| **[.gitignore](.gitignore)** | A place to tell git what _not_ to synchronise e.g. `.csv` or [weird OS files](https://gist.github.com/adamgit/3786883)|
| **[R/](R/)** | Where we store functions that get built by the package - these are then available for use in any project|
| **[Rmd/](Rmd/)** | Where we store .Rmd files and the .R scripts that call them (usually using a `drake` plan) |
| **[DESCRIPTION](DESCRIPTION)** | But only if you use this as a template for your own repo - it is a special file for packages |
| **[docs/](docs/)** | Where we put output generated by the .R/.Rmd code. This is helpful if you are using [github/lab pages](https://guides.github.com/features/pages/). Unfortunately the University of Southampton gitlab service does not currently support this. |
| **[env.R](env.R)** | Where we store all the parameters that might be re-used across our repo. Such as colour defaults, data paths etc. We avoid using a project/repo level .Rprofile because it can lead to [a **lot** of confusion](https://support.rstudio.com/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf). |
| **[howTo/](howTo/)** | Our collection of guides and `how-tos` |
| **[man/](man/)** | Where roxygen puts the package man(ual) files |
| **[notData/](notData/)** | Where we do _not_ store [data](/howTo/keepingData.md). R packages expect certain kinds of data in their 'data/' folders. Do not put your data in it. |
| **[.gitignore](.gitignore)** | A place to tell git what _not_ to synchronise e.g. `.csv` or [weird OS files](https://gist.github.com/adamgit/3786883)|
| **[CONTRIBUTING.md](CONTRIBUTING.md)** | How to contribute (nicely)|
| **[DESCRIPTION](DESCRIPTION)** | But only if you use this as a template for your own repo - it is a special file for packages |
| **[LICENSE](LICENSE)** | Edit to suit your needs |
| **[notData/](notData/)** | Where we do not store data. R packages expect certain kinds of data in their 'data/' folders. Do not put your data in it. |
| **[R/](R/)** | Where we store functions that get built by the package - these are then available for use in any project|
| **[README.md](README.md)** | Repo readme |
| **[resources.md](resources.md)** | Our collection of guides and `how-tos` |
| **[_drake_basicReport.R](_drake_basicReport.R)** | basic drake plan |
| **[bibliography.bib](bibliography.bib)** | a place to keep references (in bibtex style)|
| **[env.R](env.R)** | Where we store all the parameters that might be re-used across our repo. Such as colour defaults, data paths etc. We avoid using a project/repo level .Rprofile because it can lead to [a **lot** of confusion](https://support.rstudio.com/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf). |
| **[make_basicReport.R](make_basicReport.R)** | basic reporting script which sources the drake plan |
| **[repoAsATemplate.md](repoAsATemplate.md)** | This file |
More on data:
More on [data](/howTo/keepingData.md):
> We recommend **not** putting your data in your repo at all.
