Update plotMuso.R

RBBGCMuso/R/plotMuso.R

@@ -1,21 +1,21 @@
-#'plot the BBGCMuso output 
+#'plot the Biome-BGCMuSo output 
 #'
 #' This function runs the Biome-BGCMuSo model and reads its output file in a well structured way, and after that it plots the results automatically. plotMuso is a convenient and quick method to create nice graphs from Biome-BGCMuSo output which is quite painful in other environments. 
 #' 
 #' @author Roland HOLLOS, Dora HIDY
 #' @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 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 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 debugging If debugging is set to TRUE, after model execution the function copies the Biome-BGCMuSo log file into a LOG directory and 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 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 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 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 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 it TRUE all off the modells output to the screen will be suppressed. It can be usefull, because it increases the model-speed.
+#' @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 every possible modell-outputs from the previous modell runs.
+#' @param aggressive It deletes all previous model-outputs from previous model 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 variable Column number of the output variable which should be plotted, or "all" if you have less than 10 variables. In this case the function 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 output data? If TRUE, then the result for 31 December will be doubled in leap years which means that the results for the leap year will cover all 366 days. See the model's User's Guide for notes on leap years. 
-#' @param logfilename If you want to set a specific name for your logfiles you can set this via logfile parameter
+#' @param logfilename If you would like to set a specific name for your logfiles you can set this via the logfile parameter.
-#' @param plotType There are two options now: continious time series("cts")  or disctrete time series("dts")
+#' @param plotType There are two options implemented by now: continuous time series ("cts") or disctrete time series ("dts")
-#' @param skipSpinup If TRUE, calibMuso wont do spinup simulation
+#' @param skipSpinup If TRUE, the function won't perform the spinup simulation. In this case the endpoint file must exist that provides initial conditions for the run. 
-#' @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
+#' @return It depends on the export parameter. The function returns with a matrix with the model output, or writes this into a file, which is defined previously
 #' @usage plotMuso(settings, variable,
 #' timee="d", silent=TRUE,
 #' debugging=FALSE, keepEpc=FALSE,