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Zoltán BARCZA 2019-01-24 14:40:39 +01:00 committed by GitHub
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RBBGCMuso/R/normalMuso.R
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#' normalMuso
#'
#' This function changes the epc file and after that runs the BBGC-MuSo model in normal phase and reads in its outputfile in a well-structured way.
#' This function optionally changes the EPC file and runs the Biome-BGCMuSo model in normal phase and reads its output file in a well-structured way with debugging features. (Execution of spinup phase is possible with spinupMuso.)
#'
#' @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. I recommend to use daily data, the yearly and monthly data is not well-tested yet.
#' @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 ouxtput 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 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.
#' @param keepBinary In default RBBGCMuso to keep working area as clean as possible, deletes all the regular output files. The results are directly printed to the standard output, but you can redirect it, and save it to a variable, or you can export your results to the desired destination in a desired format. Whith this variable you can enable to keep the binary output files. If you want to set the location of the binary output, please take a look at the binaryPlace argument.
#' @param binaryPlace The place of the binary output files.
#' @param fileToChange You can change any line of the epc or the ini file, you just have to specify with this variable which file you van a change. Two options possible: "epc", "ini"
#' @return The simunation output matrix, where the columns are the choosen variables and each row is a day/month/year data.
#' @author Roland HOLLOS
#' @param settings You have to run the setupMuso function and then the spinupMuso function first as spinup phase created the so-called endpoint file for the normal simulation (endpoint=initial conditions). settings parameter contains the environment variables of the simulation as created by setupMuso.
#' @param timee The required timesteps in the model output. It can be "d", if it is daily, "m", if it is monthly, "y" if it is yearly. It is recommended to use daily data, as the yearly and monthly data is not well-tested yet.
#' @param debugging If debugging is set to TRUE, after model execution the function copies the Biome-BGCMuSo log file into a LOG directory to stores it for further processing. If debugging is set to STAMPLOG instead of TRUE, it concatenates a number before the logfile, which is one plus the maximum of those present in the LOG directory. In each case the log files will be saved.
#' @param keepEpc If keepEpc is set to TRUE, the function keeps the EPC file and stamps it, and then copies it to the EPCS directory. If debugging is set to TRUE, it copies the wrong EPC files to the wrong epc directory.
#' @param export If it is set to yes or you define a filename here, the function converts the output to the specific file format. For example, if you set export to "example.csv", it converts the output to "csv". If you set it to "example.xls" it converts the output to example.xls with the xlsx package. If the Excel converter package is not installed it gives back a warning message and converts the results to csv.
#' @param silent If you set the silent parameter to TRUE, all of the model's output normally written to the screen will be suppressed. This option can be useful to increase the speed of the model execution.
#' @param aggressive It deletes all previous model-outputs from previous model runs.
#' @param parameters Using normalMuso it is possible to change some of the EPC parameters prior to model execution. This can be achieved with this option. In the parameters variable you have set the row indices of the variables that you wish to change. In this parameters you can give an exact value for them in a vector form like c(1,2,3,4)
#' @param logfilename If you would like to set a specific name for your logfiles you can set this via the logfile parameter.
#' @param leapYear Should the function do a leapyear correction on the outputdata? If TRUE, then the 31.12 day will be doubled.
#' @param keepBinary By default RBBGCMuso keeps the working environment as clean as possible, thus deletes all the regular output files. The results are directly written to the standard output (e.g. to the screen), but you can redirect it and save them to a variable. Alternatively, you can export your results to the desired destination in a desired format. Through the keepBinary parameter you can set RBBGCMuso to keep the binary output files. If you would like to set the location of the binary output, please take a look at the binaryPlace argument.
#' @param binaryPlace The place of the binary output files (see the keepBinary parameter).
#' @param fileToChange You can change any line of the EPC or the INI file prior to model execution. All you need to do is to specify with this variable which file you want to change. Two options possible: "EPC" or "INI"
#' @return The simulation output matrix, where the columns are the chosen variables and each row is a daily/monthly/annual data.
#' @usage normalMuso(settings,parameters=NULL, timee="d", debugging=FALSE, logfilename=NULL,
#' keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
#' @import utils