Code

Pre-release fixes#104

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pratikunterwegs merged 51 commits intomainepiverse-trace/cfr:mainfrom dev/fixesepiverse-trace/cfr:dev/fixesCopy head branch name to clipboardNov 21, 2023

+801-21,831

Commits

Commits on Nov 16, 2023

• Vapply avoids loops in cfr_rolling.R

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• Correct known_onsets shifting

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• Compact iteration in cfr_time_varying.R

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• Remove duplicated date col in Readme.Rmd

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• Automatic readme update

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• Vignette edits from code review

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• Remove stray DS_Store and CSV data

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• Remove empty test file

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• Check that Poisson threshold is > 0

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• Check burn_in is a count not strictly int

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• Update function documentation

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• Guard against noSuggests check in tests

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• Correct URLs

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• Pkg title change to ascertainment, uniform ORCIDs

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• Future install instructions, correct quick example

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• Add news and CRAN comments

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• Automatic readme update

  

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• Remove old Readme figures

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• Add data description and source in data-raw

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• Update logo with text to paths

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• Required args come first in estimate_ascertainment()

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• Remove max date argument, rm related tests

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• Ignore doc/ and Meta/

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• Remove linelist to incidence2 example in data prep vig

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• Fix Readme plotting code

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• Automatic readme update

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• Rename known_onsets to expected_outcomes

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• Use vapply in estimate_outcomes()

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• Add date input checks to cfr_time_varyind

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• Add internal fn for expected outcomes

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• Internal fn does not round or rm NAs

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Commits on Nov 17, 2023

• cfr_time_varying() uses round() on internal convolve fn

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• Simplify cfr_time_varying() to assume daily data

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• Use lchoose() and round(ut * cases) in estimate_severity()

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• Update tests and docs for

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• Format code and remove DS_Store

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• Update vignettes, wordlist, Readme

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• Automatic readme update

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• Add @sbfnk as reviewer

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Commits on Nov 20, 2023

• Correct expected_outcomes calc, rev 8d7db4c, add tv_cfr test

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• Add documentation on burn_in to cfr_tv fn doc and vignette

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• Remove TODO notes

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• Update Readme with related projects

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• Automatic readme update

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• Clearer naming for ascertainment data

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• Skip test without {distributional}

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• Add test to check for index bias, WIP #108

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• Add tests for cfr_time_varying and ascertainment correctness

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• Simplify cases-PMFs convolution function

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• Update ascertainment snapshot test file

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• Update WORDLIST

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