Development

Dev environment

Set-up

To develop postcodElapse, Rstudio with the git large file storage (LFS) installed is required. Instructions can be found here. In addition, the following R packages are required:

install.packages(c("usethis", "pkgdown", "roxygen2")) #devtools

install.packages(c("dplyr", "terra","sf", "rlang")) #required by postcodElapse

install.packages(c("tidyverse", "tidyterra", "ggpubr")) #used in the docs

Cloning

After installing all the dependencies, clone: https://github.com/GRIAC-Bioinformatics/postcodElapse. Make sure to enable git LFS for the repo and pull the large file, see shell commands below.

git lfs install

git lfs pull

This will download the 125MB ELAPSE.tif. Although it is too large for a normal commit, it is required by postcodElapse. If preferred, you can switch to the dev branch.

GeoPackages

Finally create a directory named: data in the parent directory of the postcodElapse repo. Download and place into the data dir both supported GeoPackages links below:

1. BAG (Basisregistratie Adressen en Gebouwencontains) for every building in the Netherlands the location and postal code. Package size 8GB

2. PC6 (Postcode6) provides the geographic area for every Dutch postal code. Package size 0.5GB

These are used in the documentation. When setup correct everything should match the the directory tree below:

./development
├── data
│   ├── bag-light.gpkg
│   └── cbs_pc6_2024.gpkg
└── postcodElapse
    ├── data-raw
    │   └── sample_postcodes.R
    ├── DESCRIPTION
    ├── inst
    │   ├── ELAPSE.tif
    │   └── extdata
    │       ├── postcode1000.rds
    │       └── postcode100.rds
    ├── LICENSE.md
    ├── man
    │   ├── coord_zoomFeature.Rd
    │   ├── formatPostcode.Rd
    │   ├── geom_rectFeature.Rd
    │   ├── loadElapse.Rd
    │   ├── pollutionFromBag.Rd
    │   ├── pollutionFromPc6.Rd
    │   └── postcodElapse.Rd
    ├── NAMESPACE
    ├── _pkgdown.yml
    ├── postcodElapse.Rproj
    ├── R
    │   ├── extraction.R
    │   ├── helpers.R
    │   └── plotting.R
    ├── README.md
    └── vignettes
        ├── articles
        │   ├── Development.Rmd
        │   └── Spacial-plotting.Rmd
        ├── postcodElapse.Rmd
        └── postcodElapse.Rmd.orig

10 directories, 26 files

Building

When implementing new features or fixing bugs, make sure to work on the dev branch. To quickly install the package in the Rstudio ribbon, navigate to: Build > Load All. This will quickly load the package into the current R session. Alternatively, use the keybind: Control + Shift + L.

Again if you are implementing new features or fixing bugs please work on the dev branch. To quickly install the package in the Rstudio ribbon navigate: Build > Load All, this quickly loads the package into your R session. Or you can use the keybind: Control + Shift + L.

To fully build the package in the ribbon: Build > Install package or use the Control + Shift + B keybind. , This will also update any changed documentation.

After finishing developing, to build postcodElapse for release on GitHub, use: Run Build > Build Source Package. This will build package as an archive (.tar.gz or .zip) in the parent directory of the repo. Add this file as new release to GitHub. Don’t forget to merge dev to main and update the documentation.

Documentation

In package

The package documentation is used for ?postcodElapse in R. It is created with roxygen from the comment blocks above the function definitions in the postcodElapse. See their page for user information.

GitHub pages

More expanded guide style documentation can be found on the GitHub pages. This is created using pkgdown. Creating new articles or vignettes can be done with usethis, running in the R console usethis::use_article() or usethis::use_vignette(). User information can be found in the pkgdown and usethis documentation.

Local building and viewing can be done by running pkgdown::build_site(). To publish the documentation on GitHub pages, run pkgdown::deploy_to_branch() and wait until GitHub fully deploys the page.