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Clarify propagating truncation uncertainty #644

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merged 6 commits into from
May 2, 2024
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jamesmbaazam
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@jamesmbaazam jamesmbaazam commented Apr 30, 2024

Description

This PR closes #367 and further clarifies discussions in #365.

This PR expands the text on passing estimated truncation distributions to epinow(), regional_epinow(), and estimate_infections(). It explicitly points out which output from estimate_truncation() can be passed to the mentioned
functions and provides an example in the estimate_truncation() help file.

Initial submission checklist

  • My PR is based on a package issue and I have explicitly linked it.
  • I have tested my changes locally (using devtools::test() and devtools::check()).
  • I have added or updated unit tests where necessary.
  • I have updated the documentation if required and rebuilt docs if yes (using devtools::document()).
  • I have followed the established coding standards (and checked using lintr::lint_package()).
  • I have added a news item linked to this PR.

After the initial Pull Request

  • I have reviewed Checks for this PR and addressed any issues as far as I am able.

@jamesmbaazam jamesmbaazam requested a review from sbfnk April 30, 2024 15:30
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This is great! Just one suggested rewrite.

R/estimate_infections.R Outdated Show resolved Hide resolved
@sbfnk sbfnk enabled auto-merge (squash) May 2, 2024 10:57
@sbfnk sbfnk merged commit 0a1d58e into main May 2, 2024
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@sbfnk sbfnk deleted the passing-uncertainty branch May 2, 2024 13:21
sbfnk added a commit that referenced this pull request May 3, 2024
* Clarify propagating truncation uncertainty

* Add NEWS item

* Simplify wording of truncation argument

Co-authored-by: Sebastian Funk <[email protected]>

* Generate Rd files

---------

Co-authored-by: Sebastian Funk <[email protected]>
sbfnk added a commit that referenced this pull request May 3, 2024
* Clarify propagating truncation uncertainty

* Add NEWS item

* Simplify wording of truncation argument

Co-authored-by: Sebastian Funk <[email protected]>

* Generate Rd files

---------

Co-authored-by: Sebastian Funk <[email protected]>
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Clarify documentation for passing uncertainty from estimate_truncation to estimate_infections
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