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Update setupMuso.R

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Zoltán BARCZA 2019-01-23 21:54:01 +01:00 committed by GitHub
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RBBGCMuso/R/setupMuso.R
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#' setupMuso #' setupMuso
#' #'
#' This funcion is fundamental for the Biome-BGCMuSo model related functions like runMuso, spinupMuso, normalMuso, rungetMuso, as it sets the model's environment. The function reads the INI files from a given directory, analyzes them with error checking, and creates a data structure in R that contains the complete information content for the simulation. #' The setupMuso is fundamental for the Biome-BGCMuSo model related other functions like runMuso, spinupMuso, normalMuso, rungetMuso, as it sets the model's environment. The function reads the INI files from a given directory, analyzes them with error checking, and creates a data structure in R that contains the complete information content for the simulation.
#' #'
#' @author Roland Hollos #' @author Roland HOLLOS
#' @param parallel Set this variable to TRUE if you would like to implement parallel execution of the model #' @param parallel Set this variable to TRUE if you would like to implement parallel execution of the model
#' @param executable This parameter stores the location (directory) of the modell-executable file. In normal usage, you don't have to set this parameter, 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 executable This parameter stores the location (directory) of the model-executable file. In normal usage, you don't have to set this parameter, because the RBBGCMuso package always contains the latest model executable. In spite of this, if you would like to use this package for model development or just want to use different model version (for example for comparison), you will find this option 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) #' @param calibrationPar You might want to change some parameters in your EPC file before running the model. setupMuso offers possibility for this without editing the EPC file. In this situation you have to select the appropirate model parameters first. You can refer to these parameters with the number of the line in the EPC file. Indexing of lines start from one. You should use a vector for this referencing like c(1,5,8)
#' @param outputLoc Where should the modell puts its outputs. You should give a location for it via this variable, for example: outputLoc="/place/of/the/outputs/" #' @param outputLoc With this parameter the user can specify the directory for the model output. The syntax is simple, for example: outputLoc="/place/of/the/outputs/" or outputLoc="C:/my_model_directory/". Note that this output directory is specified by the user within the INI file, which means that the outputLoc parameter overrides the INI settings if specified.
#' @param inputLoc Usually it is the root directory, where you put the iniFiles for the modell #' @param inputLoc Usually it is the root (or base) directory where you store the INI files for the model. If the working directory is set by the user, this parameter can be skipped.
#' @param metInput Via metInput parameter, you can tell the modell where are the meteorological files. As default it reads this from the iniFiles. #' @param metInput Via the metInput parameter the user can specify the location of the input meteorological files. Generally this information is taken directly from the INI file. Using metInput this setting can be changed.
#' @param CO2Input Via CO2 parameter, you can tell the modell where are the CO2 data files. As default it reads this from the iniFiles. #' @param CO2Input Via CO2Input parameter the user can specify the location of the the CO2 data files. By default the package reads this information from the INI files.
#' @param plantInput Via planting parameter, you can tell the modell where are the data files, which contains the planting informations. As default it reads this from the iniFiles. #' @param plantInput Via planting parameter, you can tell the modell where are the data files, which contains the planting informations. As default it reads this from the iniFiles.
#' @param thinInput Via thining parameter, you can tell the modell where are the data files, which contains the thining informations. As default it reads this from the iniFiles. #' @param thinInput Via thining parameter, you can tell the modell where are the data files, which contains the thining informations. As default it reads this from the iniFiles.
#' @param mowInput Via mowing parameter, you can tell the modell where are the data files, which contains the mowing informations. As default it reads this from the iniFiles. #' @param mowInput Via mowing parameter, you can tell the modell where are the data files, which contains the mowing informations. As default it reads this from the iniFiles.