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riparias / pov-fishes-occurrences

DwC mapping of the fishes and crayfishes occurrences of the Provincial Center of Environmental Research (PCM) in East Flanders, Belgium
MIT License
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readme

funding fetch-data mapping and testing

Rationale

This repository contains the functionality to standardize the fishes and crayfishes data of the Province East Flanders to a Darwin Core Archive that can be harvested by a GBIF IPT.

Workflow

fetch data from WFS → save them as local source data → Darwin Core mapping script → generated Darwin Core files

Published dataset

Repo structure

The repository structure is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.

├── README.md              : Description of this repository
├── LICENSE                : Repository license
├── pov-fishes-occurrences.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
│
├── .github                
│   ├── PULL_REQUEST_TEMPLATE.md : Pull request template
│   └── workflows
│   │   ├── fetch-data.yaml    : GitHub action to fetch raw data
│   │   └── mapping_and_testing.yaml : GitHub action to map data to DwC and perform some tests on the Dwc output
|
├── src
│   ├── fetch_data.Rmd     : Fetchin data script
│   ├── dwc_mapping.Rmd    : Darwin Core mapping script
│   ├── run_fetch_data.R   : R script to run code in fetch_data.Rmd in an automatic way within a GitHub action
│   ├── run_dwc_mapping.R  : R script to run code in dcw_mapping.Rmd in an automatic way within a GitHub action
│   └── install_packages.R : R script to install all needed packages
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├── sql                    : Darwin Core transformations
│   └── dwc_event.sql
│   ├── dwc_occurrence.sql
│   └── dwc_mof.sql
│   
└── data
│   ├── raw                : Fetched data
│   └── processed          : Darwin Core output of mapping script GENERATED

Installation

  1. Clone this repository to your computer
  2. Open the RStudio project file
  3. Run install_packages.R to install any required packages
  4. Open fetch_data.Rmd R Markdown file in RStudio to fetch data manually
  5. Open the dwc_mapping.Rmd R Markdown file in RStudio to map data to DwC manually
  6. Click Run > Run All to generate the processed data

License

MIT License for the code and documentation in this repository. The included data is released under another license.