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Remove inaccurate text from README (#173)
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athowes authored Jul 17, 2024
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57 changes: 25 additions & 32 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,17 @@ cat(gsub("\n[ ]+"," ",packageDescription("epidist")$Description))

<details><summary>Installing the package</summary>

You can install the latest released version using the normal `R` function, though you need to point to `r-universe` instead of CRAN:
<!-- You can install the latest released version using the normal `R` function, though you need to point to `r-universe` instead of CRAN: -->

```{r, eval = FALSE}
install.packages(
"epidist", repos = "https://epinowcast.r-universe.dev"
)
```
<!-- ```{r, eval = FALSE} -->
<!-- install.packages( -->
<!-- "epidist", repos = "https://epinowcast.r-universe.dev" -->
<!-- ) -->
<!-- ``` -->

Alternatively, you can use the [`remotes` package](https://remotes.r-lib.org/) to install the development version from Github (warning! this version may contain breaking changes and/or bugs):
<!-- Alternatively, y -->

You can use the [`remotes` package](https://remotes.r-lib.org/) to install the development version from Github (warning! this version may contain breaking changes and/or bugs):

```{r, eval = FALSE}
remotes::install_github(
Expand Down Expand Up @@ -80,15 +82,15 @@ install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOpt
cmdstanr::install_cmdstan()
```

*Note: You can speed up CmdStan installation using the `cores` argument. If you are installing a particular version of `epinowcast`, you may also need to install a past version of CmdStan, which you can do with the `version` argument.*
*Note: You can speed up CmdStan installation using the `cores` argument. If you are installing a particular version of `epidist`, you may also need to install a past version of CmdStan, which you can do with the `version` argument.*

</details>

<details><summary>Alternative: Docker</summary>
<!-- <details><summary>Alternative: Docker</summary> -->

We also provide a [Docker](https://www.docker.com/get-started/) image with [`epinowcast` and all dependencies installed](https://github.com/orgs/epinowcast/packages/container/package/epidist). You can use this image to run `epidist` without installing dependencies.
<!-- We also provide a [Docker](https://www.docker.com/get-started/) image with [all dependencies installed](https://github.com/orgs/epinowcast/packages/container/package/epidist). You can use this image to run `epidist` without installing dependencies. -->

</details>
<!-- </details> -->

## Resources

Expand All @@ -100,30 +102,32 @@ Our [organisation website](https://www.epinowcast.org/) includes links to other

<details><summary>Community Forum</summary>

Our [community forum](https://community.epinowcast.org/) has areas for [question and answer](https://community.epinowcast.org/c/interface/15) and [considering new methods and tools](https://community.epinowcast.org/c/projects/11), among others. If you are generally interested in real-time analysis of infectious disease, you may find this useful even if do not use `epinowcast`.
Our [community forum](https://community.epinowcast.org/) has areas for [question and answer](https://community.epinowcast.org/c/interface/15) and [considering new methods and tools](https://community.epinowcast.org/c/projects/11), among others. If you are generally interested in real-time analysis of infectious disease, you may find this useful even if do not use `epidist`.

</details>

## Contributing

We welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/epidist/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/epidist/pulls) and see our [contributing guide](CONTRIBUTING.md) for more information.
We welcome contributions and new contributors! We particularly appreciate help on [identifying and identified issues](https://github.com/epinowcast/epidist/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epinowcast/epidist/pulls).

### How to make a bug report or feature request
<!-- and see our [contributing guide](CONTRIBUTING.md) for more information. -->

Please briefly describe your problem and what output you expect in an [issue](https://github.com/epinowcast/epidist/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/dist/discussions/categories/q-a). See our [contributing guide](CONTRIBUTING.md) for more information.
<!-- ### How to make a bug report or feature request -->

### Code of Conduct

Please note that the `epidist` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
<!-- Please briefly describe your problem and what output you expect in an [issue](https://github.com/epinowcast/epidist/issues). -->

## Citation
<!-- If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/dist/discussions/categories/q-a). -->
<!-- See our [contributing guide](CONTRIBUTING.md) for more information. -->

If making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [model outline](https://epidist.epinowcast.org/articles/model.html). If you use `epidist` in your work, please consider citing it with `citation("epidist")`.
<!-- ### Code of Conduct -->

## Contributors
<!-- Please note that the `epidist` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. -->

## Citation

If making use of our methodology or the methodology on which ours is based, please cite the relevant papers from our [model outline](https://epidist.epinowcast.org/articles/model.html). If you use `epidist` in your work, please consider citing it with `citation("epidist")`.

