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Review {cfr} v0.1.0 for CRAN release #78

Merged
merged 60 commits into from
Sep 15, 2023
Merged

Review {cfr} v0.1.0 for CRAN release #78

merged 60 commits into from
Sep 15, 2023

Commits on Sep 11, 2023

  1. Edits to vignettes from code review 

    This commit adds a number of edits bundled together in a batch.

Co-authored-by: Adam Kucharski <[email protected]>
Co-authored-by: James Azam <[email protected]>
    @pratikunterwegs @adamkucharski @jamesmbaazam
    3 people authored Sep 11, 2023
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  2. Add further vignette suggestions from review 

    Co-authored-by: James Azam <[email protected]>
    @pratikunterwegs @jamesmbaazam
    pratikunterwegs and jamesmbaazam authored Sep 11, 2023
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  3. Automatic readme update

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    actions-user committed Sep 11, 2023
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  4. Remove dev packages from Suggests

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    pratikunterwegs committed Sep 11, 2023
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  5. Account for changes to epidist_db(), WIP #80

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    pratikunterwegs committed Sep 11, 2023
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  6. Remove creation of empty objects

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    pratikunterwegs committed Sep 11, 2023
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  7. Style vignettes and Readme, also WIP #80

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    pratikunterwegs committed Sep 11, 2023
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  8. Update fn get_default_burn_in() for better param access 

    Fix get_default_burn_in()

Use {epiparameter} fns in get_default_burn_in()
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    pratikunterwegs committed Sep 11, 2023
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  9. CFR: case fatality risk, use 'ascertainment ratio'

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    pratikunterwegs committed Sep 11, 2023
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  10. Update Readme.Rmd with details on {epiparameter}

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    pratikunterwegs committed Sep 11, 2023
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  11. Correct for delays is default, epidist has no default value

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    pratikunterwegs committed Sep 11, 2023
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  12. Change outputs to use full names, e.g. 'mean' instead of 'me'

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    pratikunterwegs committed Sep 11, 2023
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  13. Update documentation and miscellaneous fixes

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    pratikunterwegs committed Sep 11, 2023
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  14. Updates to vignettes

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    pratikunterwegs committed Sep 11, 2023
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  15. Update Readme.Rmd and DESCRIPTION

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    pratikunterwegs committed Sep 11, 2023
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  16. Correct Readme.Rmd for correction by default

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  17. Automatic readme update

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Commits on Sep 13, 2023

  1. Update pkg data prep and documentation

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    pratikunterwegs committed Sep 13, 2023
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  2. Simplify estimate_rolling()

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    pratikunterwegs committed Sep 13, 2023
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  3. Minor tweaks to docs for estimate_severity()

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    pratikunterwegs committed Sep 13, 2023
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  4. Simplify estimate_ascertainment(), update docs

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    pratikunterwegs committed Sep 13, 2023
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  5. Add method details to estimate_static(), correct arg order

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  6. Add mthd details est_time_var(), correct arg order

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    pratikunterwegs committed Sep 13, 2023
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  7. Check for parameterised epidist for get default burnin

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    pratikunterwegs committed Sep 13, 2023
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  8. Add checks to known_outcomes(), edit docs

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    pratikunterwegs committed Sep 13, 2023
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  9. Unify prepare_data generic and method docs

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    pratikunterwegs committed Sep 13, 2023
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  10. Basic tests for default burn in

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    pratikunterwegs committed Sep 13, 2023
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  11. Add tests for time varying ascertainment, add baseline value

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    pratikunterwegs committed Sep 13, 2023
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  12. Add test for prepare_data with NAs present

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    pratikunterwegs committed Sep 13, 2023
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  13. Update test snapshots

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    pratikunterwegs committed Sep 13, 2023
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  14. Minor updates to vignettes

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    pratikunterwegs committed Sep 13, 2023
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  15. Update all Rd files

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    pratikunterwegs committed Sep 13, 2023
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  16. Update GHA workflows

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    pratikunterwegs committed Sep 13, 2023
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  17. Update .gitignore, .lintr, .Rbuildignore

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    pratikunterwegs committed Sep 13, 2023
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  18. Add citation file

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    pratikunterwegs committed Sep 13, 2023
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  19. Allow coordinate expansion in Readme plot

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    pratikunterwegs committed Sep 13, 2023
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  20. Automatic readme update

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  21. Unquote dataframe col names on creation

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    pratikunterwegs committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. Remove empty vector creation

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    pratikunterwegs committed Sep 14, 2023
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  2. Use mean method for epidist, fixes #81

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    pratikunterwegs committed Sep 14, 2023
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  3. Rename CFR functions from estimate_* to cfr_*

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    pratikunterwegs committed Sep 14, 2023
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  4. Rm logical function args

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    pratikunterwegs committed Sep 14, 2023
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  5. Update Readme and add text to vignettes

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    pratikunterwegs committed Sep 14, 2023
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  6. Automatic readme update

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Commits on Sep 15, 2023

  1. Fn arg epidist defaults to NULL

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    pratikunterwegs committed Sep 15, 2023
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  2. Update fn arg documentation and maths

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    pratikunterwegs committed Sep 15, 2023
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  3. Update math formatting in vignettes

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    pratikunterwegs committed Sep 15, 2023
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  4. Rename burn_in_value to burn_in, allow 0s

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    pratikunterwegs committed Sep 15, 2023
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  5. Minor formatting

    @pratikunterwegs
    pratikunterwegs committed Sep 15, 2023
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  6. Update wordlist

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    pratikunterwegs committed Sep 15, 2023
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  7. Update documentation for burn_in arg

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    pratikunterwegs committed Sep 15, 2023
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  8. Update example for cfr_time_varying

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    pratikunterwegs committed Sep 15, 2023
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  9. Update formatting for cfr_time_varying

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    pratikunterwegs committed Sep 15, 2023
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  10. Small possible speed up to cfr_time_varying

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    pratikunterwegs committed Sep 15, 2023
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  11. Test that known_outcomes gives no NAs

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    pratikunterwegs committed Sep 15, 2023
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  12. Vectorise loop in cfr_time_varying()

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    pratikunterwegs committed Sep 15, 2023
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  13. Remove DS_Store file

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    pratikunterwegs committed Sep 15, 2023
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  14. Rename MLE to maximum likelihood estimate

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    pratikunterwegs committed Sep 15, 2023
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  15. Add citation for Covid-19 CFR estimate, add to ref library

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    pratikunterwegs committed Sep 15, 2023
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  16. Update Rd files with new documentation

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    pratikunterwegs committed Sep 15, 2023
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