synonymize_subspecies {taxotools} | R Documentation |
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)