fixAlloc

RBBGCMuso/NAMESPACE

@@ -10,6 +10,7 @@ export(compareMuso)
 export(copyMusoExampleTo)
 export(corrigMuso)
 export(createSoilFile)
+export(fixAlloc)
 export(flatMuso)
 export(genEpc)
 export(getAnnualOutputList)
@@ -37,6 +38,7 @@ export(plotMuso)
 export(plotMusoWithData)
 export(randEpc)
 export(readObservedData)
+export(readValuesFromFile)
 export(runMuso)
 export(rungetMuso)
 export(saveAllMusoPlots)

RBBGCMuso/R/assistantFunctions.R

@@ -125,17 +125,27 @@ dynRound <- function(x,y,seqLen){
 }
 
 
-readValuesFromFile  <- function(epc, linums){
+#' readValuesFromFile  
-	epcFile <- readLines(epc)
+#' 
+#' read Muso values from file 
+#'
+#' @param  filename The name of the 
+#' @usage readValuesFromFile(filename, linums)
+#' @export 
+
+readValuesFromFile  <- function(filename, linums){
 	rows <- numeric(2)
 	values <- sapply(linums, function(x){
 	    rows[1] <- as.integer(x)
 	    rows[2] <- as.integer(round(100*x)) %% 10 + 1 
-	    epcFile <- readLines(epc)
+	    fromFile <- readLines(filename)
-	    selRow <- unlist(strsplit(epcFile[rows[1]], split= "[\t ]"))
+	    selRow <- unlist(strsplit(fromFile[rows[1]], split= "[\t ]"))
 	    selRow <- selRow[selRow!=""]
-	    return(as.numeric(selRow[rows[2]]))
+        ret <- suppressWarnings(as.numeric(selRow[rows[2]]))
-
+        if( is.na(ret) ){
+            return(selRow[rows[2]])
+        }
+	    return(ret)
 	})
 
 	return(values)

RBBGCMuso/R/calibMuso.R

@@ -33,7 +33,8 @@ calibMuso <- function(settings=setupMuso(), calibrationPar=NULL,
                       binaryPlace = "./", fileToChange = "epc",
                       skipSpinup = TRUE, modifyOriginal = FALSE, prettyOut = FALSE,
                       postProcString = NULL,
-                      doBackup=TRUE
+                      doBackup=TRUE,
+                      fixAlloc=FALSE
                       ){ #
 ########################################################################
 ###########################Set local variables and places###############
@@ -121,6 +122,9 @@ calibMuso <- function(settings=setupMuso(), calibrationPar=NULL,
                       } else {
                           NULL
                       })
+        if(fixAlloc){
+            fixAlloc(settings)
+        }
                        # fileToChange = fileToChange,)
     }
     

RBBGCMuso/R/otherUsefullFunctions.R

@@ -183,3 +183,36 @@ return(randomNorm)
 getConstMatrix <- function (filetype="epc", version = as.character(getOption("RMuso_version"))) {
     getOption("RMuso_constMatrix")[[filetype]][[version]]
 }
+
+
+#' fixAlloc 
+#' 
+#' Fix allocation parameter in the epc file
+#'
+#' @param settings the base RMuso settings variable
+#' @param type normal or spinup depending what you want to modify
+#' @usage ...
+#' @export 
+
+fixAlloc <- function(settings=NULL,type="normal"){
+    if(is.null(settings)){
+        settings <- setupMuso()
+    }
+    print("Need fix?")
+    epc_file <- settings$epcInput[type]
+    depTable <- options()$RMuso_constMatrix$epc[[as.character(options()$RMuso_version)]]
+    alloc_params<- depTable$INDEX[grep("ALLOCATION",depTable$NAME)]
+    alloc_groups <- round(100*(alloc_params - floor(alloc_params)))
+    tapply(alloc_params, alloc_groups, function(x){
+        currentValues <- readValuesFromFile(epc_file,x)
+        difference <- 1 - sum(currentValues)
+        if(difference == 0){
+            return(FALSE)
+        }
+        tomodiff <- currentValues[currentValues != 0]
+        changemulline(filePaths="c3grass_muso7.epc",
+                      contents=(tomodiff + difference/length(tomodiff)),
+                      calibrationPar=x[currentValues != 0])
+        return(TRUE)
+    })
+}

RBBGCMuso/R/parametersweep.R

@@ -18,7 +18,8 @@ paramSweep <- function(inputDir="./",
                        outputDir=NULL,
                        iterations=10,
                        outVar="daily_gpp",
-                       htmlOutName = "paramsweep.html"){
+                       htmlOutName = "paramsweep.html",
+                       fixAlloc=FALSE){
     
     if(is.null(pandoc_version())){
         stop("In order to use parameterSweep you have to have\n pandoc (1.12.3+) installed or run this function from Rstudio\n
@@ -41,13 +42,16 @@ You can download pandoc from here: 'https://pandoc.org/',\n or Rstudio from here
         varNames <- musoMapping(outVar)
         outVarIndex<-outVar
     }
+   
+    if(file.exists("parameters.csv")){
+        parameters <- read.csv("parameters.csv")
+    }
     
-    
+    if(is.null(parameters) ){
-    if(is.null(parameters)){
         parameters <- tcltk::tk_choose.files(caption = "Please select a file with the parameters and the ranges")
     }
     
