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Remove reporting templates (#604)
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* Remove reporting templates

* Add NEWS item

* Automatic readme update

---------

Co-authored-by: GitHub Action <action@github.com>
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jamesmbaazam and actions-user committed Mar 11, 2024
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1 change: 1 addition & 0 deletions NEWS.md
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* The contribution guide has been improved to include more detail on ways to contribute new features/enhancements, report bugs, and improve or suggest vignettes. By @jamesmbaazam in #464 and reviewed by @seabbs.
* Updated the code in `inst/CITATION` and added a GitHub Actions workflow to auto-generate `citation.cff` so that the two citation files are always in sync with `DESCRIPTION`. By @jamesmbazam in #467, with contributions from @Bisaloo, and reviewed by @seabbs and @sbfnk.
* Updated the documentation of the `reported_cases` argument in `estimate_infections()` and `confirm` column in the `obs` argument of `estimate_truncation()` to allow `numeric` types, not just `integer`. See #594, by @jamesmbaazam, and reviewed by @sbfnk.
* Removed the reporting templates that were previously provided. See #604 by @jamesmbaazam, and reviewed by @sbfnk.

## Package

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6 changes: 0 additions & 6 deletions README.Rmd
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</details>

<details> <summary> Reporting templates </summary>

Rmarkdown templates are provided in the package (`templates`) for semi-automated reporting of estimates. If using these templates to report your results please highlight our [limitations](https://doi.org/10.12688/wellcomeopenres.16006.1) as these are key to understanding the results from `{EpiNow2}` .

</details>

## Contributing

We welcome all contributions. If you have identified an issue with the package,
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18 changes: 3 additions & 15 deletions README.md
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`{EpiNow2}` estimates the time-varying reproduction number on cases by
date of infection (using a similar approach to that implemented in
[`{EpiEstim}`](https://github.com/mrc-ide/EpiEstim)). True infections
treated as latent and unobserved, estimated, and then mapped to observed
data (for example cases by date of report) via a series of uncertain
[`{EpiEstim}`](https://github.com/mrc-ide/EpiEstim)). True infections,
treated as latent and unobserved, are estimated and then mapped to
observed data (for example cases by date of report) via one or more
delay distributions (in the examples in the package documentation these
are an incubation period and a reporting delay) and a reporting model
that can include weekly periodicity.
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Covid-19 can be found
[here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867).

</details>
<details>
<summary>
Reporting templates
</summary>

Rmarkdown templates are provided in the package (`templates`) for
semi-automated reporting of estimates. If using these templates to
report your results please highlight our
[limitations](https://doi.org/10.12688/wellcomeopenres.16006.1) as these
are key to understanding the results from `{EpiNow2}` .

</details>

## Contributing
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52 changes: 0 additions & 52 deletions inst/templates/_region-report.Rmd

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