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https://github.com/inbo/n2khab

R package with preprocessing functions and standard reference data for Flemish Natura 2000 (N2K) habitat (HAB) analyses
https://github.com/inbo/n2khab

habitat natura2000 package preprocessing-functions r reproducibility

Last synced: about 2 months ago
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R package with preprocessing functions and standard reference data for Flemish Natura 2000 (N2K) habitat (HAB) analyses

Host: GitHub
URL: https://github.com/inbo/n2khab
Owner: inbo
License: gpl-3.0
Created: 2019-06-12T15:09:10.000Z (over 5 years ago)
Default Branch: main
Last Pushed: 2024-08-08T13:31:50.000Z (5 months ago)
Last Synced: 2024-08-09T14:54:40.460Z (5 months ago)
Topics: habitat, natura2000, package, preprocessing-functions, r, reproducibility
Language: R
Homepage: https://inbo.github.io/n2khab
Size: 1.92 MB
Stars: 1
Watchers: 6
Forks: 1
Open Issues: 10
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md

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README

        
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3631579.svg)](https://doi.org/10.5281/zenodo.3631579)

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[![R-CMD-check](https://github.com/inbo/n2khab/workflows/R-CMD-check/badge.svg)](https://github.com/inbo/n2khab/actions?query=workflow%3AR-CMD-check)

[![inbo r-universe-name](https://inbo.r-universe.dev/badges/:name?color=c04384)](https://inbo.r-universe.dev)

[![inbo r-universe package status](https://inbo.r-universe.dev/badges/n2khab)](https://inbo.r-universe.dev)

## Welcome

The **n2khab** R package provides preprocessing functions and standard reference data, supporting _reproducible_ and _transparent_ analyses on Flemish Natura 2000 (**n2k**) habitats (**hab**) and regionally important biotopes (RIBs).

The package's core aim is to **provide readily standardized (preprocessed) data** in your R environment.

This facilitates collaboration and reproducibility.

The standard reference data include: checklists, spatial habitat distribution, administrative & environmental layers, GRTSmaster_habitats.

## Installing and using the _n2khab_ package

To install the current package version from the `main` branch (latest stable release), run:

```r

install.packages("n2khab", repos = c(inbo = "https://inbo.r-universe.dev", 

                                     CRAN = "https://cloud.r-project.org"))

```

The above provides a pre-compiled package for Windows and macOS, which should be faster than below approach.

INBO staff should have the INBO repository enabled already (check with `getOption("repos")`), in which case **`install.packages("n2khab")`** is all you need!

If you want to install from the source repository, run:

```r

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = "true") # as a precaution

remotes::install_github("inbo/n2khab",

                        build_vignettes = TRUE,

                        upgrade = TRUE)

```

Note that this will install the package from the `main` branch.

If you need a version from another branch, add the `ref` argument in the above function to provide the branch name.

Repeat the installation when you wish to upgrade.

Have a look at the vignettes to quickly find your way!

```r

help(package = "n2khab")

# vignettes only: browseVignettes("n2khab")

# documentation of whole package: package?n2khab

```

### Data setup

Please take note that you must set up the needed data sources as explained in `vignette("v020_datastorage")` and demonstrated in `vignette("v022_example")`.

There is a major distinction between:

- **raw data** ([Zenodo-link](https://zenodo.org/communities/n2khab-data-raw)), to be stored in a folder `n2khab_data/10_raw`;

- **processed data** ([Zenodo-link](https://zenodo.org/communities/n2khab-data-processed)), to be stored in a folder `n2khab_data/20_processed`.

## You are welcome to contribute!

Please have a look at our [contributing guide](.github/CONTRIBUTING.md)!

## Intention for the future

At a later date, the intention is to incorporate functionality to enhance workflow reproducibility and ease the setup:

- let a user declare which versions of which data sources are used in an R workflow (at the beginning of a script or R markdown file);

- perform checks whether the needed versions of those data sources are locally present;

- if missing, download the needed data from the Zenodo collections.

Currently these aspects must be taken care of in a more manual fashion.

See `vignette("v022_example")` for example code to currently accomplish specific aspects.

## Code of Conduct

Please note that the n2khab package is released with a [Contributor Code of Conduct](https://inbo.github.io/n2khab/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.