syn2taxo: Synonym list to taxolist

In taxotools: Taxonomic List Processing

Synonym list to taxolist

Description

Converts a Synonym list with Accepted Names and Synonym columns to taxolist format

Usage

syn2taxo(synlist, canonical = "canonical", synonym = "synonym")

Arguments

synlist	Synonym list with Accepted name (canonical) and Synonym columns
canonical	Accepted names column name, Default: 'canonical'
synonym	Synonym column name , Default: 'synonym'

Details

Converts a synonyms list to taxolist format. If order and family fields are present, then they are carried forward else NAs are populated. Duplicate synomyms with same source are removed but with different sources are retained.

Value

returns a data frame in taxolist format with all the names in canonical column and accepted names linked to synonyms using id and accid fields. Order, family and (guessed) taxonlevel are added if missing. Genus, species and subspecies fields are added by melting the canonical names.

See Also

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

Examples

 synlist <- data.frame("id" = c(1,2,3),
                       "canonical" = c("Hypochlorosis ancharia",
                                       "Hypochlorosis ancharia",
                                       "Hypochlorosis ancharia"),
                       "synonym" = c( "Hypochlorosis tenebrosa",
                                      "Pseudonotis humboldti",
                                      "Myrina ancharia"),
                       "family" = c("Lycaenidae", "Lycaenidae", 
                                    "Lycaenidae"),
                       "source" = c("itis","wiki","wiki"),
                       stringsAsFactors = FALSE)
                       
 mytaxo <- syn2taxo(synlist)

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