## Contributors

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
<!-- prettier-ignore-start -->
Expand All @@ -133,33 +137,22 @@ All contributions to this project are gratefully acknowledged using the [`allcon

### Code


<a href="https://github.com/epinowcast/epidist/commits?author=seabbs">seabbs</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=athowes">athowes</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=parksw3">parksw3</a>,
<a href="https://github.com/epinowcast/epidist/commits?author=medewitt">medewitt</a>



### Issue Authors


<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Akgostic">kgostic</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3ATimTaylor">TimTaylor</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Ajamesmbaazam">jamesmbaazam</a>



### Issue Contributors


<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Apearsonca">pearsonca</a>,
<a href="https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Asbfnk">sbfnk</a>


<!-- markdownlint-enable -->
<!-- prettier-ignore-end -->
<!-- ALL-CONTRIBUTORS-LIST:END -->



68 changes: 25 additions & 43 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,20 +38,17 @@ biased conclusions.
<summary>
Installing the package
</summary>

You can install the latest released version using the normal `R`
function, though you need to point to `r-universe` instead of CRAN:

``` r
install.packages(
"epidist", repos = "https://epinowcast.r-universe.dev"
)
```

Alternatively, you can use the [`remotes`
package](https://remotes.r-lib.org/) to install the development version
from Github (warning! this version may contain breaking changes and/or
bugs):
<!-- You can install the latest released version using the normal `R` function, though you need to point to `r-universe` instead of CRAN: -->
<!-- ```{r, eval = FALSE} -->
<!-- install.packages( -->
<!-- "epidist", repos = "https://epinowcast.r-universe.dev" -->
<!-- ) -->
<!-- ``` -->
<!-- Alternatively, y -->

You can use the [`remotes` package](https://remotes.r-lib.org/) to
install the development version from Github (warning! this version may
contain breaking changes and/or bugs):

``` r
remotes::install_github(
Expand Down Expand Up @@ -96,22 +93,14 @@ cmdstanr::install_cmdstan()
```

*Note: You can speed up CmdStan installation using the `cores` argument.
If you are installing a particular version of `epinowcast`, you may also
If you are installing a particular version of `epidist`, you may also
need to install a past version of CmdStan, which you can do with the
`version` argument.*

</details>
<details>
<summary>
Alternative: Docker
</summary>

We also provide a [Docker](https://www.docker.com/get-started/) image
with [`epinowcast` and all dependencies
installed](https://github.com/orgs/epinowcast/packages/container/package/epidist).
You can use this image to run `epidist` without installing dependencies.

</details>
<!-- <details><summary>Alternative: Docker</summary> -->
<!-- We also provide a [Docker](https://www.docker.com/get-started/) image with [all dependencies installed](https://github.com/orgs/epinowcast/packages/container/package/epidist). You can use this image to run `epidist` without installing dependencies. -->
<!-- </details> -->

## Resources

Expand All @@ -136,7 +125,7 @@ Our [community forum](https://community.epinowcast.org/) has areas for
and [considering new methods and
tools](https://community.epinowcast.org/c/projects/11), among others. If
you are generally interested in real-time analysis of infectious
disease, you may find this useful even if do not use `epinowcast`.
disease, you may find this useful even if do not use `epidist`.

</details>

Expand All @@ -146,22 +135,15 @@ We welcome contributions and new contributors! We particularly
appreciate help on [identifying and identified
issues](https://github.com/epinowcast/epidist/issues). Please check and
add to the issues, and/or add a [pull
request](https://github.com/epinowcast/epidist/pulls) and see our
[contributing guide](CONTRIBUTING.md) for more information.

### How to make a bug report or feature request

Please briefly describe your problem and what output you expect in an
[issue](https://github.com/epinowcast/epidist/issues). If you have a
question, please don’t open an issue. Instead, ask on our [Q and A
page](https://github.com/epinowcast/dist/discussions/categories/q-a).
See our [contributing guide](CONTRIBUTING.md) for more information.

### Code of Conduct

Please note that the `epidist` project is released with a [Contributor
Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project,
you agree to abide by its terms.
request](https://github.com/epinowcast/epidist/pulls).

<!-- and see our [contributing guide](CONTRIBUTING.md) for more information. -->
<!-- ### How to make a bug report or feature request -->
<!-- Please briefly describe your problem and what output you expect in an [issue](https://github.com/epinowcast/epidist/issues). -->
<!-- If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epinowcast/dist/discussions/categories/q-a). -->
<!-- See our [contributing guide](CONTRIBUTING.md) for more information. -->
<!-- ### Code of Conduct -->
<!-- Please note that the `epidist` project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. -->

## Citation

Expand Down

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