34 port notebooks under modeldocs to quarto #35
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ghost
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ghost
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Mar 21, 2024
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This is ready for review, @dylanhmorris, @natemcintosh, @AFg6K7h4fhy2, or @SamuelBrand1 :) |
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Mar 25, 2024
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
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* Porting to quarto and adding a makefile entry to render them * Now it should be easier to deal with pre-commit under docs (only skipping cache) * Forgot to remove the pyrenew_demo notebook * Update model/Makefile * Fixing typos * Removes progress bar - adds doc/ figures - sets jupyter as kernel * Update model/docs/getting-started.qmd Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> --------- Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
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…39) * Copy doc from wastewater model on Hosp Admin to class * Rename metaclasses to metaclass (#36) * Create typos.yaml (#42) * Create typos.yaml * Does this make it run on the whole repo? * remove trailing whitespace * Delete .github/workflows/typos.yaml trying to use typos in pre-commit instead * Update .pre-commit-config.yaml add typos to pre-commit * fixed typos * 34 port notebooks under modeldocs to quarto (#35) * Porting to quarto and adding a makefile entry to render them * Now it should be easier to deal with pre-commit under docs (only skipping cache) * Forgot to remove the pyrenew_demo notebook * Update model/Makefile * Fixing typos * Removes progress bar - adds doc/ figures - sets jupyter as kernel * Update model/docs/getting-started.qmd Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> --------- Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> * Extra mathematical description of discrete delay distributions (#44) * Update description of discrete delay distributions * remove double desciption * minor eq fix * Update equations.md * update equations.md contents * Update equations.md * fix contents * Escaping tau * Adding deterministic obs and process to the equation * Cleaning the quarto documents and working on the getting started diagram * Flexible IHR (now RandomVariable) * Adding weekday and phosp effect to latent hosp * Adding back figures * Adding a test for deterministic/stochastic weekday effect * Typo Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> * Correcting tests (class name) and improving readme a bit * Adding deterministic module (midway, expected to fail) [skip ci] * Refactoring I0 and gen_int (expected to fail) [skip ci] * gen_int and I0 now are directly passed to the models * In latent hosp, change inf_hosp_int to inform_hosp (clearer name) * Adding missing figures (pyrenew demo was not compiling) * Renaming inform_hosp * Removing defaults for hosp rate * Changing language (initial infections) + adding section to getting-started * Update model/src/pyrenew/latent/hospitaladmissions.py Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> * Addressing comments on default priors and varnames * Rt is not default now for basic model * Commas and title * Update model/src/pyrenew/latent/hospitaladmissions.py Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> * Renaming hosp reporting variable in latent var * Renaming hosp report * Update model/src/pyrenew/latent/hospitaladmissions.py Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> * Final renaming of vars in tests * Different vector for hosp_report_prob_dist in tests --------- Co-authored-by: George G. Vega Yon <xrd4@cdc.gov> Co-authored-by: George G Vega Yon <156135298+gvegayoncdc@users.noreply.github.com> Co-authored-by: Nate McIntosh <NMcIntosh@cdc.gov> Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com> Co-authored-by: Samuel Brand <48288458+SamuelBrand1@users.noreply.github.com> Co-authored-by: George G. Vega Yon <g.vegayon@gmail.com> Co-authored-by: Dylan H. Morris <dzl1@cdc.gov>
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qmdversions of the jupyter notebooks (and their md versions).*_cache, if needed.