Code

Bring clean up and fixes to dev#19

Code

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davidsantiagoquevedo merged 64 commits intodevepiverse-trace/vaccineff:devfrom mainepiverse-trace/vaccineff:mainCopy head branch name to clipboardAug 8, 2023

+1,764-612

Commits

Commits on Jul 5, 2023

• Initial styler run on R files

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• Styler run on vignette

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• Styler run on regenerated documentation

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• Correct spellings and update WORDLIST

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• Automatic readme update

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• Remove empty file visualisation.R

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• Add author ORCIDs, URL, BugReports to DESCRIPTION

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• Add author ORCID

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• Update title and description in DESCRIPTION

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• Add R dependency >= 3.5.0 for serialised data

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• Update WORDLIST and pkg doc Rd with study authors

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• Edit Readme to allow automated packagename and GH repo

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• Add contributing guide

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• Automatic readme update

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

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• Automatic readme update

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• Update WORDLIST for Readme updates

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• Add {qtl} to Suggests to avoid GHA R CMD check Note

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• Update WORDLIST with word in paper title

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• Update LICENSE files with correct year and pkg name

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• Add input checking get_age_group

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• Minor formatting edits get_age_group()

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• Update documentation get_age_groups()

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• Add testthat.R file

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• Add tests for get_age_groups()

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• Add {checkmate} to Imports

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• Update documentation get_age_group()

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• Ignore scratch file for development

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Commits on Jul 7, 2023

• Add input checking for set_status()

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• Update documentation for set_status()

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• Add operator argument options for set_status()

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• Add basic tests for set_status()

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• Update set_status() Rd file

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• Do not lint any and all usage in tests

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• Input checking, minor rearrangement, and docs for coh_effectiveness()

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• Nolint surv object for coxph, avoid warning from coxph

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Commits on Jul 10, 2023

• Add snapshot test for get_immunization_date()

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• Add input checking for get_immunization_date()

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• Simplify calculations in get_immunization_date(), rm dependencies

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• Run examples for get_immunization_date(), update Rd documentation, format test file

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• Remove {rlang} from Imports

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• Add tests for immunization_date()

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• Make coh_eff_noconf return p-val as a numeric

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• Input checking, inherit params for fn coh_test_noconf()

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• Add tests, update documentation for cohort effectiveness fns

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• Add tests for time_to_event()

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• Add input checking for time_to_event()

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• Clean up code time_to_event()

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• Handle case of full immunity after cohort end

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• Handle case of death before full immunity

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• Cleanup of option from cohort start date

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• Minor formatting and run examples in time_to_event()

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• Update tests for time to event

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• Update documentation time_to_event()

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• Correct comments in tests for immunisation_date

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• Add tests for immunization_dose()

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• Add input checking, shorten fn get_immunization_dose()

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• Add tests for immunizing_vaccine - fn broken

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• Add snapshot test for immunizing_vaccine()

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• Simplify immunization_vaccine() fn

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• Update documentation immunization_vaccine()

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

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Commits on Aug 5, 2023

• Merge branch 'main' into dev-fixes-pratik

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• Merge pull request #13 from epiverse-trace/dev-fixes-pratik

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