genEpc, changemulline -> creation, bugfix

RBBGCMuso/DESCRIPTION

@@ -37,7 +37,7 @@ Imports:
     rpart,
     rpart.plot
 Maintainer: Roland Hollo's <hollorol@gmail.com>
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.0
 Suggests: knitr,
     rmarkdown,
 VignetteBuilder: knitr

RBBGCMuso/NAMESPACE

@@ -11,6 +11,7 @@ export(copyMusoExampleTo)
 export(corrigMuso)
 export(createSoilFile)
 export(flatMuso)
+export(genEpc)
 export(getAnnualOutputList)
 export(getConstMatrix)
 export(getDailyOutputList)

RBBGCMuso/R/calibration.R

@@ -273,7 +273,8 @@ musoGlue <- function(presCalFile, w, delta = 0.17, settings=setupMuso(), paramet
     maxParValues <- unlist(preservedCalibtop5[which.max(preservedCalibtop5$combined),])[1:length(paramIndex)]
     maxParIndexes <- paramIndex
     maxLikelihoodParameters <- data.frame(parameter_index=maxParIndexes,parameter_value=maxParValues)
-    write.csv(cbind.data.frame(calibrationPar=maxParValues,parameters=maxParIndexes),"maxLikelihood.csv")
+    write.csv(cbind.data.frame(parameters=maxParIndexes, calibrationPar=maxParValues),
+              "maxlikelihood_parameters.csv")
     cat("\n\n- A file containing the parameters with the maximum likelihood (maxlikelihood_parameters.csv) has been created.\n")
     write.csv(optRanges,"optRanges.csv")
     cat("- GLUE interval values have been written into optRanges.csv\n")

RBBGCMuso/R/changeMuso.R

@@ -5,7 +5,7 @@
 #' @author Roland Hollos
 #' @export
 
-changemulline <- function(filePaths, calibrationPar, contents, src, outFiles=filePaths){
+changemulline <- function(filePaths, calibrationPar, contents, src=NULL, outFiles=filePaths){
     # browser()
     if(is.null(src)){
         src <- filePaths

RBBGCMuso/R/genEpc.R

@@ -33,3 +33,18 @@ randEpc <- function(parameterFile = "parameters.csv", location = "./epcDir",
     }
    setwd(currDir)
 }
+
+#' genEpc
+#'
+#' randEpc is a random epc creator based on musoMonte
+#' @author Roland HOLLOS
+#' @param sourceEpc the original epc file-the template
+#' @param parameters dataframe where in the first column there are the indices and the second column the values
+#' @param location output location directory
+#' @export
+
+genEpc <- function (sourceEpc, targetEpc, parameters) {
+   changemulline(filePaths=sourceEpc,outFiles=targetEpc,
+                 calibrationPar=parameters[,1],contents=parameters[,2]) 
+}
+

RBBGCMuso/R/plotMuso.R

@@ -275,28 +275,29 @@ plotMusoWithData <- function(mdata, plotName=NULL,
                        modellSettings = settings,
                        startDate = startDate,
                        endDate = endDate, leapYear = leapYearHandling, continious = continious),envir=environment())
-    mesData <- numeric(settings$numYears*365)
-    k <- 1
-    for(i in seq(mesData)){
-        if(i %in% modIndex){
-            mesData[i] <- measuredData[k]
-            k <- k + 1
-        } else {
-            mesData[i] <- NA
-        }
-    }
-    rm(k)
+    # mesData <- numeric(settings$numYears*365)
+    # k <- 1
+    # for(i in seq(mesData)){
+    #     if(i %in% modIndex){
+    #         mesData[i] <- measuredData[k]
+    #         k <- k + 1
+    #     } else {
+    #         mesData[i] <- NA
+    #     }
+    # }
+    # rm(k)
     # modIndex and measuredData are created.
     ## measuredData is created
     ## baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
-    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)
+    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
     baseData[,1] <- as.Date(baseData[,1],format = "%d.%m.%Y")
     selVarName <- colnames(baseData)[selVar]
     if(!all.equal(colnames(baseData),unique(colnames(baseData)))){
         notUnique <- setdiff((unlist(settings$dailyVarCodes)),unique(unlist(settings$dailyVarCodes)))
         stop(paste0("Error: daily output variable list in the ini file must contain unique numbers. Check your ini files! Not unique codes: ",notUnique))
     }
-    mesData<-cbind.data.frame(baseData[,1],mesData)
+    # mesData<-cbind.data.frame(baseData[,1],mesData)
+    mesData<-cbind.data.frame(baseData[,1],measuredData)
     colnames(mesData) <- c("date", "measured")
     p <- baseData  %>%
         ggplot(aes_string("date",selVarName)) +

RBBGCMuso/man/calibrateMuso.Rd

@@ -24,7 +24,7 @@ calibrateMuso(
   naVal = NULL,
   postProcString = NULL,
   thread_prefix = "thread",
-  numCores = (parallel::detectCores() - 1),
+  numCores = max(c(parallel::detectCores() - 1, 1)),
   pb = txtProgressBar(min = 0, max = iterations, style = 3),
   maxLikelihoodEpc = TRUE,
   pbUpdate = setTxtProgressBar,

RBBGCMuso/man/changemulline.Rd

@@ -4,7 +4,13 @@
 \alias{changemulline}
 \title{changemulline}
 \usage{
-changemulline(filePaths, calibrationPar, contents, src, outFiles = filePaths)
+changemulline(
+  filePaths,
+  calibrationPar,
+  contents,
+  src = NULL,
+  outFiles = filePaths
+)
 }
 \description{
 The function uses the previous changspecline function to operate.

RBBGCMuso/man/readObservedData.Rd

@@ -11,7 +11,9 @@ readObservedData(
   leapYearHandling = TRUE,
   convert.var = NULL,
   convert.scalar = 1,
-  convert.fun = (function(x) {     x * convert.scalar }),
+  convert.fun = (function(x) {
+     x * convert.scalar
+ }),
   convert.file = NULL,
   filterCol = NULL,
   filterVal = 1,