warning of chains not mixing, when there is a correlation which is NA
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Description
Summary:
I get a false alarm of chains not mixing, because an Rhat is NA, which should be fine. It's related to https://github.com/paul-buerkner/brms/issues/864
Reproducible Steps:
I was a bit lazy and generated the code with brms.
library(brms)
library(rstan)
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
data <- data.frame(x= rnorm(1000), y = rnorm(1000), z = rnorm(1000), g =rep(1:10,100))
code <- make_stancode(y ~ x + (x|g), data= data, control = list(adapt_delta =.9))
ls_data <- make_standata(y ~ x + (x|g), data= data, control = list(adapt_delta =.9))
f <- stan(model_code = code,data =ls_data)
Current Output:
Warning messages:
1: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
2: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
3: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Expected Output:
No warning
RStan Version:
2.19.3
R Version:
R version 3.6.3 (2020-02-29)
Operating System:
Ubuntu 18.04
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by running the supplied RStan 2.19.3 reproduction on the stated R and Ubuntu versions, then trace where the R-hat warning is generated when its largest value is NA. Check related issue #864 for context. Done means this case no longer emits the false chain-mixing warning while genuine diagnostics remain reported.
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