@@ -1,63 +1,96 @@
-spinupMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, silent=FALSE, aggressive=FALSE){
+#' Run the BBGCMuso modell only in spinup phase, and debugging. 
+#'
+#' This function runs the BBGC-MuSo model's in the spinup phase.
+#' 
+#' @author Roland Hollos
+#' @param settings You have to run the setupMuso function before spinupMuso. It is its output which contains all of the necessary system variables. It sets the whole running environment.
+#' @param debugging If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles
+#' @param keepEpc If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.
+#' @param silent If you set it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.
+#' @param aggressive It deletes every possible modell-outputs from the previous modell runs.
+#' @param parameters In the settings variable you have set the row indexes of the variables, you wish to change. In this parameter you can give an exact value for them in a vector like: c(1,2,3,4)
+#' @param logfilename If you want to set a specific name for your logfiles you can set this via logfile parameter
+#' @return No return, outputs are written to file 
+#' @usage spinupMuso(settings, parameters=NULL, debugging=FALSE,
+#' logfilename=NULL, keepEpc=FALSE, silent=FALSE, aggressive=FALSE)
+#' @export
+
+spinupMuso <- function(settings, parameters=NULL, debugging=FALSE, logfilename=NULL, keepEpc=FALSE, silent=FALSE, aggressive=FALSE){
+
+##########################################################################
+###########################Set local variables########################
+########################################################################
+    
+    Linuxp <-(Sys.info()[1]=="Linux")
     ##Copy the variables from settings
     inputloc <- settings$inputloc
+    outputloc <- settings$outputloc
     executable <- settings$executable
     ininput <- settings$ininput
     epc <- settings$epcinput
     calibrationpar <- settings$calibrationpar
+    whereAmI<-getwd()
 
-    ##Sometimes a bug occure due to logfiles and controlfiles in the input loc directory
+
+#############################################################
+############################spinup run############################
+########################################################## 
+    
+##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")
-
-        }
-        
-    }
+            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()
-    }
+        cleanupMuso(location=outputloc)}
 
     
     ##change the epc file if and only if there are given parameters
     if(!is.null(parameters)){
-        changemulline(settings, parameters)
-    }
+        changemulline(filename=epc[1], calibrationpar, parameters)}
 
     ##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
     
-    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$",list.files(inputloc))]
-    perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1))))
+
+
+    if(silent){#silenc mode
+        if(Linuxp){
+            #In this case, in linux machines
+            system(paste(executable,ininput[1],"> /dev/null",sep=" "))
+        } else {
+            #In windows machines there is a show.output.on.console option
+            system(paste(executable,ininput[1],sep=" "),show.output.on.console = FALSE)}        
+    } else {
+        system(paste(executable,ininput[1],sep=" "))}
+
+###############################################
+#############LOG SECTION#######################
+###############################################
+    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]
+    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0
+    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]
+
     dirName<-paste(inputloc,"/LOG",sep="")
     dirERROR<-paste(inputloc,"/ERROR",sep="")
     ERROR_EPC<-paste(inputloc,"/ERROR_EPC",sep="")
-
-
-
     
     if(!dir.exists(dirName)){
-        dir.create(dirName)
-    }
+        dir.create(dirName)}
 
     if(!dir.exists(dirERROR)){
-        dir.create(dirERROR)
-    }
+        dir.create(dirERROR)}
 
-    if(length(perror)>sum(perror)){
+    if(spincrash){
         errorsign <- 1
     } else {
-        errorsign <- 0
-    }
-
-
+        errorsign <- 0}
+    
     if(keepEpc){#if keepepc option tured on
         
         if(length(unique(dirname(epc)))>1){

RBBGCMuso/R/stamplog.R

@@ -0,0 +1,33 @@
+#' This function returns only the starting numbers of a string
+#' 
+#' This function returns only the starting numbers of a string
+#' @author Roland Hollos
+#' @keywords internal
+
+numcut<-function(string){
+    #This function returns only the starting numbers of a string
+    unlist(strsplit(grep("^[0-9]",string,value = TRUE),"[aAzZ-]"))[1]
+}
+
+#' numcutall
+#'
+#' apply numcut for all elements of a string vector
+#' @author Roland Hollos
+#' @keywords internal
+numcutall<-function(vector){
+    #numcall apply numcut for all elements of a string vector
+as.numeric(unlist(apply(as.matrix(vector),1,numcut)))
+}
+
+#' It gives back a stamp wich is the maximum number of the output numcall
+#'
+#' It gives back a stamp wich is the maximum number of the output numcall
+#' @author Roland Hollos
+#' @keywords internal
+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))}
+}

