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Merge contributions from summit's challenge #22

Merged
merged 80 commits into from
Aug 13, 2023
Merged

Merge contributions from summit's challenge #22

merged 80 commits into from
Aug 13, 2023

Commits on Jun 26, 2023

  1. Merge pull request #2 from TRACE-LAC/dev 

    readme basics
    @GeraldineGomez
    GeraldineGomez authored Jun 26, 2023
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Commits on Jun 28, 2023

  1. Merge pull request #4 from TRACE-LAC/dev 

    first release cohort study design
    @tracelac
    tracelac authored Jun 28, 2023
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Commits on Jul 5, 2023

  1. Merge pull request #9 from TRACE-LAC/dev 

    Dev
    @GeraldineGomez
    GeraldineGomez authored Jul 5, 2023
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  2. Merge pull request #11 from epiverse-trace/dev 

    adding etdev package to description file
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Jul 5, 2023
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  3. Initial styler run on R files

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  5. Styler run on regenerated documentation

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  7. Automatic readme update

    @actions-user
    actions-user committed Jul 5, 2023
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  8. Remove empty file visualisation.R

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  10. Add author ORCID

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

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

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  15. Add contributing guide

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  16. Automatic readme update

    @actions-user
    actions-user committed Jul 5, 2023
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  17. Add general reference to Readme & vignette, add CSL refs file

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  18. Automatic readme update

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  21. Update WORDLIST with word in paper title

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  22. Update LICENSE files with correct year and pkg name

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  23. Add input checking get_age_group

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  26. Add testthat.R file

    @pratikunterwegs
    pratikunterwegs committed Jul 5, 2023
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  27. Add tests for get_age_groups()

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

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

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

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

  1. Add input checking for set_status()

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

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

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

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

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

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

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

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

  1. Use epiverse pkgdown theme 

    This adds a link to the code of conduct in Spanish, as well as google analytics
    @Bisaloo
    Bisaloo committed Jul 10, 2023
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  2. Add snapshot test for get_immunization_date()

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

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

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

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  8. Make coh_eff_noconf return p-val as a numeric

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  9. Input checking, inherit params for fn coh_test_noconf()

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

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  11. Add tests for time_to_event()

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

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  15. Handle case of death before full immunity

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

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

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

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

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  22. Add input checking, shorten fn get_immunization_dose()

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  23. Add tests for immunizing_vaccine - fn broken

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

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

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  26. Update documentation immunization_vaccine()

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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  27. Remove {dplyr} and {data.table} dependencies

    @pratikunterwegs
    pratikunterwegs committed Jul 10, 2023
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Commits on Aug 1, 2023

  1. Merge pull request #14 from epiverse-trace/epiversetheme 

    Use epiverse pkgdown theme
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 1, 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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Commits on Aug 8, 2023

  1. Merge pull request #19 from epiverse-trace/main 

    Bring clean up and fixes to dev
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 8, 2023
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  2. added new logo

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  3. updated contributions

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  4. updated contribution list on README

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  5. updated ORCID and contributions

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  6. fix: minor typo on authorship

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  7. fix: indentations

    @davidsantiagoquevedo
    davidsantiagoquevedo committed Aug 8, 2023
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  8. Merge pull request #20 from epiverse-trace/dev-minor-fixes 

    Dev minor fixes
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 8, 2023
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  9. Automatic readme update

    @actions-user
    actions-user committed Aug 8, 2023
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  10. Merge pull request #21 from epiverse-trace/dev 

    Dev
    @davidsantiagoquevedo
    davidsantiagoquevedo authored Aug 8, 2023
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