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Rely more on posterior #1171

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Rely more on posterior #1171

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fb9e112
Update monitor to use functions from posterior
VisruthSK Oct 21, 2025
3371eac
Wrap posterior functions
VisruthSK Oct 21, 2025
1ef5c29
Deleted unexported functions
VisruthSK Oct 21, 2025
1e915bb
Fixed typo
VisruthSK Oct 21, 2025
bbbb54c
Added posterior as a dependency
VisruthSK Oct 22, 2025
90ae295
Don't use names from posterior::quantile2
VisruthSK Oct 24, 2025
4aca466
Add a snapshot test whose baseline values need to be set since I can'…
VisruthSK Oct 24, 2025
4605a6b
use fixed set of posterior draws in monitor test
jgabry Oct 24, 2025
6937428
respect `probs` argument and don't hardcode any internally
jgabry Oct 24, 2025
48bc313
update test and generate snapshot
jgabry Oct 24, 2025
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3 changes: 2 additions & 1 deletion rstan/rstan/DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@ Imports:
loo (>= 2.4.1),
pkgbuild (>= 1.2.0),
QuickJSR,
ggplot2 (>= 3.3.5)
ggplot2 (>= 3.3.5),
posterior (>= 1.6.1)
Depends:
R (>= 3.4.0),
StanHeaders (>= 2.36.0)
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6 changes: 3 additions & 3 deletions rstan/rstan/R/check_hmc_diagnostics.R
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Expand Up @@ -74,19 +74,19 @@ throw_sampler_warnings <- function(object) {
call. = FALSE, noBreaks. = TRUE)

sims <- as.array(object)
rhat <- apply(sims, MARGIN = 3, FUN = Rhat)
rhat <- apply(sims, MARGIN = 3, FUN = posterior::rhat)
if (any(rhat > 1.05, na.rm = TRUE))
warning("The largest R-hat is ", round(max(rhat), digits = 2),
", indicating chains have not mixed.\n",
"Running the chains for more iterations may help. See\n",
"https://mc-stan.org/misc/warnings.html#r-hat", call. = FALSE)
bulk_ess <- apply(sims, MARGIN = 3, FUN = ess_bulk)
bulk_ess <- apply(sims, MARGIN = 3, FUN = posterior::ess_bulk)
if (any(bulk_ess < 100 * ncol(sims), na.rm = TRUE))
warning("Bulk Effective Samples Size (ESS) is too low, ",
"indicating posterior means and medians may be unreliable.\n",
"Running the chains for more iterations may help. See\n",
"https://mc-stan.org/misc/warnings.html#bulk-ess", call. = FALSE)
tail_ess <- apply(sims, MARGIN = 3, FUN = ess_tail)
tail_ess <- apply(sims, MARGIN = 3, FUN = posterior::ess_tail)
if (any(tail_ess < 100 * ncol(sims), na.rm = TRUE))
warning("Tail Effective Samples Size (ESS) is too low, indicating ",
"posterior variances and tail quantiles may be unreliable.\n",
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