RBBGCMuso/man/calibMuso.Rd

@@ -4,10 +4,11 @@
 \alias{calibMuso}
 \title{calibMuso}
 \usage{
-calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL,
+keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 }
 \arguments{
-\item{settings}{You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment}
+\item{settings}{You have to run the setupMuso function before calibMuso. It is its output which contains all of the necessary system variables. It sets the whole running environment}
 
 \item{parameters}{In the settings variable you have set the row indexes of the variables, you wish to change. In this parameter you can give an exact value for them in a vector like: c(1,2,3,4)}
 
@@ -15,6 +16,8 @@ calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL
 
 \item{debugging}{If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles}
 
+\item{logfilename}{If you want to set a specific name for your logfiles you can set this via logfile parameter}
+
 \item{keepEpc}{If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.}
 
 \item{export}{if it is yes or you give a filename here, it converts the output to the specific extension. For example, if you set export to "example.csv", it converts the output to "csv", if you set it to "example.xls" it converts to example.xls with the xlsx package. If it is not installed it gives back a warning message and converts it to csv.}
@@ -23,7 +26,7 @@ calibMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL
 
 \item{aggressive}{It deletes every possible modell-outputs from the previous modell runs.}
 
-\item{leapyear}{future feature.}
+\item{leapYear}{Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.}
 }
 \value{
 No return, outputs are written to file
@@ -32,5 +35,5 @@ No return, outputs are written to file
 This function changes the epc file and after that  runs the BBGC-MuSo model and reads in its outputfile in a very structured way.
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/changemulline.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/changeMuso.R
+\name{changemulline}
+\alias{changemulline}
+\title{This is the function which is capable change multiple specific lines to other using their row numbers.}
+\usage{
+changemulline(filename, calibrationpar, contents)
+}
+\description{
+he function uses the previous changspecline function to operate.
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/corrigMuso.Rd

@@ -18,5 +18,5 @@ It returns the modells leapyear-corrigated output data.
 This function leapyear-corrigate the output of the modell
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/dayOfMonths.Rd

@@ -17,9 +17,4 @@ vector with 12 element. First is January, the last is December. All of the vecto
 \description{
 This function gives as a vector which contains the number of the days per each month
 }
-\examples{
-dayOfMonths(2004, corrigated=TRUE)
-
-dayOfMonths(2004, corrigated=FALSE)
-
-}
+\keyword{internal}

RBBGCMuso/man/dayOfYears.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/musoTime.R
+\name{dayOfYears}
+\alias{dayOfYears}
+\title{This function tells us how many days are in the given year.}
+\usage{
+dayOfYears(year, corrigated = TRUE)
+}
+\description{
+This function tells us how many days are in the given year.
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/fextension.Rd

@@ -16,5 +16,5 @@ the extension of the given file
 A function for extracting the extension name from the filename string
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/getyearlycum.Rd

@@ -7,7 +7,7 @@
 getyearlycum(daily_observations)
 }
 \arguments{
-\item{A}{vector of the daily observations.}
+\item{daily_observations}{vector of the daily observations.}
 }
 \value{
 A vector of yearly data
@@ -16,5 +16,5 @@ A vector of yearly data
 Funtion for getting cumulative yearly data from observations
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/getyearlymax.Rd

@@ -16,5 +16,5 @@ A vector of yearly data
 Function for getting the maximum values of the years, from daily data
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/isLeapyear.Rd

@@ -15,8 +15,4 @@ TRUE, if leapyear, FALSE if dont.
 \description{
 This function tells us if its argument a leapyear or not.
 }
-\examples{
-isLeapyear(2004)
-isLeapyear(2000)
-isLeapyear(2100)
-}
+\keyword{internal}

RBBGCMuso/man/musoDate.Rd

@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/musoTime.R
+\name{musoDate}
+\alias{musoDate}
+\title{It generates BiomeBGC-MuSo dates}
+\usage{
+musoDate(settings, timestep = "d", combined = TRUE, corrigated = TRUE,
+  format = "en")
+}
+\arguments{
+\item{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.}
+
+\item{timestep}{timestep, which can be daily ("d"), monthly ("m"), yearly("y")}
+
+\item{combined}{If FALSE the output is a vector of 3 string: day, month year, if true, these strings will be concatenated.}
+
+\item{corrigated}{If True it counts with leapyears, else dont.}
+
+\item{format}{This is the format of the date. It can be "en" (dd.mm.yyyy), or "hu" (yyyy.mm.dd)}
+}
+\value{
+The exact date-vectors for the BioBGC-MuSo output. You can use this for labelling purpose for example.
+}
+\description{
+It generates all of the day-dates which are between the start and endyear of BiomeBGC-MuSo run.
+How many days are from the given date and given period length(periodlen)?
+}
+\author{
+Roland Hollos
+}

