Cover TODO Next-Step Material Across Documentation

[AFg6K7h4fhy2]

Goal

Cover the TODOs previously specified across documentation files.

Context

With first-pass documentation (#47) maturing, a noteworthy point brought up by DHM concerned the presence of TODOs in the Notes sections of the docstrings. These were out of place, given the issue, but still somewhat important to address for enhancing the richness of the documentation. As such, these TODOs have been aggregated here. Expect some changes to this issue's contents as the TODOs are ported over.

Specifications

This checklist covers the historical TODOs in each file:

• Latent Folder
  • Add Notes in class HospAdmissionsSample in hospitaladmissions.py
  • Add Notes in class InfectHospRateSample in hospitaladmissions.py
  • Complete method validate() in infections.py
• Model Folder
  • Add See Also in def __init__() in class HospitalizationModel(Model) in hospitalizations.py
  • Add Examples in def sample_hospitalizations_latent() in class HospitalizationModel(Model) in hospitalizations.py
  • Add Examples in def sample_hospitalizations_obs() in class HospitalizationModel(Model) in hospitalizations.py
  • Add Examples in def sample_infections_obs() in class RtInfectionsRenewalModel(Model) in rtinfectionsrenewal.py
  • Add See Also in def sample() in class RtInfectionsRenewalModel(Model) in rtinfectionsrenewal.py
• Top Level Folder (pyrenew)
  • Add Examples in file docstring for convolve.py
  • convolve.py, new_convolve_scanner: Add Examples section.
  • convolve.py, new_convolve_scanner: Expand and or verify Returns section.

The remainder will be filled in w/ the completion of the corresponding PRs and issue 47.

Reference the files here (produced with tree | grep -Ev "\.png|\.pyc|\.txt|\.csv|\.doctree|\.rst":

.
├── pyrenew
│   ├── convolve.py
│   ├── datasets
│   │   ├── __init__.py
│   │   ├── data-raw
│   │   │   ├── README.md
│   │   │   ├── generation_interval.py
│   │   │   ├── infection_admission_interval.py
│   │   │   └── wastewater.R
│   │   ├── generation_interval.py
│   │   ├── generation_interval.tsv
│   │   ├── infection_admission_interval.py
│   │   ├── infection_admission_interval.tsv
│   │   ├── wastewater.py
│   │   └── wastewater.tsv
│   ├── deterministic
│   │   ├── __init__.py
│   │   ├── deterministic.py
│   │   ├── deterministicpmf.py
│   │   └── process.py
│   ├── distutil.py
│   ├── latent
│   │   ├── __init__.py
│   │   ├── hospitaladmissions.py
│   │   ├── i0.py
│   │   ├── infection_functions.py
│   │   └── infections.py
│   ├── math.py
│   ├── mcmcutils.py
│   ├── metaclass.py
│   ├── model
│   │   ├── __init__.py
│   │   ├── hospitalizations.py
│   │   └── rtinfectionsrenewal.py
│   ├── observation
│   │   ├── __init__.py
│   │   ├── negativebinomial.py
│   │   └── poisson.py
│   ├── process
│   │   ├── __init__.py
│   │   ├── ar.py
│   │   ├── firstdifferencear.py
│   │   ├── rtrandomwalk.py
│   │   └── simplerandomwalk.py
│   ├── regression.py
│   └── transform.py
└── test
    ├── __init__.py
    ├── baseline
    ├── test_ar_process.py
    ├── test_datasets.py
    ├── test_deterministic.py
    ├── test_first_difference_ar.py
    ├── test_latent_hospitalizations.py
    ├── test_latent_infections.py
    ├── test_leslie_matrix.py
    ├── test_logistic_susceptibility_adjustment.py
    ├── test_model_basic_renewal.py
    ├── test_model_hospitalizations.py
    ├── test_observation_negativebinom.py
    ├── test_observation_poisson.py
    ├── test_process_asymptotics.py
    ├── test_random_walk.py
    ├── test_regression.py
    └── test_transforms.py

10 directories, 56 files

Related Documents

• PR for top-level folder files documentation: [pending]
• PR for latent folder documentation: First Pass Documentation (docstrings) For Latent Folder #73
• PR for model folder documentation: First Pass Documentation (docstrings) For Model Folder #74
• PR for process folder documentation: [pending]
• PR for observation folder documentation: First Pass Documentation (docstrings) For Observation Folder #76
• PR for deterministic folder documentation: [pending]
• PR for quarto docs documentation: Issue 47 - pyrenew_demo.qmd #77