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Add generic observation processes which combine the convolution with the noise model. #644
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #644 +/- ##
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+ Coverage 96.98% 97.32% +0.33%
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Files 42 47 +5
Lines 1094 1270 +176
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+ Hits 1061 1236 +175
- Misses 33 34 +1
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…ents, 'aggregate' instead of 'jurisdiction'
…ents, 'aggregate' instead of 'jurisdiction'
for more information, see https://pre-commit.ci
… into mem_generic_observations
for more information, see https://pre-commit.ci
… into mem_generic_observations
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Thanks @cdc-mitzimorris! A high-level suggested changes before re-review
- Change "expected" --> "predicted" throughout, as nothing in the design requires or enforces that the prediction be the expected value, though in many concrete cases it is, and that's desirable.
- Throughout, avoid custom names for the observed quantity, if any, to the
sample()call. Instead useobs, for API mirroring ofnumpyro.sample(). - Revise the measurements tutorial to be stricter about what is specific to the wastewater example and what is general to delay-ascertained measurements.
- Remove the provided helper classes for sampling priors (i.e.
pyrenew/randomvariable/hierarchical.pyfrom this PR. That will keep it more narrowly focused on observation processes.
RE: the helper classes for sampling priors: I am open to the possibility that we could want those helper classes in Pyrenew, but as I mention in my line-by-line comments, I think it requires a broader rethink of how we do distributional variables, etc. Would also appreciate thoughts from @damonbayer on that point.
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
Co-authored-by: Dylan H. Morris <[email protected]>
… into mem_generic_observations
…randomvariable/hierarchical.py), per reviewer comments
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ready for re-review - high-level concerns addressed:
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This PR adds work that was done in https://github.com/cdcent/cfa-pyrenew-hierarchical/pull/4 to PyRenew.
It adds the base observation process class, concrete implementations for Count processes and the abstract base class for Measurement processes, together with unit tests and two new tutorials for count and measurement observation processes respectively.
Once this PR and the work done in https://github.com/cdcent/cfa-pyrenew-hierarchical/pull/5 have been added to PyRenew, subsequent PRs will deprecate unused features and harmonize the documentation and tutorials.