stan-dev / stan-dev/rstanarm

Reloading `stanreg` objects cannot be used with `bridgesampling::bridge_sampler`

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R
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Description

Summary:

Reloading stanreg objects cannot be used with bridgesampling::bridge_sampler.

Description:

When saving a stanreg model, with a defined diagnostic_file, and reloading it into a new R session, bridgesampling::bridge_sampler does not run even though the diagnostic file is available.

Reproducible Steps:
library(rstanarm)

count_data <- data.frame(
  counts = c(18,17,15,20,10,20,25,13,12),
  outcome = gl(3,1,9),
  treatment = gl(3,3)
)

fit <- stan_glm(
  counts ~ treatment + outcome, 
  data = count_data, 
  family = poisson(link="log"),
  diagnostic_file = "df.csv"
)

bridgesampling::bridge_sampler(fit)
#> Iteration: 1
#> Iteration: 2
#> Iteration: 3
#> Iteration: 4
#> Iteration: 5
#> Bridge sampling estimate of the log marginal likelihood: -38.62193
#> Estimate obtained in 5 iteration(s) via method "normal".


saveRDS(fit,"fit.rds")

Close R and restart.

library(rstanarm)
fit <- readRDS("fit.rds")
bridgesampling::bridge_sampler(fit)
#> Error in .local(object, ...) : 
#>  the model object is not created or not valid
RStanARM Version:
packageVersion("rstanarm")
#> [1] '2.18.2'
R Version:
getRversion()
#> [1] '3.5.3'
Operating System:

Windows 10

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the failure with the supplied rstanarm example: save and reload the stanreg object, then call bridgesampling::bridge_sampler with the diagnostic file present. The payload names no source files or tests, so trace the reload path and bridge_sampler integration before deciding where to work. Done means the reloaded object runs bridge_sampler successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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