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

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pratikunterwegs merged 60 commits intomainepiverse-trace/cfr:mainfrom reviewepiverse-trace/cfr:reviewCopy head branch name to clipboardSep 15, 2023

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Commits on Sep 11, 2023

• Edits to vignettes from code review

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• Add further vignette suggestions from review

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• Remove dev packages from Suggests

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• Account for changes to epidist_db(), WIP #80

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• Remove creation of empty objects

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• Style vignettes and Readme, also WIP #80

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• Update fn get_default_burn_in() for better param access

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• CFR: case fatality risk, use 'ascertainment ratio'

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• Update Readme.Rmd with details on {epiparameter}

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• Correct for delays is default, epidist has no default value

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• Change outputs to use full names, e.g. 'mean' instead of 'me'

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• Update documentation and miscellaneous fixes

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• Updates to vignettes

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• Update Readme.Rmd and DESCRIPTION

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Commits on Sep 13, 2023

• Update pkg data prep and documentation

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• Simplify estimate_rolling()

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• Minor tweaks to docs for estimate_severity()

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• Simplify estimate_ascertainment(), update docs

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• Add method details to estimate_static(), correct arg order

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• Add mthd details est_time_var(), correct arg order

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• Check for parameterised epidist for get default burnin

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• Add checks to known_outcomes(), edit docs

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• Unify prepare_data generic and method docs

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• Basic tests for default burn in

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• Add tests for time varying ascertainment, add baseline value

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• Add test for prepare_data with NAs present

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• Update test snapshots

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• Minor updates to vignettes

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• Update all Rd files

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• Update GHA workflows

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• Update .gitignore, .lintr, .Rbuildignore

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• Add citation file

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• Allow coordinate expansion in Readme plot

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• Unquote dataframe col names on creation

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Commits on Sep 14, 2023

• Remove empty vector creation

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• Use mean method for epidist, fixes #81

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• Rename CFR functions from estimate_* to cfr_*

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• Rm logical function args

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• Update Readme and add text to vignettes

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Commits on Sep 15, 2023

• Fn arg epidist defaults to NULL

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• Update fn arg documentation and maths

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• Update math formatting in vignettes

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• Rename burn_in_value to burn_in, allow 0s

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• Minor formatting

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• Update wordlist

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• Update documentation for burn_in arg

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• Update example for cfr_time_varying

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• Update formatting for cfr_time_varying

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• Small possible speed up to cfr_time_varying

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• Test that known_outcomes gives no NAs

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• Vectorise loop in cfr_time_varying()

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• Remove DS_Store file

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• Rename MLE to maximum likelihood estimate

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• Add citation for Covid-19 CFR estimate, add to ref library

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• Update Rd files with new documentation

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