Summary:
rstan::read_stan_csv() no longer works for for .csv files produced by cmdstanr
Description:
It seems that rstan expects the save_warmup field to be an integer value, but cmdstanr instead writes this as a logical value (e.g., false) to the conversion to integer fails in rstan:::parse_stancsv_comments() resulting in an NA value for save_warmup. This used to work with earlier versions of cmdstanr/CmdStan.
Reproducible Steps:
library("cmdstanr")
#> This is cmdstanr version 0.8.1
#> - CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
#> - CmdStan path: C:/Users/Santtu/.cmdstan/cmdstan-2.35.0
#> - CmdStan version: 2.35.0
file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan")
mod <- cmdstan_model(file)
data_list <- list(N = 10, y = c(0, 1, 0, 0, 0, 0, 0, 0, 0, 1))
samples <- mod$sample(
data = data_list,
refresh = 0,
chains = 1,
iter_sampling = 10,
iter_warmup = 10
)
#> Running MCMC with 1 chain...
#>
#> Chain 1 WARNING: No variance estimation is
#> Chain 1 performed for num_warmup < 20
#> Chain 1 finished in 0.0 seconds.
rstan::read_stan_csv(samples$output_files())
#> Warning in parse_stancsv_comments(comments): NAs introduced by coercion
#> Error in if (max(save_warmup) == 0L) {: missing value where TRUE/FALSE neededCreated on 2024-07-10 with reprex v2.1.1
RStan Version:
2.32.6
R Version:
R version 4.4.0 (2024-04-24 ucrt)
Operating System:
Windows 11 Pro 23H2
Summary:
rstan::read_stan_csv()no longer works for for .csv files produced bycmdstanrDescription:
It seems that
rstanexpects thesave_warmupfield to be an integer value, butcmdstanrinstead writes this as a logical value (e.g.,false) to the conversion to integer fails inrstan:::parse_stancsv_comments()resulting in anNAvalue forsave_warmup. This used to work with earlier versions ofcmdstanr/CmdStan.Reproducible Steps:
Created on 2024-07-10 with reprex v2.1.1
RStan Version:
2.32.6
R Version:
R version 4.4.0 (2024-04-24 ucrt)
Operating System:
Windows 11 Pro 23H2