Open anddis opened 1 year ago
rstanarm's modeling functions won't save warm-up draws even if save_warmup = TRUE is specified.
rstanarm
save_warmup = TRUE
(refresh, otoh is correctly passed to stan(), for example).
refresh
stan()
> library(rstanarm) > sglm <- stan_glm(vs ~ wt, data = mtcars, family = "binomial", chains = 1, + seed = 1234, iter = 2000, refresh = 400, save_warmup = TRUE) SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 1.7e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup) Chain 1: Iteration: 800 / 2000 [ 40%] (Warmup) Chain 1: Iteration: 1001 / 2000 [ 50%] (Sampling) Chain 1: Iteration: 1400 / 2000 [ 70%] (Sampling) Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling) Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.041092 seconds (Warm-up) Chain 1: 0.037098 seconds (Sampling) Chain 1: 0.07819 seconds (Total) Chain 1: > sglm$stanfit@stan_args[[1]]$save_warmup [1] FALSE > sglm$stanfit@stan_args[[1]]$refresh [1] 400
Code only:
library(rstanarm) sglm <- stan_glm(vs ~ wt, data = mtcars, family = "binomial", chains = 1, seed = 1234, iter = 2000, refresh = 400, save_warmup = TRUE) sglm$stanfit@stan_args[[1]]$save_warmup sglm$stanfit@stan_args[[1]]$refresh
> packageVersion("rstanarm") [1] ‘2.21.3’ > packageVersion("rstan") [1] ‘2.21.7’
4.2.0
OS X 10.14.6
Description:
rstanarm
's modeling functions won't save warm-up draws even ifsave_warmup = TRUE
is specified.(
refresh
, otoh is correctly passed tostan()
, for example).Reproducible example:
Code only:
Package version:
R Version:
4.2.0
Operating System:
OS X 10.14.6