create_taxonomicCoverage: Create taxonomicCoverage EML node from taxonomic data

In CAPLTER/capeml: CAP LTER package for generating EML

Create taxonomicCoverage EML node from taxonomic data

Description

This function reads a taxa data file in the working directory (taxa_map.csv) and generates EML-compliant taxonomicClassification node(s) suitable for use with the EML R package. It uses create_taxa_list() to generate a list of single-rank taxonomic classification records. The resulting EML node can be incorporated as a taxonomicCoverage element as part of a EML coverage. In addition to returning a list of taxonomicClassification(s), the resulting content is written to taxonomicCoverage.xml in the working directory.

Usage

create_taxonomicCoverage()

Details

The input taxa data file (taxa_map.csv) must contain at least the columns taxonRank, taxa_clean (the value for the specified rank), taxonID (e.g., "ITIS:12345" or "GBIF:67890"), and optionally vernacularName (common names, possibly comma- or semicolon-separated).

Only the rank specified in taxonRank is included for each record. The function is robust to missing or empty vernacularName and taxonID fields (these are omitted). The output is suitable for use in EML metadata or other workflows requiring a flat, single-rank taxonomic classification structure.

The name of the function is a bit misleading as it does not actually return a taxonomicCoverage but rather a list of taxonomicClassification(s) that are added to coverage as a taxonomicCoverage sensu coverage$taxonomicCoverage <- taxaCoverage. taxonomicCoverage is part of the title as that is the essence and taxonomicClassification could have added a different confusion of suggesting that it constructs only a single taxonomicClassification.

It is important to note that a taxonomic tree for each organism is not generated. Rather, the function builds a 'taxonomicClassification' element for each taxon that features only the derived rank of the organism. For example, if the taxon Larrea tridentata is submitted, the output will include content (authority, authority ID, and common name (if relevant)) for that species. That is, the result will not include content related to the family, order, class, etc. to which the organism is associated. This approach is contrast to other tools, such as taxonomyCleanr, that build a complete taxonomic tree.

Value

A list EML-compliant taxonomicClassification nodes. The function also writes taxonomicCoverage.xml to the working directory.

See Also

create_taxa_list, set_taxonomic_coverage

Examples

## Not run: 
  # Assumes taxa_df.csv is present in the working directory
  coverage <- create_taxonomicCoverage()
  str(coverage, max.level = 3)

## End(Not run)

CAPLTER/capeml documentation built on July 16, 2025, 3:57 p.m.