CmdStan User's guide - sampler auxiliary output file option `diagnostic-file` needs more doc
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Description
The CmdStan documentation should say a bit more about the output diagnostic-file option.
The sample methods use the output option diagnostic-file to designate files which contain the per-draw gradients of all parameters.
This is a .csv file, almost like the output file option's Stan CSV file (default name output.csv).
-
Explain difference between CmdStan utility
diagnose, Stan sampler methoddiagnose, andoutput diagnostics-file. -
Document the format of the output diagnostics-file - compare to
output file=output.csvfile:- Both files have config, header-rows, and timing.
- The first columns of the data tables are the sampler state variables,
lp__,accept_stat__, etc. - Only the
output.csvfile has adaptation information (as a comment following the data table header row)
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- 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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Research direction
Start in the CmdStan User's guide section covering sample output options, then compare the diagnostic-file output with the output.csv description. Document the distinction between CmdStan diagnose, the Stan sampler diagnose method, and diagnostic-file, including the shared configuration, headers, timing, and sampler-state columns and the adaptation information unique to output.csv.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- tex
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100