From b15d6a7af630aa4e8c07a7b5acd0ddbe5fe50251 Mon Sep 17 00:00:00 2001
From: Matthew Pitkin <matthew.pitkin@ligo.org>
Date: Fri, 14 Sep 2018 10:18:54 +0100
Subject: [PATCH] sampler.py: add help for PyMC3
---
tupak/core/sampler.py | 39 ++++++++++++++++++++++++++++++++++++++-
1 file changed, 38 insertions(+), 1 deletion(-)
diff --git a/tupak/core/sampler.py b/tupak/core/sampler.py
index 6ef63b94e..719731dd1 100644
--- a/tupak/core/sampler.py
+++ b/tupak/core/sampler.py
@@ -1155,7 +1155,44 @@ class Ptemcee(Emcee):
class Pymc3(Sampler):
- """ tupak wrapper of the pymc3 sampler (https://docs.pymc.io/) """
+ """ tupak wrapper of the PyMC3 sampler (https://docs.pymc.io/)
+
+ All keyword arguments (i.e., the kwargs) passed to `run_sampler` will be
+ propogated to `pymc3.sample` where appropriate, see documentation for that
+ class for further help. Under Keyword Arguments, we list commonly used
+ kwargs and the tupak, or where appropriate, PyMC3 defaults.
+
+ Keyword Arguments
+ -----------------
+ draws: int, (1000)
+ The number of sample draws from the posterior per chain.
+ chains: int, (2)
+ The number of independent MCMC chains to run.
+ cores: int, (1)
+ The number of CPU cores to use.
+ tune: int, (500)
+ The number of tuning (or burn-in) samples per chain.
+ discard_tuned_samples: bool, True
+ Set whether to automatically discard the tuning samples from the final
+ chains.
+ step: str, dict
+ Provide a step method name, or dictionary of step method names keyed to
+ particular variable names (these are case insensitive). If no method is
+ provided for any particular variable then PyMC3 will automatically
+ decide upon a default, with the first option being the NUTS sampler.
+ The currently allowed methods are 'NUTS', 'HamiltonianMC',
+ 'Metropolis', 'BinaryMetropolis', 'BinaryGibbsMetropolis', 'Slice', and
+ 'CategoricalGibbsMetropolis'. Note: you cannot provide a PyMC3 step
+ method function itself here as it is outside of the model context
+ manager.
+ nuts_kwargs: dict
+ Keyword arguments for the NUTS sampler.
+ step_kwargs: dict
+ Options for steps methods other than NUTS. The dictionary is keyed on
+ lowercase step method names with values being dictionaries of keywords
+ for the given step method.
+
+ """
def _verify_parameters(self):
"""
--
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