README.qmd

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# `hgp: HandelGroupPackage`

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`hgp` is a package for storing utility functions for use across handelgroup.
Right now, `hgp` contains the following utilities:

* A group-standard `ggplot2` theme function;
* A set of functions for working with HAI data;
* A function to standardize influenza strain names for the strains used in the
datasets we have available to us; along with a corresponding data set of
standardized strain names.

**Because this repo is public, absolutely NO sensitive or confidential
information should be stored here. This repo is strictly for shared utilities.**

## Installation

You can install the development version of hgp from [GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("ahgroup/hgp")
```

Or if you are in a repository with `renv` enabled (recommended):

``` r
renv::install("ahgroup/hgp")
```

## Using the `ggplot2` theme

If you have a `ggplot2` plot already created, you can add an `hgp` theme to
it in the same way as any other theme

```r
library(ggplot2)
## basic example code
ggplot(mtcars) +
	aes(x = wt, y = mpg) +
	geom_point() +
	hgp::theme_ms()
```

You can also implement an `hgp` theme at the global (script) level. After
executing this code, all `ggplot` objects you produce afterwards will use this
theme.

```r
ggplot2::theme_set(hgp::theme_ms())
```

## Contributions

* If you contribute to `hgp`, please follow the following steps.
* We recommend referring to the appropriate section(s) in
[R Packages, 2e](https://r-pkgs.org/) for any confusing steps.
* Ensure that you run `usethis::git_vaccinate()` on every local environment
(typically new machine) that you intend to edit this package on. This helps
to prevent leakage of PII.
* All functions should be documented using standard `roxygen2` syntax, and you
should use `devtools::document()` to generate the documentation files.
* Please run `devtools:check()` before merging any new functionality to the
main branch and fix any resulting messages. It is unnecessary to `build` the
package, we just need to ensure that any checks pass.
* `renv` is initialized for this repository using the EXPLICIT snapshot mode.
	* If you need to import a new package, you MUST update the `NAMESPACE` file
	appropriately before invoking `renv::snapshot()`.
	* Remember to keep the `NAMESPACE` and lockfile up to date as you add new
	functionality. You can update the `NAMESPACE` via `usethis::use_package()`.
	* Developer-only dependencies like `devtools` and `usethis` will thus not
	appear in the lockfile, which is the currently recommended best practice.
* If you are a new author, you should add your information to the `DESCRIPTION`
file. The easiest way is to use `usethis::use_author()`. See again the
R packages book for information on the different fields here.
* If you update the `README`, you should only edit `README.qmd`. Make sure to
render the file manually after updating.
* If you intend to add new functionality, you should either fork the repo or
make a new branch. This way, other users can continue to install the working
version of the package while you develop new features. Remember to commit
your work regularly.