added requested docstrings #2692
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Pull Request Overview
Adds and improves documentation for adaptive Hamiltonian sampling in Turing, addressing requested docstrings and minor formatting.
- Add comprehensive docstring for AbstractMCMC.sample with AdaptiveHamiltonian, detailing adaptation/warmup controls.
- Add docstring for DynamicPPL.initialstep to clarify initialization behavior and keywords.
- Normalize NUTS docstring section header to “# Arguments”.
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src/mcmc/hmc.jl
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| ```julia | ||
| NUTS() # Use default NUTS configuration. | ||
| NUTS(1000, 0.65) # Use 1000 adaption steps, and target accept ratio 0.65. |
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Correct 'adaption' to 'adaptation' for clarity and consistency.
| NUTS(1000, 0.65) # Use 1000 adaption steps, and target accept ratio 0.65. | |
| NUTS(1000, 0.65) # Use 1000 adaptation steps, and target accept ratio 0.65. |
src/mcmc/hmc.jl
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| """ | ||
| struct NUTS{AD,metricT<:AHMC.AbstractMetric} <: AdaptiveHamiltonian | ||
| n_adapts::Int # number of samples with adaption for ϵ |
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Correct 'adaption' to 'adaptation' in the field comment.
| n_adapts::Int # number of samples with adaption for ϵ | |
| n_adapts::Int # number of samples with adaptation for ϵ |
|
Turing.jl documentation for PR #2692 is available at: |
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src/mcmc/hmc.jl
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| - `initial_params`: Initial parameter values for sampling. See `DynamicPPL.initialstep` for details. | ||
| Additional keyword arguments are passed to the underlying sampling implementation. |
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Are all the other keyword arguments specific to HMC, or do they include generic ones joint to all samplers, like verbose or something?
Relatedly, may be worth linking to this in the docstring: https://turinglang.org/docs/usage/sampling-options Maybe already above?
src/mcmc/hmc.jl
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| # Keyword Arguments | ||
| - `initial_params`: Initial parameter values to use for sampling. If `nothing` (the default), |
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initial_params and verbose work the same way for all samplers, not just HMC, so I would not document them here, but rather refer to the docstring of the more generic initialstep function or method. That docstring may need writing too, but would make sense to postpone that after github.com//pull/2676, because the way initial_params works is going to change quite drastically.
AoifeHughes
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- Improved docstring for initial_params to reference DynamicPPL.initialstep - Added link to sampling options documentation for keyword arguments - Fixed typos: "adaption" → "adaptation" throughout HMCDA and NUTS
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WRT: #2684