This repository contains the functionality to standardize the alien plants data of the Province East Flanders to a Darwin Core Archive that can be harvested by a GBIF IPT.
fetch data from WFS → save them as local source data → Darwin Core mapping script → generated Darwin Core files
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-ias-plants-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
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├── src
│ ├── fetch_data.Rmd : Fetching 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_occurrence.sql
│
└── data
│ ├── raw : Fetched data
│ ├── interim : sqlite database, input for mapping script
│ └── processed : Darwin Core output of mapping script GENERATED
install_packages.R
to install any required packagesfetch_data.Rmd
R Markdown file in RStudio to fetch data manuallydwc_mapping.Rmd
R Markdown file in RStudio to map data to DwC manuallyRun > Run All
to generate the processed dataMIT License for the code and documentation in this repository. The included data is released under another license.