Latest install of rstanarm stan_surv() fails with random effects.
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Description
Summary:
I downloaded rstanarm in my usual way and tried to run a stan_surv model with random effects and it errors.
Description:
When I run the example from stan_surv() that includes random I get the error:
Error : Exception: model_surv_namespace::model_surv: V_event[i_0__][i_1__] is 0, but must be greater than or equal to 1 (in 'model_surv' at line 648)
In addition: Warning messages:
1: In status < 0 || status > 3 :
'length(x) = 40 > 1' in coercion to 'logical(1)'
2: In status < 0 || status > 3 :
'length(x) = 40 > 1' in coercion to 'logical(1)'
3: In status < 0 || status > 3 :
'length(x) = 40 > 1' in coercion to 'logical(1)'
4: In status < 0 || status > 3 :
'length(x) = 40 > 1' in coercion to 'logical(1)'
failed to create the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Reproducible Steps:
I download rstanarm by running: git clone -b feature/survival https://github.com/stan-dev/rstanarm.git in the Terminal. I then run devtools::document() and Build the R package locally.
I then ran:
m_frail <- stan_surv(
formula = Surv(eventtime, status) ~ trt + (1 | site),
data = frail[1:40,],
basehaz = "exp",
chains = 1,
refresh = 0,
iter = 600,
seed = 123)
And got the error above. Other random effects model also fail.
RStanARM Version:
I am running rstanarm v2.21.3
R Version:
I am running R version v4.2.2
Operating System:
Your operating system (e.g., OS X 13.2.1)
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Research direction
Start by reproducing the supplied stan_surv() call with the frail[1:40,] data and random-effects formula. Trace the random-effects path into model_surv around the reported validation error at line 648; done means the example creates a valid fit without the V_event error or status warnings.
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