Link to the new warnings page from `diagnose` output
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Description
Summary:
The new warning page (https://mc-stan.org/misc/warnings.html) hopefully provides better context for understanding and diagnosing warnings from diagnose output (divergences, treedepth, ...). So the current short description and hints (e.g. increase adapt_delta or reparametrize) should be replaced with a link to the site.
Description:
Describe the issue as clearly as possible.
Current Output:
9 of 4000 (0.23%) transitions ended with a divergence.
These divergent transitions indicate that HMC is not fully able to explore the posterior distribution.
Try increasing adapt delta closer to 1.
If this doesn't remove all divergences, try to reparameterize the model.
Checking E-BFMI - sampler transitions HMC potential energy.
The E-BFMI, 0.078, is below the nominal threshold of 0.3 which suggests that HMC may have trouble exploring the target distribution.
If possible, try to reparameterize the model.
The following parameters had split R-hat greater than 1.1:
y
Such high values indicate incomplete mixing and biased estimation.
You should consider regularizing your model with additional prior information or a more effective parameterization.
Proposed Output:
9 of 4000 (0.23%) transitions ended with a divergence.
These divergent transitions indicate that HMC is not fully able to explore the posterior distribution.
Checking E-BFMI - sampler transitions HMC potential energy.
The E-BFMI, 0.078, is below the nominal threshold of 0.3 which suggests that HMC may have trouble exploring the target distribution.
The following parameters had split R-hat greater than 1.1:
y
Such high values indicate incomplete mixing and biased estimation.
Visit https://mc-stan.org/misc/warnings.html for a more thorough description of what the warnings mean and hints how to resolve the issues.
Current Version:
v2.29.2
Contributor guide
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.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Search the CmdStan source for the existing diagnose warning strings and identify where their output is assembled. Compare the current and proposed output in this issue, then verify that the detailed guidance is replaced by the warnings-page URL without changing the diagnostic results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp
- Domain
- cli
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100