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Bring clean up and fixes to dev #19

Merged
merged 64 commits into from
Aug 8, 2023
Merged

Bring clean up and fixes to dev #19

merged 64 commits into from
Aug 8, 2023

Commits on Jul 5, 2023

  1. Initial styler run on R files

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  2. Styler run on vignette

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  3. Styler run on regenerated documentation

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    pratikunterwegs committed Jul 5, 2023
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  4. Correct spellings and update WORDLIST

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    pratikunterwegs committed Jul 5, 2023
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  5. Automatic readme update

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  6. Remove empty file visualisation.R

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    pratikunterwegs committed Jul 5, 2023
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  7. Add author ORCIDs, URL, BugReports to DESCRIPTION

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    pratikunterwegs committed Jul 5, 2023
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  8. Add author ORCID

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    pratikunterwegs committed Jul 5, 2023
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  9. Update title and description in DESCRIPTION

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    pratikunterwegs committed Jul 5, 2023
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  10. Add R dependency >= 3.5.0 for serialised data

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    pratikunterwegs committed Jul 5, 2023
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  11. Update WORDLIST and pkg doc Rd with study authors

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    pratikunterwegs committed Jul 5, 2023
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  12. Edit Readme to allow automated packagename and GH repo

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    pratikunterwegs committed Jul 5, 2023
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  13. Add contributing guide

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    pratikunterwegs committed Jul 5, 2023
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  14. Automatic readme update

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  15. Add general reference to Readme & vignette, add CSL refs file

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    pratikunterwegs committed Jul 5, 2023
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  16. Automatic readme update

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    actions-user committed Jul 5, 2023
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  17. Update WORDLIST for Readme updates

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    pratikunterwegs committed Jul 5, 2023
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  18. Add {qtl} to Suggests to avoid GHA R CMD check Note

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  19. Update WORDLIST with word in paper title

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  20. Update LICENSE files with correct year and pkg name

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  21. Add input checking get_age_group

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    pratikunterwegs committed Jul 5, 2023
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  22. Minor formatting edits get_age_group()

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    pratikunterwegs committed Jul 5, 2023
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  23. Update documentation get_age_groups()

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    pratikunterwegs committed Jul 5, 2023
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  24. Add testthat.R file

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  25. Add tests for get_age_groups()

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    pratikunterwegs committed Jul 5, 2023
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  26. Add {checkmate} to Imports

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    pratikunterwegs committed Jul 5, 2023
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  27. Update documentation get_age_group()

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    pratikunterwegs committed Jul 5, 2023
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  28. Ignore scratch file for development

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    pratikunterwegs committed Jul 5, 2023
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Commits on Jul 7, 2023

  1. Add input checking for set_status()

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    pratikunterwegs committed Jul 7, 2023
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  2. Update documentation for set_status()

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    pratikunterwegs committed Jul 7, 2023
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  3. Add operator argument options for set_status()

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    pratikunterwegs committed Jul 7, 2023
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  4. Add basic tests for set_status()

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    pratikunterwegs committed Jul 7, 2023
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  5. Update set_status() Rd file

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    pratikunterwegs committed Jul 7, 2023
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  6. Do not lint any and all usage in tests

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    pratikunterwegs committed Jul 7, 2023
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  7. Input checking, minor rearrangement, and docs for coh_effectiveness()

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    pratikunterwegs committed Jul 7, 2023
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  8. Nolint surv object for coxph, avoid warning from coxph

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    pratikunterwegs committed Jul 7, 2023
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Commits on Jul 10, 2023

  1. Add snapshot test for get_immunization_date()

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    pratikunterwegs committed Jul 10, 2023
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  2. Add input checking for get_immunization_date()

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    pratikunterwegs committed Jul 10, 2023
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  3. Simplify calculations in get_immunization_date(), rm dependencies

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    pratikunterwegs committed Jul 10, 2023
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  4. Run examples for get_immunization_date(), update Rd documentation, fo… 

    …rmat test file
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    pratikunterwegs committed Jul 10, 2023
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  5. Remove {rlang} from Imports

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    pratikunterwegs committed Jul 10, 2023
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  6. Add tests for immunization_date()

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  7. Make coh_eff_noconf return p-val as a numeric

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  8. Input checking, inherit params for fn coh_test_noconf()

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    pratikunterwegs committed Jul 10, 2023
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  9. Add tests, update documentation for cohort effectiveness fns

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  10. Add tests for time_to_event()

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    pratikunterwegs committed Jul 10, 2023
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  11. Add input checking for time_to_event()

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    pratikunterwegs committed Jul 10, 2023
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  12. Clean up code time_to_event()

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    pratikunterwegs committed Jul 10, 2023
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  13. Handle case of full immunity after cohort end

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  14. Handle case of death before full immunity

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    pratikunterwegs committed Jul 10, 2023
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  15. Cleanup of option from cohort start date

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    pratikunterwegs committed Jul 10, 2023
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  16. Minor formatting and run examples in time_to_event()

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    pratikunterwegs committed Jul 10, 2023
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  17. Update tests for time to event

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    pratikunterwegs committed Jul 10, 2023
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  18. Update documentation time_to_event()

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    pratikunterwegs committed Jul 10, 2023
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  19. Correct comments in tests for immunisation_date

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    pratikunterwegs committed Jul 10, 2023
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  20. Add tests for immunization_dose()

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  21. Add input checking, shorten fn get_immunization_dose()

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  22. Add tests for immunizing_vaccine - fn broken

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    pratikunterwegs committed Jul 10, 2023
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  23. Add snapshot test for immunizing_vaccine()

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    pratikunterwegs committed Jul 10, 2023
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  24. Simplify immunization_vaccine() fn

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  25. Update documentation immunization_vaccine()

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  26. Remove {dplyr} and {data.table} dependencies

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    pratikunterwegs committed Jul 10, 2023
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Commits on Aug 5, 2023

  1. Merge branch 'main' into dev-fixes-pratik

    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 5, 2023
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  2. Merge pull request #13 from epiverse-trace/dev-fixes-pratik 

    Package cleanup
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 5, 2023
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