stan-dev / stan-dev/rstanarm

Error: passing unknown arguments: warmup in stan_jm()

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R
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Description

Summary:

not able to set warmup parameter in Stan_jm() function

Description:

When I am trying to change default warmup parameter, stan_jm() giving an Error: passing unknown arguments: warmup.
In sampling function from rstan I can see the warmup parameter with default value floor(iter/2)

Reproducible Steps:

The code I am running from the example section in rstanarm

f1 <- stan_jm(formulaLong = logBili ~ year + (1 | id),
dataLong = pbcLong,
formulaEvent = Surv(futimeYears, death) ~ sex + trt,
dataEvent = pbcSurv,
time_var = "year",
# this next line is only to keep the example small in size!
chains = 1, cores = 1, algorithm = "sampling",seed = 12345, iter = 1000,warmup = 100)

RStanARM Version:

2.21.3

R Version:

4.2.1

Operating System:

macOS Monterey 12.5

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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 with the stan_jm() argument handling and compare it with the sampling function behavior described in the issue. Run the provided pbcLong and pbcSurv example using warmup = 100; done means stan_jm() accepts the argument without reporting it as unknown and applies the requested warmup setting.

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
35/100

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