create_taxa_list: Create a list of taxonomic classifications

In CAPLTER/capeml: CAP LTER package for generating EML

Create a list of taxonomic classifications

Description

This function generates a list of taxonomic classification records where each record is a single-rank list corresponding to the value in the taxonRank column of the input data frame. The output structure is designed to match the EML (Ecological Metadata Language) classifications format, with each element containing only the specified rank, its value, and (if present) associated common names and taxon identifiers.

Usage

create_taxa_list(taxa_df)

Arguments

taxa_df

A data frame containing taxonomic information. Must include 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).

Details

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

Value

A list of lists:

• taxonRankName: The rank name (from taxonRank).

• taxonRankValue: The value for that rank (from taxa_clean).

• commonName: A list of common names (if present in vernacularName); omitted if not present.

• taxonId: A list with provider and taxonId

Examples

## Not run: 
  taxa_df <- data.frame(
    taxonRank = c("family", "genus"),
    taxa_clean = c("Felidae", "Panthera"),
    taxonID = c("ITIS:183833", "ITIS:180544"),
    vernacularName = c("cats", "big cats")
  )
  taxon_trees <- create_taxa_list(taxa_df)
  str(taxon_trees[[1]], max.level = 2)

## End(Not run)

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