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Update runMuso.R

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Zoltán BARCZA 2019-01-24 15:04:13 +01:00 committed by GitHub
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RBBGCMuso/R/runMuso.R
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#' runMuso
#'
#' This function changes the epc file and after that runs the BBGC-MuSo model and reads in its outputfile in a well-structured way.
#' This function runs the Biome-BGCMuSo model (with option to change the EPC file), then it reads its output file in a well-structured way. As the result is passed to R, the results can be easily post-processed in R environment.
#'
#' @author Roland Holl\'{o}s
#' @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
#' @author Roland HOLL\'{O}S
#' @param settings RBBGCMuso uses variables that define the entire simulation environment. Those environment variables include the name of the INI files, the name of the meteorology files, the path to the model executable and its file name, the entire output list, the entire output variable matrix, the dependency rules for the EPC parameters etc. Using the runMuso function RBBGCMuso can automatically create those environment variables by inspecting the files in the working directory (this happens through the setupMuso function). It means that by default model setup is performed automatically in the background and the user has nothing to do. With this settings parameter we can force runMuso to skip automatic environment setup as we provide the environment settings to runMuso. In a typical situation the user can skip this option.
#' @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.