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fix #281: allow restarting/continuing of a one-element mcmcSamplerList with runMCMC() #282

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fix #281: allow restarting/continuing of a one-element mcmcSamplerList with runMCMC() #282

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5 changes: 3 additions & 2 deletions BayesianTools/R/mcmcRun.R
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Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,9 @@ runMCMC <- function(bayesianSetup , sampler = "DEzs", settings = NULL){

if(restart == T) if(!getPossibleSamplerTypes()$restartable[which(getPossibleSamplerTypes()$BTname == settings$sampler)]) stop("This sampler can not be restarted")

########### Recursive call in case multiple chains are to be run
if(settings$nrChains >1){
########### Recursive call for multiple chains or restarting a sampler list
if(settings$nrChains > 1 ||
(restart && inherits(bayesianSetup, "mcmcSamplerList"))){

# Initialize output list
out<- list()
Expand Down
48 changes: 48 additions & 0 deletions BayesianTools/tests/testthat/test-runMCMC-singleton-list.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
# Suggested regression test for BayesianTools/tests/testthat/.
for (sampler in c("DEzs", "DREAMzs")) {
testthat::test_that(paste(sampler, "resumes singleton and longer sampler lists"), {
set.seed(1)
setup <- createBayesianSetup(
likelihood = function(x) sum(dnorm(x, log = TRUE)),
lower = rep(-10, 2),
upper = rep(10, 2)
)
fit <- runMCMC(
setup, sampler = sampler,
settings = list(iterations = 30, burnin = 0, nrChains = 1,
startValue = 3, message = FALSE)
)
testthat::expect_s3_class(fit, "mcmcSampler")

for (settings in list(NULL, list(iterations = 15, burnin = 0,
message = FALSE))) {
# A singleton list should resume just like the first entry of a longer list.
set.seed(2)
longer <- runMCMC(createMcmcSamplerList(list(fit, fit)), settings = settings)
set.seed(2)
singleton <- runMCMC(createMcmcSamplerList(list(fit)), settings = settings)

testthat::expect_s3_class(singleton, "mcmcSamplerList")
testthat::expect_length(singleton, 1L)
testthat::expect_s3_class(longer, "mcmcSamplerList")
testthat::expect_length(longer, 2L)
testthat::expect_identical(singleton[[1]]$chain, longer[[1]]$chain)
testthat::expect_identical(singleton[[1]]$X, longer[[1]]$X)
testthat::expect_identical(singleton[[1]]$Z, longer[[1]]$Z)

for (output in list(singleton, longer)) {
for (i in seq_along(output)) {
testthat::expect_s3_class(output[[i]], "mcmcSampler")
for (j in seq_along(fit$chain)) {
before <- as.matrix(fit$chain[[j]])
after <- as.matrix(output[[i]]$chain[[j]])
testthat::expect_gt(nrow(after), nrow(before))
testthat::expect_identical(
unname(after[seq_len(nrow(before)), , drop = FALSE]), unname(before)
)
}
}
}
}
})
}