Updated helper function for the functions whose name starts with mcmc.

BayesianTools/R/mcmcDREAM_helperFunctions.R

@@ -1,75 +1,73 @@
-
-
-##' Generates matrix of CR values based on pCR
-##' @param pCR Vector of crossover probabilities. Needs to be of length nCR.
-##' @param settings settings list
-##' @param Npop number of chains
-##' @return Matrix with CR values
-#' @keywords internal
-generateCRvalues <- function(pCR,settings, Npop){
-
- # Random vector, add zero to get first position 
- RandomVec <- c(0,cumsum(as.numeric(rmultinom(1, size = Npop*settings$updateInterval, prob = pCR))))
-
- # get candidate points
- cand <- sample(Npop*settings$updateInterval)
- CR <- rep(NA, Npop*settings$updateInterval)
-
- ## Now loop over chains to generate CR values
- for(i in 1:settings$nCR){
- #Start and End
- Start <- RandomVec[i]+1
- End <- RandomVec[i+1]
-
- # get candidates
- candx <- cand[Start:End]
-
- # Assign these indices settings$CR
- CR[candx] <- i/settings$nCR
- }
- ## Reshape CR
- CR <- matrix(CR,Npop,settings$updateInterval)
-
- return(CR)
-} 
-
-
-
-
-#' Adapts pCR values
-#' @param CR Vector of crossover probabilities. Needs to be of length nCR.
-#' @param settings settings list
-#' @param delta vector with differences
-#' @param lCR values to weight delta
-#' @param Npop number of chains.
-#' @return Matrix with CR values
-#' @keywords internal
-AdaptpCR <- function(CR, delta ,lCR, settings, Npop){
- if(any(delta >0)){ ## Adaptions can only be made if there are changes in X
-
- # Change CR to vector
- CR <- c(CR)
-
- # Store old lCR values
- lCROld <- lCR
- ## Determine lCR
- lCR <- rep(NA,settings$nCR)
-
- for (k in 1:settings$nCR){
-
- ## how many times a CR value is used. This is used to weight delta
- CR_counter <- length(which(CR==k/settings$nCR))
- lCR[k] <- lCROld[k]+ CR_counter
- } 
-
- ## Adapt pCR 
- pCR <- Npop * (delta / lCR) / sum(delta)
-
- pCR[which(is.nan(pCR))] <- 1/settings$nCR # catch possible error if delta and lCR = 0
-
- ## Normalize values
- pCR <- pCR/sum(pCR)
-
- }
- return(list(pCR=pCR,lCR=lCR))
-} ##AdaptpCR
+##' Generates matrix of CR values based on pCR
+##' @param pCR vector of crossover probabilities. Needs to be of length nCR.
+##' @param settings list of settings
+##' @param Npop number of chains
+##' @return Matrix with CR values
+#' @keywords internal
+generateCRvalues <- function(pCR,settings, Npop){
+
+ # Random vector, add zero to get first position 
+ RandomVec <- c(0,cumsum(as.numeric(rmultinom(1, size = Npop*settings$updateInterval, prob = pCR))))
+
+ # get candidate points
+ cand <- sample(Npop*settings$updateInterval)
+ CR <- rep(NA, Npop*settings$updateInterval)
+
+ ## Now loop over chains to generate CR values
+ for(i in 1:settings$nCR){
+ #Start and End
+ Start <- RandomVec[i]+1
+ End <- RandomVec[i+1]
+
+ # get candidates
+ candx <- cand[Start:End]
+
+ # Assign these indices settings$CR
+ CR[candx] <- i/settings$nCR
+ }
+ ## Reshape CR
+ CR <- matrix(CR,Npop,settings$updateInterval)
+
+ return(CR)
+} 
+
+
+
+
+#' Adapts pCR values
+#' @param CR vector of crossover probabilities. Needs to be of length nCR.
+#' @param settings list of settings
+#' @param delta vector with differences
+#' @param lCR values to weight delta
+#' @param Npop number of chains.
+#' @return Matrix with CR values
+#' @keywords internal
+AdaptpCR <- function(CR, delta ,lCR, settings, Npop){
+ if(any(delta >0)){ ## Adaptions can only be made if there are changes in X
+
+ # Change CR to vector
+ CR <- c(CR)
+
+ # Store old lCR values
+ lCROld <- lCR
+ ## Determine lCR
+ lCR <- rep(NA,settings$nCR)
+
+ for (k in 1:settings$nCR){
+
+ ## how many times a CR value is used. This is used to weight delta
+ CR_counter <- length(which(CR==k/settings$nCR))
+ lCR[k] <- lCROld[k]+ CR_counter
+ } 
+
+ ## Adapt pCR 
+ pCR <- Npop * (delta / lCR) / sum(delta)
+
+ pCR[which(is.nan(pCR))] <- 1/settings$nCR # catch possible error if delta and lCR = 0
+
+ ## Normalize values
+ pCR <- pCR/sum(pCR)
+
+ }
+ return(list(pCR=pCR,lCR=lCR))
+} ##AdaptpCR