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add randomization feature to sensitivity and calibration with musoMonte

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This commit is contained in:
Roland Hollós 2023-06-19 10:09:54 +02:00
parent 216f2109fe
commit b9e829951e
3 changed files with 14 additions and 2 deletions
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11
RBBGCMuso/R/calibrateMuso.R
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@ -12,6 +12,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s
skipSpinup = TRUE, plotName = "calib.jpg", skipSpinup = TRUE, plotName = "calib.jpg",
modifyOriginal=TRUE, likelihood, uncertainity = NULL, modifyOriginal=TRUE, likelihood, uncertainity = NULL,
naVal = NULL, postProcString = NULL, naVal = NULL, postProcString = NULL,
sourceFile=NULL, # bases for musoRand if dependecy group is not fully defined by parameters.csv
thread_prefix="thread", numCores = max(c(parallel::detectCores()-1,1)), pb = txtProgressBar(min=0, max=iterations, style=3), thread_prefix="thread", numCores = max(c(parallel::detectCores()-1,1)), pb = txtProgressBar(min=0, max=iterations, style=3),
maxLikelihoodEpc=TRUE, maxLikelihoodEpc=TRUE,
pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){
@ -127,6 +128,14 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s
switch(method, switch(method,
"GLUE"={ "GLUE"={
musoGlue(results, parameters=parameters,settings=settings, w=w, lg=lg) musoGlue(results, parameters=parameters,settings=settings, w=w, lg=lg)
liks <- results[,sprintf("%s_likelihood",names(likelihood))]
epcIndexes <- future::value(fut[[1]], stdout = FALSE, signal=FALSE)
epcVals <- results[which.max(liks),1:length(epcIndexes)]
epcPlace <- file.path(dirname(settings$inputFiles),settings$epc)[2]
changemulline(filePaths= epcPlace, epcIndexes,
epcVals, src =epcPlace,# settings$epcInput[2],
outFiles = file.path(outputLoc, "maxLikelihood_epc.epc"))
names(epcVals) <- epcIndexes
}, },
"agromo"={ "agromo"={
liks <- results[,sprintf("%s_likelihood",names(likelihood))] liks <- results[,sprintf("%s_likelihood",names(likelihood))]
@ -234,7 +243,7 @@ musoSingleThread <- function(measuredData, parameters = NULL, startDate = NULL,
## row numbers ## row numbers
print("optiMuso is randomizing the epc parameters now...",quote = FALSE) print("optiMuso is randomizing the epc parameters now...",quote = FALSE)
if(iterations < 3000){ if(iterations < 3000){
randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = 3000) randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = 3000,sourceFile=sourceFile)
randVals[[2]]<- randVals[[2]][sample(1:3000,iterations),] randVals[[2]]<- randVals[[2]][sample(1:3000,iterations),]
} else { } else {
randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = iterations) randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = iterations)

3
RBBGCMuso/R/musoMonte.R
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@ -18,6 +18,7 @@
musoMonte <- function(settings=NULL, musoMonte <- function(settings=NULL,
parameters=NULL, parameters=NULL,
sourceFile=NULL,
inputDir = "./", inputDir = "./",
outLoc = "./calib", outLoc = "./calib",
iterations = 10, iterations = 10,
@ -100,7 +101,7 @@ musoMonte <- function(settings=NULL,
##reading the original epc file at the specified ##reading the original epc file at the specified
## row numbers ## row numbers
if(iterations < 3000){ if(iterations < 3000){
randVals <- musoRand(parameters = parameters,fileType="epc", iterations = 3000) randVals <- musoRand(parameters = parameters,fileType="epc", iterations = 3000,sourceFile=sourceFile)
randVals[[2]]<- randVals[[2]][sample(1:3000,iterations),] randVals[[2]]<- randVals[[2]][sample(1:3000,iterations),]
} else { } else {
randVals <- musoRand(parameters = parameters,fileType="epc", iterations = iterations) randVals <- musoRand(parameters = parameters,fileType="epc", iterations = iterations)

2
RBBGCMuso/R/musoSensi.R
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@ -31,6 +31,7 @@ musoSensi <- function(monteCarloFile = NULL,
plotTitle = "Sensitivity", plotTitle = "Sensitivity",
skipSpinup = TRUE, skipSpinup = TRUE,
skipZero = TRUE, skipZero = TRUE,
sourceFile=NULL,
postProcString=NULL, postProcString=NULL,
modifyOut=TRUE, modifyOut=TRUE,
dpi=300){ dpi=300){
@ -87,6 +88,7 @@ musoSensi <- function(monteCarloFile = NULL,
if(is.null(monteCarloFile)){ if(is.null(monteCarloFile)){
M <- musoMonte(parameters = parameters, M <- musoMonte(parameters = parameters,
settings = settings, settings = settings,
sourceFile=NULL,
inputDir = inputDir, inputDir = inputDir,
outLoc = outLoc, outLoc = outLoc,
iterations = iterations, iterations = iterations,