RBBGCMuso/man/musoLeapYears.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/musoTime.R
+\name{musoLeapYears}
+\alias{musoLeapYears}
+\title{Musoleapyear}
+\usage{
+musoLeapYears(settings)
+}
+\description{
+How many days are from the given date and given period length(periodlen)?
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/numcut.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stamplog.R
+\name{numcut}
+\alias{numcut}
+\title{This function returns only the starting numbers of a string}
+\usage{
+numcut(string)
+}
+\description{
+This function returns only the starting numbers of a string
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/numcutall.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stamplog.R
+\name{numcutall}
+\alias{numcutall}
+\title{numcutall}
+\usage{
+numcutall(vector)
+}
+\description{
+apply numcut for all elements of a string vector
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/plotMuso.Rd

@@ -4,8 +4,11 @@
 \alias{plotMuso}
 \title{plot the BBGCMuso output}
 \usage{
-rungetMuso(settings, timee="d", debugging=FALSE, logfilename=NULL,
-keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
+plotMuso(settings, variable,
+timee="d", silent=TRUE,
+debugging=FALSE, keepEpc=FALSE,
+logfilename=NULL, aggressive=FALSE,
+leapYear=FALSE, export=FALSE)
 }
 \arguments{
 \item{settings}{You have to run the setupMuso function before rungetMuso. It is its output which contains all of the necessary system variables. It sets the whole environment}
@@ -20,9 +23,11 @@ keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 
 \item{keepEpc}{If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.}
 
+\item{logfilename}{If you want to set a specific name for your logfiles you can set this via logfile parameter}
+
 \item{aggressive}{It deletes every possible modell-outputs from the previous modell runs.}
 
-\item{leapyear}{Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.}
+\item{leapYear}{Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.}
 
 \item{export}{if it is yes or you give a filename here, it converts the output to the specific extension. For example, if you set export to "example.csv", it converts the output to "csv", if you set it to "example.xls" it converts to example.xls with the xlsx package. If it is not installed it gives back a warning message and converts it to csv.}
 }
@@ -33,5 +38,5 @@ It depends on the export parameter. The function returns with a matrix with the
 This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way, and after that plot the results automaticly
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/rungetMuso.Rd

@@ -14,6 +14,8 @@ keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 
 \item{debugging}{If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles}
 
+\item{logfilename}{If you want to set a specific name for your logfiles you can set this via logfile parameter}
+
 \item{keepEpc}{If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.}
 
 \item{export}{if it is yes or you give a filename here, it converts the output to the specific extension. For example, if you set export to "example.csv", it converts the output to "csv", if you set it to "example.xls" it converts to example.xls with the xlsx package. If it is not installed it gives back a warning message and converts it to csv.}
@@ -22,7 +24,7 @@ keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 
 \item{aggressive}{It deletes every possible modell-outputs from the previous modell runs.}
 
-\item{leapyear}{Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.}
+\item{leapYear}{Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.}
 }
 \value{
 It depends on the export parameter. The function returns with a matrix with the modell output, or writes this in a file, which is given previously
@@ -31,5 +33,5 @@ It depends on the export parameter. The function returns with a matrix with the
 This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way.
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/setupMuso.Rd

@@ -4,10 +4,14 @@
 \alias{setupMuso}
 \title{setupMuso}
 \usage{
-setupMuso(executable=NULL, parallel = F, calibrationpar =c(1), outputloc=NULL, inputloc=NULL,
-metinput=NULL, CO2input=NULL, plantinput=NULL, thininput=NULL,
-mowinput=NULL, grazinput=NULL, harvinput=NULL, plouginput=NULL, fertinput=NULL,
-irrinput=NULL, nitinput=NULL, ininput=NULL, epcinput=NULL)
+setupMuso(executable=NULL, parallel = F, calibrationpar =c(1),
+outputloc=NULL, inputloc=NULL,
+metinput=NULL, CO2input=NULL,
+plantinput=NULL, thininput=NULL,
+mowinput=NULL, grazinput=NULL,
+harvinput=NULL, plouginput=NULL,
+fertinput=NULL, irrinput=NULL,
+nitinput=NULL, ininput=NULL, epcinput=NULL)
 }
 \arguments{
 \item{executable}{This parameter stores the place of the modell-executable file. In normal usage, you don't have to be set this, because a RBBgcmuso package contains allways the latest modell executable. In spite of this, if you would like to use this package for modell development or just want to use different models (for example for comparison), you will find it useful}
@@ -54,5 +58,5 @@ executable, calibrationpar, outputloc, outputname, inputloc, ininput, metinput,
 This funcion is fundamental for the BiomBGC-MuSo modell related functions like spinupMuso, normalMuso, rungetMuso, because it sets the modells environment.
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/man/spinupMuso.Rd

