Add comprehensive documentation for Chains object internal fields #486
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MCMCChains.jl documentation for PR #486 is available at: |
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| - **`log_density`**: The log probability density of the target distribution at each sample point. | ||
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| - **`lp`**: An alias for log probability density (may be identical to `log_density`). |
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log_density includes the Jacobian term (i.e. is calculated in linked space), whereas lp doesn't (on Turing >= v0.40).
More generally though is MCMCChains really the right place to document these? The sampler stats are generated by AdvancedHMC, whereas lp itself is generated in Turing. It seems like these should be documented in one of those two packages.
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(my preference would be Turing itself because subpackages docs are not very discoverable -- in fact ideally the fields would be documented in AdvancedHMC itself and we would put a link to it in the main Turing docs)
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Perhaps a good task for @AoifeHughes?
This PR addresses the lack of documentation for internal fields in
Chainsobjects returned by NUTS and other HMC samplers. Previously, users could see fields likeacceptance_rate,hamiltonian_energy,tree_depth, etc., but had no explanation of what these fields represented or how to use them.Changes Made
Added a comprehensive "Internals Fields" section to
docs/src/chains.mdthat documents:12 common internal fields including all those mentioned in the original issue:
acceptance_rate: The acceptance rate of the samplerhamiltonian_energy: Total energy used for diagnostic plotshamiltonian_energy_error: Energy integration errorsis_accept: Whether samples were acceptedlog_densityandlp: Log probability density valuesn_steps: Number of leapfrog steps takenstep_size: Integrator step sizetree_depth: NUTS binary tree depthPractical code examples showing how to access internal fields:
Diagnostic applications explaining how these fields are used for:
energyplot()Example Usage
Before this PR, users saw output like:
But had no way to understand what these fields meant. Now the documentation provides clear explanations and usage examples for each field.
Fixes #339.
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