Argument `save_warmup` is ignored?
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Description
Description:
rstanarm's modeling functions won't save warm-up draws even if save_warmup = TRUE is specified.
(refresh, otoh is correctly passed to stan(), for example).
Reproducible example:
> 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
Package version:
> packageVersion("rstanarm")
[1] ‘2.21.3’
> packageVersion("rstan")
[1] ‘2.21.7’
R Version:
4.2.0
Operating System:
OS X 10.14.6
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the reproducible stan_glm example and inspecting sglm$stanfit@stan_args[[1]]$save_warmup alongside refresh. Trace how the modeling function forwards arguments to stan(); done when save_warmup=TRUE is preserved and warm-up draws are saved as requested.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100