Rationale

This repository contains the functionality to standardize the macrophytes data of the Flanders Environment Agency (VMM) to a Darwin Core Archive that can be harvested by GBIF.

Workflow

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

For an overview of the mapping of the fields, see issue 23.

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
├── vmm-macrophytes-occurrences.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
│
├── src
│   └── dwc_mapping.Rmd    : Darwin Core mapping script
|
├── sql                    : Darwin Core transformations
│   ├── dwc_event.sql
│   ├── dwc_occurrence.sql
│   └── dwc_mof.sql
|
├── tests
│   └── test_dwc_event_occurrence_mof.R : Tests to check DwC mapping
|
└── 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
4. Install any required packages
5. 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.