Targeted monitoring of invasive alien crayfishes in the Flemish part of the LIFE RIPARIAS areas

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Rationale

This repository contains the functionality to standardize the crayfishes data from a targeted monitoring of the Agentschap voor Natuur en Bos (ANB) to a Darwin Core Archive that can be harvested by a GBIF IPT.

Workflow

source data → Darwin Core mapping script → generated Darwin Core files

Published dataset

• Dataset on the IPT
• Dataset on GBIF

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
├── anb-crayfishes-occurrences.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
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├── sql                    : Darwin Core transformations
│   ├── dwc_event.sql
│   └── dwc_occurrence.sql
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├── src
│   ├── dwc_mapping.Rmd    : Darwin Core mapping script
│   ├── _site.yml          : Settings to build website in docs/
│   └── index.Rmd          : Template for website homepage
├── tests
│   └── test_dwc_occurrence.R : some basic tests to check DwC mapping
│
├── docs                   : Repository website GENERATED
│
└── data
    ├── raw                : Source data, input for mapping script
    └── processed          : Darwin Core output of mapping script GENERATED

Installation

1. Clone this repository to your computer
2. Open the RStudio project file
3. Open the dwc_mapping.Rmd R Markdown file in RStudio to map data to DwC manually
4. 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.