checkMeteoBGC

RBBGCMuso/NAMESPACE

@@ -2,6 +2,7 @@
 
 export(calibMuso)
 export(changeMusoC)
+export(checkMeteoBGC)
 export(cleanupMuso)
 export(compareMuso)
 export(copyMusoExampleTo)

RBBGCMuso/R/calibMuso.R

@@ -36,6 +36,7 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
 ########################################################################
 ###########################Set local variables and places###############
 ########################################################################
+    cat("Biome-BGC simulation started\n") # ZOLI
     if(is.null(settings)){
         settings <- setupMuso()
     }

RBBGCMuso/R/setupMuso.R

@@ -267,6 +267,7 @@ setupMuso <- function(executable=NULL,
         soilFiles <- tryCatch(sapply(iniFiles,function(x){(searchBellow(x,"SOIL_FILE"))}),error = function(e){""})
     }
     epcFiles <- tryCatch(sapply(iniFiles,function(x){(searchBellow(x,"EPC_FILE"))}),error = function(e){""}) 
+    metInput <- tryCatch(sapply(iniFiles,function(x){(searchBellow(x,"MET_INPUT"))}),error = function(e){""})
     
     settings = list(executable = executable,
                     calibrationPar = calibrationPar,
@@ -274,7 +275,7 @@ setupMuso <- function(executable=NULL,
                     outputNames=outputName,
                     inputLoc=inputLoc,
                     iniInput=iniInput,
-                    # metInput=inputs$metInput,
+                    metInput=metInput,
                     epcInput=epcFiles,
                     # thinInput=inputs$thinInput,
                     # CO2Input=inputs$CO2Input,

RBBGCMuso/man/runMuso.Rd

@@ -10,14 +10,10 @@ keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 \arguments{
 \item{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.}
 
-\item{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).}
-
 \item{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.}
 
 \item{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.}
 
-\item{logfilename}{If you would like to set a specific name for your logfiles you can set this via the logfile parameter.}
-
 \item{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.}
 
 \item{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.}
@@ -26,6 +22,10 @@ keepEpc=FALSE, export=FALSE, silent=FALSE, aggressive=FALSE, leapYear=FALSE)
 
 \item{aggressive}{It deletes all previous model-outputs from previous model runs.}
 
+\item{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).}
+
+\item{logfilename}{If you would like to set a specific name for your logfiles you can set this via the logfile parameter.}
+
 \item{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.}
 
 \item{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.}