plot optimized muso

RBBGCMuso/R/calibration.R

@@ -44,6 +44,7 @@ optiMuso <- function(measuredData, parameters = NULL, startDate,
 		     modelVar = 3009,
                      postProcString = NULL)
 {
+    mdata <- measuredData
     dataCol <- grep(dataVar, colnames(measuredData))
 
     if(is.null(parameters)){
@@ -104,6 +105,7 @@ optiMuso <- function(measuredData, parameters = NULL, startDate,
     randValues <- randVals[[2]]
     settings$calibrationPar <- randVals[[1]]
     list2env(alignData(measuredData,dataCol = dataCol,modellSettings = settings,startDate = startDate,endDate = endDate,leapYear = leapYearHandling, continious = continious),envir=environment())
+    ## modIndex and measuredData are created.  
 
     modellOut <- numeric(iterations + 1) # single variable solution
     rmse <- numeric(iterations + 1)
@@ -149,12 +151,21 @@ optiMuso <- function(measuredData, parameters = NULL, startDate,
     preservedCalib <- preservedCalib[-1,]
     dontInclude <-c((ncol(preservedCalib)-1),ncol(preservedCalib))
     for(i in seq_along(colnames(preservedCalib)[-dontInclude])){
-        p[[i]] <- ggplot(as.data.frame(preservedCalib),aes_string(colnames(preservedCalib)[i],"likelihood"))+geom_point(shape='.',size=1,alpha=0.8)
+        p[[i]] <- ggplot(as.data.frame(preservedCalib),aes_string(colnames(preservedCalib)[i],"likelihood")) +
+            geom_point(shape='.',size=1,alpha=0.8)
     }
 
-    ggsave(plotName,grid.arrange(grobs = p, ncol = floor(sqrt(ncol(preservedCalib)-1))),dpi = 3000)
+    ggsave(plotName,grid.arrange(grobs = p, ncol = floor(sqrt(ncol(preservedCalib)-1))),dpi = 300)
+    maxLikelihoodPlace  <- which(preservedCalib[,"likelihood"]==max(preservedCalib[,"likelihood"],na.rm = TRUE))
+    resPlot <- plotMusoWithData(mdata = mdata, startDate = startDate, endDate = endDate,
+                                dataVar = dataVar, modelVar = modelVar, settings = settings, continious = continious) +
+        plotMuso(settings = settings, parameters = randValues[maxLikelihoodPlace,],
+                 postProcString = postProcString, skipSpinup = FALSE, variable = colNumb, layerPlot = TRUE, colour = "green")
 
-    return(preservedCalib[preservedCalib[,"likelihood"]==max(preservedCalib[,"likelihood"],na.rm = TRUE),])
+    print(resPlot)
+    tempEpc <- paste0(tools::file_path_sans_ext(basename(settings$epcInput[2])),"-tmp.",tools::file_ext(settings$epcInput[2]))
+    file.rename(tempEpc, "optimizedEpc.epc")
+    return(preservedCalib[maxLikelihoodPlace,])
 }
 
 

RBBGCMuso/R/musoTime.R

@@ -59,17 +59,22 @@ musoDate <- function(startYear, endYears = NULL, numYears, combined = TRUE, leap
 #' This function align the data to the model and the model to the data
 #' @importFrom lubridate leap_year
 #' @keywords internal
-alignData  <- function(mdata, dataCol, modellSettings = NULL, startDate=NULL, endDate=NULL, formatString = "%Y-%m-%d", leapYear = TRUE, continious = TRUE){
+alignData  <- function(mdata, dataCol, modellSettings = NULL, startDate=NULL, endDate=NULL, formatString = "%Y-%m-%d", leapYear = TRUE, continious = FALSE){
 
-    
+    if(continious){
-    startDate <- as.Date(startDate, format = formatString)
+        if((is.null(startDate) | is.null(endDate))){
-    endDate <- as.Date(endDate, format = formatString)
+            stop("If your date is continuous, you have to provide both startDate and endDate. ")
-    mdata <- as.data.frame(mdata)
+        }
+        startDate <- as.Date(startDate, format = formatString)
+        endDate <- as.Date(endDate, format = formatString)
+    }
 
     if(is.null(modellSettings)){
         modellSettings <- setupMuso()
     }
 
+    mdata <- as.data.frame(mdata)
+
     if(continious){
         dates <- seq(startDate, to = endDate, by= "day")
     } else{

RBBGCMuso/R/plotMuso.R

@@ -251,8 +251,12 @@ plotMuso <- function(settings = NULL, variable = 1,
 #' @importFrom ggplot2 ggplot geom_line geom_point aes aes_string labs theme element_blank 
 #' @export
 plotMusoWithData <- function(mdata, plotName=NULL,
-                             startDate, endDate,
+                             startDate = NULL, endDate = NULL,
-                             colour=c("black","blue"),dataVar, modelVar, settings = setupMuso(), silent = TRUE, continious = TRUE){
+                             colour=c("black","blue"), dataVar, modelVar, settings = setupMuso(), silent = TRUE, continious = FALSE){
+
+    if(continious  & (is.null(startDate) | is.null(endDate))){
+        stop("If your date is continuous, you have to provide both startDate and endDate. ")
+    }
 
     dataCol<- grep(paste0("^",dataVar,"$"), colnames(mdata))
     selVar <- grep(modelVar,(settings$dailyVarCodes))+4
@@ -261,21 +265,33 @@ plotMusoWithData <- function(mdata, plotName=NULL,
                        modellSettings = settings,
                        startDate = startDate,
                        endDate = endDate, leapYear = FALSE, continious = continious),envir=environment())
-    
+    mesData <- numeric(settings$numYears*365)
-    
+    k <- 1
+    for(i in seq(mesData)){
+        if(i %in% modIndex){
+            mesData[i] <- measuredData[k]
+            k <- k + 1
+        } else {
+            mesData[i] <- NA
+        }
+    }
+    rm(k)
+    # modIndex and measuredData are created.
     ## measuredData is created
-    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
+    ## baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
+    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)
     baseData[,1] <- as.Date(baseData[,1],format = "%d.%m.%Y")
     selVarName <- colnames(baseData)[selVar]
     if(!all.equal(colnames(baseData),unique(colnames(baseData)))){
         notUnique <- setdiff((unlist(settings$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)
+    colnames(mesData) <- c("date", "measured")
     p <- baseData  %>%
         ggplot(aes_string("date",selVarName)) +
         geom_line(colour=colour[1]) +
-        geom_point(colour=colour[2], aes(date,measuredData)) +
+        geom_point(data = mesData, colour=colour[2], aes(date,measured)) +
         labs(y = paste0(selVarName,"_measured"))+
         theme(axis.title.x = element_blank())
     if(!is.null(plotName)){