Hierarchical Causal Models#236

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Commits on Feb 28, 2025

functions for creating and querying HCMs with pygraphviz

Adam Rupe
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adamrupe
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functionality to collapse phygraphviz HCMs to nxmixedgraphs

Adam Rupe
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adamrupe
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added __all__

Adam Rupe
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added test_hierarchical

Adam Rupe
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pygraphviz dep and lint exception for hierarchical in pyproject

Adam Rupe
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auto lint hierarchical

Adam Rupe
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auto lint test_hierarchical

Adam Rupe
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added docstrings to hierarchical.py

Adam Rupe
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adamrupe
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added docstrings to test_hierarchical.py

Adam Rupe
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more ignores in pyproject.toml

Adam Rupe
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imperative docstrings

Adam Rupe
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cleaned whitespace

Adam Rupe
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lint HCM_from_lists

Adam Rupe
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more linting

Adam Rupe
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added typing to hierarchical.py

Adam Rupe
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added typing to test_hierarchical.py

Adam Rupe
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HCM notebook with Fig 2 up to collapsed models

Adam Rupe
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lint fixes

Adam Rupe
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docstring lint

Adam Rupe
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test fixtures for Fig 2 augmented models

Adam Rupe
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added augment_collapsed_model function that implements Algorithm 2

Adam Rupe
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tox formatting

Adam Rupe
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tests for augmentation and formatting

Adam Rupe
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added augmented models to notebook

Adam Rupe
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add marginalize function implementing Algorithm 3

Adam Rupe
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Instrument test for algorithm 3

Adam Rupe
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Clean up literals

cthoyt
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adamrupe
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update collapse_HCM to preserve unit-level edges

Adam Rupe
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adamrupe
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update augment and marginalize functions to return new objects instead of mutate input

Adam Rupe
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added copy_HCM

Adam Rupe
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Fig 2 fixture tests for copy_HCM

Adam Rupe
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added convert_to_HCGM

Adam Rupe
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tests for convert to HCGM

Adam Rupe
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minor lint

Adam Rupe
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update HCGM styles for consistency with observed vars

Adam Rupe
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update convert_to_HCGM to handle unobserved Q vars

Adam Rupe
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add functions to parse semiMarkov edges from HCMs with latent variables

Adam Rupe
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updated collapse_HCM with intermediate convert_to_HCGM; follows paper pseudocode much closer and has option to return intermediate HCGM

Adam Rupe
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lint and fix bug on direct_unit_descendents

Adam Rupe
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bug fix augment_collapsed_model

Adam Rupe
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added sorting to create_Qvar

Adam Rupe
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update test with sorted Qvar

Adam Rupe
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Update hierarchical.py

cthoyt
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adamrupe
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Add type checking for tests

cthoyt
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adamrupe
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Update test_hierarchical.py

cthoyt
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adamrupe
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Update tox.ini

cthoyt
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adamrupe
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function and unit tests for getting ancestors

Adam Rupe
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linted

Adam Rupe
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mid update of augmentation mechanism, previous tests modified and passing

Adam Rupe
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tests for augmentation_mechanism

Adam Rupe
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update augmentation_mechanism to use direct subunit descendents rather than subunit parents

Adam Rupe
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test aug mech for complicated subunit graph HCM

Adam Rupe
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update augment_collapsed_model

Adam Rupe
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commit before rebase

Adam Rupe
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added subunit_graph and fixed bug in collapse_HCM

Adam Rupe
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fixed bug in marginalize

Adam Rupe
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add demote_Qvar

Adam Rupe
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update HCM notebook with all Figs from paper

Adam Rupe
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update HCM images

Adam Rupe
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add identification to HCM nb

Adam Rupe
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add parse_Qvar

Adam Rupe
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generalize augmentation code

Adam Rupe
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update augmentation tests

Adam Rupe
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add tests for parse_Qvar

Adam Rupe
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add more tests for subunit_graph and parse_Qvar

Adam Rupe
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add convert_to_HSCM

Adam Rupe
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Refactor

cthoyt
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Switch fully to nx from pygraphviz

cthoyt
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adamrupe
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Refactor while loops

cthoyt
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adamrupe
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Cleanup typing

cthoyt
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Remove warnings

cthoyt
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Clean up variable names

cthoyt
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Reuse some example graphs

cthoyt
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Update Hierarchical Causal Models.ipynb

cthoyt
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Keep track of stochastic variables

cthoyt
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adamrupe
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minor commit before pull

Adam Rupe
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merge nb

Adam Rupe
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finish nb merge

Adam Rupe
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change HCM attribute name stochastic to deterministic

Adam Rupe
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fix to_hscm and update to_pygraphviz for exogenous variables

Adam Rupe
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add collapse_hcm_function

Adam Rupe
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refactor with HSCM subclass

Adam Rupe
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add HSCM examples

Adam Rupe
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add tests for HCM.to_hscm and HSCM.to_hcm

Adam Rupe
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lint

Adam Rupe
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adamrupe
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minor lint and bug fixes

Adam Rupe
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adamrupe
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minor bug fix for collapse_hcm

Adam Rupe
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trying fix for mypy bug

Adam Rupe
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lint

Adam Rupe
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try again

Adam Rupe
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minor clean

Adam Rupe
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Commits on Mar 1, 2025

Commits on Mar 5, 2025

raise exception if collapsing HCM with unobserved subunits
Adam Rupe
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allow strings for marginal_parents in marginalize_augmented_model
Adam Rupe
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minor clean to HCM nb
Adam Rupe
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add tests for augment_collapsed_model and lint
Adam Rupe
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Commits on Mar 13, 2025

switch Q variables to upper case to match paper
Adam Rupe
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Commits on Mar 14, 2025

Commits on Mar 17, 2025

rename current HCM nb
Adam Rupe
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add HCM nb
Adam Rupe
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lint
Adam Rupe
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Commits on Mar 18, 2025

update HCM Figs nb with new Q variable format
Adam Rupe
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Update Hierarchical Causal Models.ipynb
cthoyt
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Cleanup unused code
cthoyt
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Rerun
cthoyt
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Commits on Jun 11, 2025

Started the process of converting unit-level and subunit-level variables to english names that capture the unit-level (school) and subunit (student) hierarchical distributions
djinnome
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Commits on Jun 20, 2025

Commits on Jun 21, 2025

Update README.md
cthoyt
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Commits on Sep 18, 2025

Focusing the narrative on test scores in schools
djinnome
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Commits on Sep 24, 2025

Added narrative to Hierarchical Causal Models
Nathaniel Merrill
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more small Narrative changes
Nathaniel Merrill
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Show Identifiability before technical discussion
Nathaniel Merrill
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Cleanup markdown code statements. Make descriptions less technical
Nathaniel Merrill
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Commits on Nov 14, 2025

Commits on Nov 19, 2025

Changed explanation of Collapse
Nathaniel Merrill
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Resolved merge conflict in Hierarchical Causal Models.ipynb
Nathaniel Merrill
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Commits on Dec 8, 2025

Rewrite the Augment section to be more readable
Nathaniel Merrill
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