-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
3902b14
commit dff5cd6
Showing
1 changed file
with
62 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,62 @@ | ||
# Contributing to `GeoTox` | ||
This outlines how to (1) propose a change to `GeoTox` and (2) serves as log of potential enhancements for `GeoTox`. | ||
|
||
## Best Practices | ||
|
||
If you’ve found a bug, please file an issue that illustrates the bug with a minimal | ||
[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). | ||
See tidyverse team's guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice. | ||
When adding a new function to the package, always add working examples of the new function in roxygen2 documentation under `#' @examples`. | ||
|
||
### Pull request process | ||
|
||
* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("NIEHS/GeoTox", fork = TRUE)`. | ||
|
||
* Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. | ||
If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. | ||
* Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`. | ||
|
||
* Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser. | ||
The title of your PR should briefly describe the change. | ||
The body of your PR should contain `Fixes #issue-number`. | ||
|
||
* For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). | ||
|
||
### Code style | ||
|
||
* Please abide by 80-character line rules (as default settings in `lintr`) | ||
|
||
* We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation. | ||
|
||
* We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. | ||
Contributions with test cases included are easier to accept. | ||
|
||
## Fixing typos | ||
|
||
You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. | ||
This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. | ||
You can find the `.R` file that generates the `.Rd` by reading the comment in the first line. | ||
|
||
## GeoTox Open Issues and Enhancements | ||
|
||
This section serves as log of potential enhancements for `GeoTox`. Community members are welcomed and encouraged to use our contributing guide to address the open issues and enhancements to this package. Additionally, new enhancements can be proposed by using our `enhancements` template request. If you want to address an open enchancement or suggest a new one, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. | ||
|
||
|
||
### Scientific | ||
|
||
1) Non-steady state toxicokinetics. This will likely require additional usage of the `httk` package. | ||
2) Complete integration of the multiple end-point analysis into the GeoTox objects | ||
3) Integration of Reflected Generalized Concentration Addition ([RGCA](https://github.com/NIEHS/RGCA)), which will allow 3+ parameter hill models to be used for additive mixture predictions. | ||
4) Benchmark Dose modeling (BMD) as a metric for risk assessment. Suggested ingetrations include [BMDexpress2.0](https://www.sciome.com/bmdexpress/) or [transcryptR](https://github.com/NIEHS/transcryptR) - note `transcryptR` is also currently a [](https://www.repostatus.org/#wip) | ||
|
||
### Computational | ||
|
||
1) `targets` pipeline template. If we provide a make-like targets pipeline, then new users will have a reproducible template to run their analysis with ease. | ||
|
||
|
||
|
||
## Code of Conduct | ||
|
||
Please note that the chopin 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. |