synonymize_subspecies: Convert all subspecies into synonyms of the species

In taxotools: Taxonomic List Processing

Convert all subspecies into synonyms of the species

Description

used in generating master lists

Usage

synonymize_subspecies(master, return_unmatched = FALSE, verbose = TRUE)

Arguments

master	List of names with a field named canonical
return_unmatched	If the return values should be unmatched (orphan) subspecies records. Default: FALSE
verbose	display process messages, Default: TRUE

Details

While dealing with taxonomic names only at species level, to take advantage of sub-specific names already available in the lists are sometimes treated as synonyms of the names at species rank. To convert all the subspecies names as synonyms this function is very handy. This function will add id, accid and taxonrank columns ro return data if missing from original data.

Value

Same list of names with id and accid fields added (or data updated the fields exists) with all subspecies linked to the species names as synonyms

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples

master <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                     "Hypochlorosis tenebrosa",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia ancharia",
                                     "Hypochlorosis ancharia tenebrosa",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c(0,1,1,0,0,0,0),
                     "source" = c("itis","itis","wiki","wiki","itis",
                                  "itis","itis"),
                     stringsAsFactors = FALSE)

synonymize_subspecies(master)
synonymize_subspecies(master,return_unmatched = TRUE)

taxotools documentation built on May 29, 2024, 3:09 a.m.