Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Implement interventions on model rates #91

Merged
merged 62 commits into from
Sep 19, 2023
Merged

Implement interventions on model rates #91

merged 62 commits into from
Sep 19, 2023

Commits on Aug 18, 2023

  1. WIP interventions on rates

    @pratikunterwegs
    pratikunterwegs committed Aug 18, 2023
    Configuration menu
    Copy the full SHA
    1ab7208 View commit details
    Browse the repository at this point in the history

Commits on Aug 21, 2023

  1. Use unordered_map, temp params map for efficient access

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    ca435c5 View commit details
    Browse the repository at this point in the history

  2. Document and add constructor for C++ intervention class

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    d1dded0 View commit details
    Browse the repository at this point in the history

  3. C++ fn to convert interventions from R

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    ec54e17 View commit details
    Browse the repository at this point in the history

  4. Update fn for applying interventions on rate params

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    252f9f2 View commit details
    Browse the repository at this point in the history

  5. Remove infection param fn, superseded by translate_intervention

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    4b246fb View commit details
    Browse the repository at this point in the history

  6. Fn check_args_default adds dummy interv on beta for null

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    020e5b2 View commit details
    Browse the repository at this point in the history

  7. Update intervention checking default args

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    39fd190 View commit details
    Browse the repository at this point in the history

  8. Update intervention prep for default args

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    6f29e9c View commit details
    Browse the repository at this point in the history

  9. Update .epidemic_default_cpp()

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    ba4bef5 View commit details
    Browse the repository at this point in the history

  10. Update epidemic_default_cpp and RcppExports

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    00c7f5c View commit details
    Browse the repository at this point in the history

  11. R implementation, intervention on rates

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    0094d7f View commit details
    Browse the repository at this point in the history

  12. Add checks for args to default model

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    edfef6c View commit details
    Browse the repository at this point in the history

  13. Update test files

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    f76ed20 View commit details
    Browse the repository at this point in the history

  14. Update vignettes and docs for interventions on rates

    @pratikunterwegs
    pratikunterwegs committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    61acf16 View commit details
    Browse the repository at this point in the history

  15. Automatic readme update

    @actions-user
    actions-user committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    138240d View commit details
    Browse the repository at this point in the history

Commits on Aug 22, 2023

  1. Intervention constructor allows sub-classes

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    679d7ce View commit details
    Browse the repository at this point in the history

  2. Constructors for contacts and rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    07b6f03 View commit details
    Browse the repository at this point in the history

  3. Update fn intervention() with type and reduction arg

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    6f1e372 View commit details
    Browse the repository at this point in the history

  4. Validator for contacts intervention

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    301d370 View commit details
    Browse the repository at this point in the history

  5. Validator for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    7c4cf43 View commit details
    Browse the repository at this point in the history

  6. Remove redundant example for is_intervention

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    842e595 View commit details
    Browse the repository at this point in the history

  7. Fns to check for contacts and rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    cc01dd3 View commit details
    Browse the repository at this point in the history

  8. Rename no_intervention() to no_contacts_intervention()

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    f653026 View commit details
    Browse the repository at this point in the history

  9. Print methods for rate and contacts interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    4763c9e View commit details
    Browse the repository at this point in the history

  10. Update format method for intervention subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    0ffd744 View commit details
    Browse the repository at this point in the history

  11. Update as.intervention() for intervention subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    0009a90 View commit details
    Browse the repository at this point in the history

  12. Update c() method for contacts interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    cc7201a View commit details
    Browse the repository at this point in the history

  13. Add c() method for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    1dce52a View commit details
    Browse the repository at this point in the history

  14. Rename cumulative_intervention() to cumulative_contacts_intervention()

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    437f97c View commit details
    Browse the repository at this point in the history

  15. Call cumulative_contacts_intervention() in CM interv

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    3b11756 View commit details
    Browse the repository at this point in the history

