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add iterationTotal to MCMC #1602

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Merged
merged 3 commits into from
Dec 2, 2025
+10 −7
Merged

add iterationTotal to MCMC #1602

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e769a28
can specify thin, so long as unaltered, when using reset=FALSE
danielturek Nov 26, 2025
3b7cd06
added iterationTotal to core mcmc run method
danielturek Nov 26, 2025
87b7c4d
Merge branch 'devel' into mcmc_thin
paciorek Nov 28, 2025
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17 changes: 10 additions & 7 deletions packages/nimble/R/MCMC_build.R
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,7 @@ buildMCMC <- nimbleFunction(
monitors2 <- mcmc_processMonitorNames(model, conf$monitors2)
thinFromConfVec <- c(conf$thin, conf$thin2) ## vector
thinToUseVec <- c(0, 0) ## vector, needs to member data
samplerTimes <- c(0,0) ## establish as a vector
samplerTimes <- c(0, 0) ## establish as a vector
progressBarLength <- 52 ## multiples of 4 only
progressBarDefaultSetting <- getNimbleOption('MCMCprogressBar')
##nimbleVerboseOption <- getNimbleOption('verbose') ## not currently used anywhere
Expand All @@ -244,6 +244,7 @@ buildMCMC <- nimbleFunction(
thinWAIC <- FALSE
nburnin_extraWAIC <- 0
}
iterationTotal <- 0
firstRun <- TRUE
setupOutputs(derivedTypes)
},
Expand Down Expand Up @@ -287,12 +288,13 @@ buildMCMC <- nimbleFunction(
for(i in seq_along(samplerFunctions)) samplerFunctions[[i]]$before_chain(niter, nburnin, chain)
for(i in seq_along(derivedFunctions)) derivedFunctions[[i]]$before_chain(niter-nburnin, nburnin, thinToUseVec, chain)
samplerTimes <<- numeric(length(samplerFunctions) + 1) ## default inititialization to zero
iterationTotal <<- 0
mvSamples_copyRow <- 0
mvSamples2_copyRow <- 0
} else {
if(nburnin != 0) stop('cannot specify nburnin when using reset = FALSE.')
if(thin != -1) stop('cannot specify thin when using reset = FALSE.')
if(thin2 != -1) stop('cannot specify thin2 when using reset = FALSE.')
if((thin != -1) & (thin != thinToUseVec[1])) stop('cannot alter the value of thin, when using reset = FALSE.')
if((thin2 != -1) & (thin2 != thinToUseVec[2])) stop('cannot alter the value of thin2, when using reset = FALSE.')
if(dim(samplerTimes)[1] != length(samplerFunctions) + 1) samplerTimes <<- numeric(length(samplerFunctions) + 1) ## first run: default inititialization to zero
if (resetMV) {
mvSamples_copyRow <- 0
Expand All @@ -304,8 +306,8 @@ buildMCMC <- nimbleFunction(
}
nimCopy(from = model, to = mvSaved, row = 1, logProb = TRUE)
if(onlineWAIC & resetWAIC) waicFun[[1]]$reset()
resize(mvSamples, mvSamples_copyRow + floor((niter-nburnin) / thinToUseVec[1]))
resize(mvSamples2, mvSamples2_copyRow + floor((niter-nburnin) / thinToUseVec[2]))
resize(mvSamples, floor((iterationTotal+niter-nburnin) / thinToUseVec[1]))
resize(mvSamples2, floor((iterationTotal+niter-nburnin) / thinToUseVec[2]))
## reinstate samplerExecutionOrder as a runtime argument, once we support non-scalar default values for runtime arguments:
##if(dim(samplerExecutionOrder)[1] > 0 & samplerExecutionOrder[1] == -1) { ## runtime argument samplerExecutionOrder was not provided
## lengthSamplerExecutionOrderFromConf <- dim(samplerExecutionOrderFromConfPlusTwoZeros)[1] - 2
Expand All @@ -322,6 +324,7 @@ buildMCMC <- nimbleFunction(
progressBarNextFloor <- floor(progressBarNext)
if(niter < 1) return()
for(iter in 1:niter) {
iterationTotal <<- iterationTotal + 1
checkInterrupt()
## execute samplerFunctions
if(time) {
Expand All @@ -337,7 +340,7 @@ buildMCMC <- nimbleFunction(
}
if(iter > nburnin) {
## save samples
iterPostBurnin <- iter - nburnin
iterPostBurnin <- iterationTotal - nburnin
if(iterPostBurnin %% thinToUseVec[1] == 0) {
mvSamples_copyRow <- mvSamples_copyRow + 1
nimCopy(from = model, to = mvSamples, row = mvSamples_copyRow, nodes = monitors)
Expand All @@ -362,7 +365,7 @@ buildMCMC <- nimbleFunction(
}
}
## progress bar
if(progressBar & (iter == progressBarNextFloor)) {
if(progressBar & (iter == progressBarNextFloor)) { ## keep this one as 'iter'
cat('-')
progressBarNext <- progressBarNext + progressBarIncrement
progressBarNextFloor <- floor(progressBarNext)
Expand Down
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