@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/spinupMuso.R
+\name{spinupMuso}
+\alias{spinupMuso}
+\title{Run the BBGCMuso modell only in spinup phase, and debugging.}
+\usage{
+spinupMuso(settings, parameters=NULL, debugging=FALSE,
+logfilename=NULL, keepEpc=FALSE, silent=FALSE, aggressive=FALSE)
+}
+\arguments{
+\item{settings}{You have to run the setupMuso function before spinupMuso. It is its output which contains all of the necessary system variables. It sets the whole running environment.}
+
+\item{parameters}{In the settings variable you have set the row indexes of the variables, you wish to change. In this parameter you can give an exact value for them in a vector like: c(1,2,3,4)}
+
+\item{debugging}{If it is TRUE, it copies the log file to a Log directory to store it, if it is stamplog it contatenate a number before the logfile, which is one more than the maximum of the represented ones in the LOG directory. If it is true or stamplog it collects the "wrong" logfiles}
+
+\item{logfilename}{If you want to set a specific name for your logfiles you can set this via logfile parameter}
+
+\item{keepEpc}{If TRUE, it keeps the epc file and stamp it, after these copies it to the EPCS directory. If debugging True or false, it copies the wrong epc files to the wrong epc directory.}
+
+\item{silent}{If you set it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.}
+
+\item{aggressive}{It deletes every possible modell-outputs from the previous modell runs.}
+}
+\value{
+No return, outputs are written to file
+}
+\description{
+This function runs the BBGC-MuSo model's in the spinup phase.
+}
+\author{
+Roland Hollos
+}

RBBGCMuso/man/stamp.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stamplog.R
+\name{stamp}
+\alias{stamp}
+\title{It gives back a stamp wich is the maximum number of the output numcall}
+\usage{
+stamp(path = "./")
+}
+\description{
+It gives back a stamp wich is the maximum number of the output numcall
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/sumDaysOfPeriod.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/musoTime.R
+\name{sumDaysOfPeriod}
+\alias{sumDaysOfPeriod}
+\title{How many days are from the given date and given period length(periodlen)?}
+\usage{
+sumDaysOfPeriod(year, periodlen, corrigated = TRUE)
+}
+\description{
+How many days are from the given date and given period length(periodlen)?
+}
+\author{
+Roland Hollos
+}
+\keyword{internal}

RBBGCMuso/man/supportedMuso.Rd

@@ -16,5 +16,5 @@ if you choose "outputs", it gives you a simple vector of the formats, if you cho
 A function for getting the list of the output formats which is supported by RBBGCMuso
 }
 \author{
-Roland Hollós
+Roland Hollos
 }

RBBGCMuso/vignettes/my-vignette.Rmd

@@ -0,0 +1,58 @@
+---
+title: "Vignette Title"
+author: "Vignette Author"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format:
+
+- Never uses retina figures
+- Has a smaller default figure size
+- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style
+
+## Vignette Info
+
+Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette.
+
+## Styles
+
+The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
+
+    output: 
+      rmarkdown::html_vignette:
+        css: mystyles.css
+
+## Figures
+
+The figure sizes have been customised so that you can easily put two images side-by-side. 
+
+```{r, fig.show='hold'}
+plot(1:10)
+plot(10:1)
+```
+
+You can enable figure captions by `fig_caption: yes` in YAML:
+
+    output:
+      rmarkdown::html_vignette:
+        fig_caption: yes
+
+Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**.
+
+## More Examples
+
+You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`.
+
+```{r, echo=FALSE, results='asis'}
+knitr::kable(head(mtcars, 10))
+```
+
+Also a quote using `>`:
+
+> "He who gives up [code] safety for [code] speed deserves neither."
+([via](https://twitter.com/hadleywickham/status/504368538874703872))