{"id":19891823,"url":"https://github.com/inbo/n2khab","last_synced_at":"2025-05-02T18:31:29.889Z","repository":{"id":36100367,"uuid":"191594504","full_name":"inbo/n2khab","owner":"inbo","description":"R package with preprocessing functions and standard reference data for Flemish Natura 2000 (N2K) habitat (HAB) 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badges: start --\u003e\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3631579.svg)](https://doi.org/10.5281/zenodo.3631579)\n[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)\n[![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)\n[![inbo r-universe-name](https://inbo.r-universe.dev/badges/:name?color=c04384)](https://inbo.r-universe.dev)\n[![inbo r-universe package status](https://inbo.r-universe.dev/badges/n2khab)](https://inbo.r-universe.dev)\n\u003c!-- badges: end --\u003e\n\n## Welcome\n\nThe **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).\n\nThe package's core aim is to **provide readily standardized (preprocessed) data** in your R environment.\nThis facilitates collaboration and reproducibility.\n\nThe standard reference data include: checklists, spatial habitat distribution, administrative \u0026 environmental layers, GRTSmaster_habitats.\n\n## Installing and using the _n2khab_ package\n\nTo install the current package version from the `main` branch (latest stable release), run:\n\n```r\ninstall.packages(\"n2khab\", repos = c(inbo = \"https://inbo.r-universe.dev\", \n                                     CRAN = \"https://cloud.r-project.org\"))\n```\n\nThe above provides a pre-compiled package for Windows and macOS, which should be faster than below approach.\nINBO staff should have the INBO repository enabled already (check with `getOption(\"repos\")`), in which case **`install.packages(\"n2khab\")`** is all you need!\n\nIf you want to install from the source repository, run:\n\n```r\nSys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = \"true\") # as a precaution\nremotes::install_github(\"inbo/n2khab\",\n                        build_vignettes = TRUE,\n                        upgrade = TRUE)\n```\n\nNote that this will install the package from the `main` branch.\nIf you need a version from another branch, add the `ref` argument in the above function to provide the branch name.\n\nRepeat the installation when you wish to upgrade.\n\nHave a look at the vignettes to quickly find your way!\n\n```r\nhelp(package = \"n2khab\")\n# vignettes only: browseVignettes(\"n2khab\")\n# documentation of whole package: package?n2khab\n```\n\n### Data setup\n\nPlease take note that you must set up the needed data sources as explained in `vignette(\"v020_datastorage\")` and demonstrated in `vignette(\"v022_example\")`.\nThere is a major distinction between:\n\n- **raw data** ([Zenodo-link](https://zenodo.org/communities/n2khab-data-raw)), to be stored in a folder `n2khab_data/10_raw`;\n- **processed data** ([Zenodo-link](https://zenodo.org/communities/n2khab-data-processed)), to be stored in a folder `n2khab_data/20_processed`.\n\n\n## You are welcome to contribute!\n\nPlease have a look at our [contributing guide](.github/CONTRIBUTING.md)!\n\n\n## Intention for the future\n\nAt a later date, the intention is to incorporate functionality to enhance workflow reproducibility and ease the setup:\n\n- 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);\n- perform checks whether the needed versions of those data sources are locally present;\n- if missing, download the needed data from the Zenodo collections.\n\nCurrently these aspects must be taken care of in a more manual fashion.\nSee `vignette(\"v022_example\")` for example code to currently accomplish specific aspects.\n\n## Code of Conduct\n\nPlease 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finbo%2Fn2khab","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finbo%2Fn2khab","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finbo%2Fn2khab/lists"}