diff --git a/.Rhistory b/.Rhistory index 5bee821..3009bb5 100644 --- a/.Rhistory +++ b/.Rhistory @@ -3,3 +3,4 @@ install.packages("RBBGCMuso_0.1.8.tar.gz") install.packages("RBBGCMuso_0.1.8.tar.gz") install.packages("RBBGCMuso_0.1.8.tar.gz") install.packages("RBBGCMuso_0.1.8.tar.gz") +install.packages("RBBGCMuso_0.2.0.0-1.tar.gz") diff --git a/RBBGCMuso/DESCRIPTION b/RBBGCMuso/DESCRIPTION index 1bd6ed1..4ca8b2c 100644 --- a/RBBGCMuso/DESCRIPTION +++ b/RBBGCMuso/DESCRIPTION @@ -9,3 +9,4 @@ NeedsCompilation: no Packaged: 2016-11-15 13:58:04 UTC; hollorol Author: First Last [aut, cre] Maintainer: First Last +RoxygenNote: 6.0.1 diff --git a/RBBGCMuso/R/rungetMuso.R b/RBBGCMuso/R/rungetMuso.R index 8923ecf..029e0d8 100644 --- a/RBBGCMuso/R/rungetMuso.R +++ b/RBBGCMuso/R/rungetMuso.R @@ -1,13 +1,22 @@ -#' This runs the BBGC-MuSo model +#' This function runs the BBGC-MuSo model and reads in its outputfile in a very structured way. +#' #' @author Roland Hollós -#' @param filename Name of the initialisation files +#' @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 +#' @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. #' @return No return, outputs are written to file #' @usage The function works only, if ... +#' @export + -Linuxp <-(Sys.info()[1]=="Linux") rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE){ - +Linuxp <-(Sys.info()[1]=="Linux") ############################################################# ############################spinup run############################ ########################################################## @@ -235,3 +244,6 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k setwd(whereAmI) return(Reva)} } + + + diff --git a/RBBGCMuso/RBBGCMuso.Rproj b/RBBGCMuso/RBBGCMuso.Rproj index 3a76475..eaa6b81 100644 --- a/RBBGCMuso/RBBGCMuso.Rproj +++ b/RBBGCMuso/RBBGCMuso.Rproj @@ -13,4 +13,6 @@ RnwWeave: Sweave LaTeX: pdfLaTeX BuildType: Package +PackageUseDevtools: Yes PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace diff --git a/RBBGCMuso/man/#setup.Rd# b/RBBGCMuso/man/#setup.Rd# deleted file mode 100644 index 1e5e3d1..0000000 --- a/RBBGCMuso/man/#setup.Rd# +++ /dev/null @@ -1,23 +0,0 @@ -% 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 -} - diff --git a/RBBGCMuso/man/changspecline.Rd b/RBBGCMuso/man/changspecline.Rd deleted file mode 100644 index bcd5ac7..0000000 --- a/RBBGCMuso/man/changspecline.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% 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 -} - diff --git a/RBBGCMuso/man/getyearlycum.Rd b/RBBGCMuso/man/getyearlycum.Rd index 87a3168..9563d37 100644 --- a/RBBGCMuso/man/getyearlycum.Rd +++ b/RBBGCMuso/man/getyearlycum.Rd @@ -1,5 +1,5 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/other_usefull_functions.R +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/otherUsefullFunctions.R \name{getyearlycum} \alias{getyearlycum} \title{'Funtion for getting cumulative yearly data from observations} @@ -18,4 +18,3 @@ A vector of yearly data \author{ Roland Hollós } - diff --git a/RBBGCMuso/man/getyearlymax.Rd b/RBBGCMuso/man/getyearlymax.Rd index 68f01f3..17812a6 100644 --- a/RBBGCMuso/man/getyearlymax.Rd +++ b/RBBGCMuso/man/getyearlymax.Rd @@ -1,5 +1,5 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/other_usefull_functions.R +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/otherUsefullFunctions.R \name{getyearlymax} \alias{getyearlymax} \title{'Function for getting the maximum values of the years, from daily data} @@ -18,4 +18,3 @@ A vector of yearly data \author{ Roland Hollós } - diff --git a/RBBGCMuso/man/runMuso.Rd b/RBBGCMuso/man/runMuso.Rd deleted file mode 100644 index fb4c5d4..0000000 --- a/RBBGCMuso/man/runMuso.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% 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 -} - diff --git a/RBBGCMuso/man/setup.Rd b/RBBGCMuso/man/setup.Rd deleted file mode 100644 index 1e5e3d1..0000000 --- a/RBBGCMuso/man/setup.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% 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 -} - diff --git a/RBBGCMuso_0.2.0.0-1.tar.gz b/RBBGCMuso_0.2.0.0-1.tar.gz deleted file mode 100644 index 57d77eb..0000000 Binary files a/RBBGCMuso_0.2.0.0-1.tar.gz and /dev/null differ