Darwin Core mapping

[LienReyserhove]

This PR includes a detailed description of how the following Darwin Core files are generated:

1. taxon.csv
2. vernacular_names.csv
3. distribution.csv
4. description.csv

These files are generated using several .Rmd files:

1. 1_pre_processing.Rmd
2. 2_dwc_taxon_mapping.Rmd
3. 3_dwc_vernacularname_mapping.Rmd
4. 4_dwc_distribution_mapping.Rmd
5. 5_dwc_description_mapping.Rmd

This is an overview of all Darwin Core terms in the files + a reference to the .Rmd files needed to generate these files.

Taxon core

Remarks:

• Cleaning of the taxonomic information is outside of the scope of the mapping. Some issues on this topic:

  • https://github.com/trias-project/daisie-checklist/issues/17
  • https://github.com/trias-project/daisie-checklist/issues/24

• taxonRank information should be verified/corrected as it is based on, sometimes dubious, scientific names, see #17

• References are integrated under taxonRemarks

• [x] language

• [x] license

• [x] rightsHolder

• [x] datasetID

• [x] institutionCode

• [x] datasetName

• [x] taxonID

• [x] scientificName

• [x] kingdom

• [x] phylum

• [x] class

• [x] order

• [x] family

• [x] genus

• [x] specificEpithet

• [x] infraspecificEpithet

• [x] taxonRank

• [x] taxonRemarks

Vernacular names

• [x] taxonID
• [x] vernacularName
• [x] source
• [x] language

Distribution

• [x] taxonID
• [x] locationID (see #12 and #13)
• [x] locality
• [x] countryCode
• [x] occurrenceStatus
• [x] establishmentMeans
• [x] eventDate
• [ ] source (see #22)
• [x] occurrenceRemarks

Description

• [x] Habitat
  • [x] taxonID
  • [x] description
  • [x] type
  • [x] source
• [x] Native range
  • [x] taxonID
  • [x] description
  • [x] type
  • [x] source
• [x] Ecofunctional group
  • [x] taxonID
  • [x] description
  • [x] type
  • [x] source

[LienReyserhove]

Integrated the requested changes, ready for review

[peterdesmet]

Nice work! 👏

[peterdesmet]

Important: see #31