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burnin period

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Hollos Roland 2021-04-19 15:26:45 +02:00
parent 6d77b4074b
commit 6fe00f9e29
2 changed files with 4 additions and 8 deletions
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8
RBBGCMuso/R/multiSite.R
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@ -33,6 +33,7 @@ multiSiteCalib <- function(measurements,
parameters,
dataVar,
iterations = 100,
burnin =ifelse(iterations < 3000, 3000, NULL),
likelihood,
execPath,
thread_prefix="thread",
@ -247,12 +248,7 @@ multiSiteThread <- function(measuredData, parameters = NULL, startDate = NULL,
}}
print("optiMuso is randomizing the epc parameters now...",quote = FALSE)
if(iterations < 3000){
randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = 3000)
randVals[[2]]<- randVals[[2]][sample(1:3000,iterations),]
} else {
randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = iterations)
}
randVals <- musoRand(parameters = parameters,constrains = NULL, iterations = iterations, burnin = burnin)
origEpc <- readValuesFromFile(epcFile, randVals[[1]])
partialResult <- matrix(ncol=length(randVals[[1]])+2*length(dataVar))

4
RBBGCMuso/R/musoRand.R
View File

@ -8,7 +8,7 @@
#' @importFrom limSolve xsample
#' @export
musoRand <- function(parameters, iterations=3000, fileType="epc", constrains = NULL){
musoRand <- function(parameters, iterations=3000, fileType="epc", constrains = NULL, burnin = ifelse(iterations < 3000, 3000, NULL)){
if(is.null(constrains)){
constMatrix <- constrains
constMatrix <- getOption("RMuso_constMatrix")[[fileType]][[as.character(getOption("RMuso_version"))]]
@ -176,7 +176,7 @@ musoRand <- function(parameters, iterations=3000, fileType="epc", constrains = N
E <- do.call(rbind,lapply(Ef,function(x){x$E}))
f <- do.call(c,lapply(Ef,function(x){x$f}))
# browser()
randVal <- suppressWarnings(limSolve::xsample(G=G,H=h,E=E,F=f,iter = iterations))$X
randVal <- suppressWarnings(limSolve::xsample(G=G,H=h,E=E,F=f,burninlength=burnin, jiter = iterations))$X
} else{
Gh0<-genMat0(dependences)
randVal <- suppressWarnings(xsample(G=Gh0$G,H=Gh0$h, iter = iterations))$X