Should stan_jm throw an error when the survival submodel has zero events?
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Description
Summary:
Getting this error attempting to run stam_jm
"error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug"
Description:
Model attempting to run:
mod1 <- stan_jm(formulaLong = dsmcc_sumanxiety ~ ses + race + time + (time | id),
dataLong = longd,
formulaEvent = survival::Surv(max.pt, attrit) ~ ses + race,
dataEvent = eventd,
time_var = "time",
chains = 1, refresh = 2000, seed = 12345)
Getting this Error:
Chain 1: Rejecting initial value:
Chain 1: Error evaluating the log probability at the initial value.
Chain 1: Exception: Exception: normal_lpdf: Random variable[9] is nan, but must not be nan! (in '/functions/mvmer_functions.stan' at line 291; included from 'model_jm' at line 12)
(in 'model_jm' at line 119)
Chain 1:
Chain 1: Initialization between (-2, 2) failed after 100 attempts.
Chain 1: Try specifying initial values, reducing ranges of constrained values, or reparameterizing the model.
[1] "Error in sampler$call_sampler(args_list[[i]]) : Initialization failed."
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Reproducible Steps:
If applicable, the steps required to reproduce the issue. If you have a reproducible example, please include it.
Screenshot of Data for Longitudinal model:

Screenshot of Data for Event

model:
tried the following:
xcode-select --install
result: xcode-select: error: command line tools are already installed
install.packages("rstanarm", type = "source")
library(devtools)
install_github("stan-dev/rstanarm")
and none of these fixed the problem.
RStanARM Version:
The version of the rstanarm package you are running (e.g., from packageVersion("rstanarm"))
R Version:
The version of R you are running (e.g., from getRversion())
RStudio
Version 1.4.1106
R Version: ‘4.0.4’
Operating System:
Catalina, OS X 10.15.7
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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.
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- Open a pull request that references the issue number.
Research direction
Start at the stan_jm entry point and inspect the generated model_jm code, including the failure reported from functions/mvmer_functions.stan around line 291. Check how a survival submodel with zero events reaches Stan initialization and identify the existing validation tests or model-fitting tests. Done means the case produces a clear, intentional error rather than an invalid stanfit error.
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