  16. Add fn for cumulative rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    3f8b8a8 View commit details
    Browse the repository at this point in the history

  17. Update fn for interventions on rates

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    339014f View commit details
    Browse the repository at this point in the history

  18. Fn for null intervention on rates

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    8504a9c View commit details
    Browse the repository at this point in the history

  19. Update fns to account for intervention subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    4a78923 View commit details
    Browse the repository at this point in the history

  20. Update tests for new intervention subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    440cd11 View commit details
    Browse the repository at this point in the history

  21. Update vignettes with default model for interv subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    c5bfd87 View commit details
    Browse the repository at this point in the history

  22. Update NAMESPACE, WORDLIST, and Rd files

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    0805983 View commit details
    Browse the repository at this point in the history

  23. Update assert_intervention() for subclasses

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    51ca290 View commit details
    Browse the repository at this point in the history

  24. Fn check_args_default handles missing contact interv

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    ff5384e View commit details
    Browse the repository at this point in the history

  25. Fns for is_*() updated to remove intervention expectation

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    4f094c7 View commit details
    Browse the repository at this point in the history

  26. WIP vignette on modelling rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    9db6d45 View commit details
    Browse the repository at this point in the history

  27. Remove unnecessary concat

    @pratikunterwegs
    pratikunterwegs committed Aug 22, 2023
    Configuration menu
    Copy the full SHA
    f1f64c7 View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2023

  1. C++ rate_intervention struct holds double vectors

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    def43eb View commit details
    Browse the repository at this point in the history

  2. Rename C++ translate_intervs() to rate_intervs_cpp()

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    fb98e27 View commit details
    Browse the repository at this point in the history

  3. Rename cumulative_intervs to cumulative_contacts_intervs()

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    40f5483 View commit details
    Browse the repository at this point in the history

  4. C++ fn for cumulative rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    eca6d04 View commit details
    Browse the repository at this point in the history

  5. Update C++ fn intervention_on_rates()

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    017f03b View commit details
    Browse the repository at this point in the history

  6. Update vacamole model header with rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    b2ed175 View commit details
    Browse the repository at this point in the history

  7. Update default model header with rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    768e39f View commit details
    Browse the repository at this point in the history

  8. Update check_args_vacamole for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    3e56e43 View commit details
    Browse the repository at this point in the history

  9. Update epidemic_vacamole_x() for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    8ab3d7f View commit details
    Browse the repository at this point in the history

  10. Update .epidemic_vacamole_cpp() for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    09cbad6 View commit details
    Browse the repository at this point in the history

  11. Update .epidemic_default_cpp for rate interventions

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    f1a5750 View commit details
    Browse the repository at this point in the history

  12. Update Vacamole tests with rate interventions allowed

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    0832278 View commit details
    Browse the repository at this point in the history

  13. Add pkdown article in index, update docs and RcppExports

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    fdafe3a View commit details
    Browse the repository at this point in the history

  14. C++ linting and formatting

    @pratikunterwegs
    pratikunterwegs committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    4da5445 View commit details
    Browse the repository at this point in the history

Commits on Aug 24, 2023

  1. Remove type choices from default args

    @pratikunterwegs
    pratikunterwegs committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    9b18713 View commit details
    Browse the repository at this point in the history

  2. Correct intervention calls in vignettes and tests

    @pratikunterwegs
    pratikunterwegs committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    e8a8f31 View commit details
    Browse the repository at this point in the history

  3. Update intervention docs, remove extra message

    @pratikunterwegs
    pratikunterwegs committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    7956d63 View commit details
    Browse the repository at this point in the history

  4. Correct intervention calls in vignettes

    @pratikunterwegs
    pratikunterwegs committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    ad016de View commit details
    Browse the repository at this point in the history

  5. Update rate interventions vignette

    @pratikunterwegs
    pratikunterwegs committed Aug 24, 2023
    Configuration menu
    Copy the full SHA
    de4ee5a View commit details
    Browse the repository at this point in the history