-    rmdFile <- "---\ntitle: \"ParameterSweep basic\"\n---\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n```{r, echo=FALSE}\nsuppressWarnings(library(RBBGCMuso))\n```\n```{r, echo=FALSE}\nparameters <- read.csv(\"parameters.csv\")\n```\n```{r,fig.width=10, fig.height=3, echo=FALSE}\nnumPar\nfor(i in 1:numPar){\n  suppressWarnings(musoQuickEffect(calibrationPar=parameters[i,2],startVal = parameters[i,3], endVal = parameters[i,4],\nnSteps = 9,\noutVar = \"daily_gpp\",\nparName = parameters[i,1]))\n}\n```"
+    rmdFile <- sprintf("---\ntitle: \"ParameterSweep basic\"\n---\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n```{r, echo=FALSE}\nsuppressWarnings(library(RBBGCMuso))\n```\n```{r, echo=FALSE}\nparameters <- read.csv(\"parameters.csv\")\n```\n```{r,fig.width=10, fig.height=3, echo=FALSE}\nnumPar\nfor(i in 1:numPar){\n  suppressWarnings(musoQuickEffect(calibrationPar=parameters[i,2],startVal = parameters[i,3], endVal = parameters[i,4],\nnSteps = 9,\noutVar = \"daily_gpp\",\nparName = parameters[i,1],fixAlloc=%s))\n}\n```",fixAlloc)
     rmdVec <- unlist(strsplit(rmdFile,"\n"))
     rmdVec[11] <- paste0("parameters <- read.csv(\"",parameters,"\", stringsAsFactor = FALSE)")
     rmdVec[14] <- "numPar <- nrow(parameters)"

RBBGCMuso/R/quickeffect.R

@@ -15,7 +15,7 @@
 #' @importFrom tidyr separate
 #' @export
 
-musoQuickEffect <- function(settings = setupMuso(), calibrationPar = NULL,  startVal, endVal, nSteps = 1, fileToChange="epc",modifyOriginal=TRUE, outVar, parName = "parVal", yearNum=1, year=(settings$startYear + yearNum -1)){
+musoQuickEffect <- function(settings = setupMuso(), calibrationPar = NULL,  startVal, endVal, nSteps = 1, fileToChange="epc",modifyOriginal=TRUE, outVar, parName = "parVal", yearNum=1, year=(settings$startYear + yearNum -1),fixAlloc=FALSE){
 
     if(is.character(outVar)){
                       varNames <- as.data.frame(musoMappingFind(outVar))
@@ -45,7 +45,7 @@ musoQuickEffect <- function(settings = setupMuso(), calibrationPar = NULL,  star
                                         parameters = parVal,
                                         outVars = outVarIndex,
                                         silent = TRUE,
-                                        fileToChange = fileToChange), error = function(e){NULL})
+                                        fileToChange = fileToChange,fixAlloc=fixAlloc), error = function(e){NULL})
         if(is.null(calResult)){
             b <- cbind(rep(NA,365),parVal)
             rownames(b) <- musoDate(startYear = year, numYears = 1)

RBBGCMuso/man/createSoilFile.Rd

@@ -10,7 +10,7 @@ createSoilFile(
   outputFile = "recent.soi",
   method = "constant",
   apiURL,
-  template = system.file("examples/hhs/hhs.soi", package = "RBBGCMuso")
+  template = system.file("examples/hhs/hhs_MuSo7.soi", package = "RBBGCMuso")
 )
 }
 \description{

RBBGCMuso/man/fixAlloc.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/otherUsefullFunctions.R
+\name{fixAlloc}
+\alias{fixAlloc}
+\title{fixAlloc}
+\usage{
+...
+}
+\arguments{
+\item{settings}{the base RMuso settings variable}
+
+\item{type}{normal or spinup depending what you want to modify}
+}
+\description{
+Fix allocation parameter in the epc file
+}

RBBGCMuso/man/musoQuickEffect.Rd

@@ -15,7 +15,8 @@ musoQuickEffect(
   outVar,
   parName = "parVal",
   yearNum = 1,
-  year = (settings$startYear + yearNum - 1)
+  year = (settings$startYear + yearNum - 1),
+  fixAlloc = FALSE
 )
 }
 \arguments{

RBBGCMuso/man/paramSweep.Rd

@@ -10,7 +10,8 @@ paramSweep(
   outputDir = NULL,
   iterations = 10,
   outVar = "daily_gpp",
-  htmlOutName = "paramsweep.html"
+  htmlOutName = "paramsweep.html",
+  fixAlloc = FALSE
 )
 }
 \arguments{

RBBGCMuso/man/readValuesFromFile.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assistantFunctions.R
+\name{readValuesFromFile}
+\alias{readValuesFromFile}
+\title{readValuesFromFile}
+\usage{
+readValuesFromFile(filename, linums)
+}
+\arguments{
+\item{filename}{The name of the}
+}
+\description{
+read Muso values from file
+}

RBBGCMuso/man/tuneMusoUI.Rd

@@ -10,5 +10,5 @@
 \item{parameterFile}{optional, the parameter csv file}
 }
 \description{
-This is a simple parameter tuner function which works great in a flat directory systemj
+This is a simple parameter tuner function which works great in a flat directory system
 }