taxize (version 0.7.9)

lowest_common: Retrieve the lowest common taxon and rank for a given taxon name or ID

Description

Retrieve the lowest common taxon and rank for a given taxon name or ID

Usage

lowest_common(...)
"lowest_common"(x, db = NULL, rows = NA, class_list = NULL, low_rank = NULL, ...)
"lowest_common"(x, class_list = NULL, low_rank = NULL, ...)
"lowest_common"(x, class_list = NULL, low_rank = NULL, ...)
"lowest_common"(x, class_list = NULL, low_rank = NULL, ...)

Arguments

...

Other arguments passed to get_tsn, get_uid, get_eolid, get_colid, get_tpsid, get_gbifid.

x

Vector of taxa names (character) or id (character or numeric) to query.

db

character; database to query. either ncbi, itis, or gbif.

rows

(numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn, colid. NCBI has a method for this function but rows doesn't work.

class_list

(list) A list of classifications, as returned from classification

low_rank

(character) taxonomic rank to return, of length 1

Value

NA when no match, or a data.frame with columns

• name
• rank
• id

Examples

## Not run: 
# id <- c("9031", "9823", "9606", "9470")
# id_class <- classification(id, db = 'ncbi')
# lowest_common(id[2:4], db = "ncbi")
# lowest_common(id[2:4], db = "ncbi", low_rank = 'class')
# lowest_common(id[2:4], db = "ncbi", low_rank = 'family')
# lowest_common(id[2:4], class_list = id_class)
# lowest_common(id[2:4], class_list = id_class, low_rank = 'class')
# lowest_common(id[2:4], class_list = id_class, low_rank = 'family')
# 
# spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang")
# lowest_common(spp, db = "ncbi")
# lowest_common(get_uid(spp))
# 
# lowest_common(spp, db = "itis")
# lowest_common(get_tsn(spp))
# 
# gbifid <- c("2704179", "3119195")
# lowest_common(gbifid, db = "gbif")
# 
# spp <- c("Poa annua", "Helianthus annuus")
# lowest_common(spp, db = "gbif")
# lowest_common(get_gbifid(spp))
# 
# cool_orchid <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea")
# orchid_ncbi <- get_uid(cool_orchid)
# orchid_gbif <- get_gbifid(cool_orchid)
# orchid_itis <- get_tsn(cool_orchid)
# 
# orchid_hier_ncbi <- classification(orchid_ncbi, db = 'ncbi')
# orchid_hier_gbif <- classification(orchid_gbif, db = 'gbif')
# orchid_hier_itis <- classification(orchid_itis, db = 'itis')
# 
# lowest_common(orchid_ncbi, low_rank = 'class')
# lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'class')
# lowest_common(orchid_gbif, low_rank = 'class')
# lowest_common(orchid_gbif, orchid_hier_gbif, low_rank = 'class')
# lowest_common(get_uid(cool_orchid), low_rank = 'class')
# lowest_common(get_uid(cool_orchid), low_rank = 'family')
# 
# lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'subfamily')
# lowest_common(orchid_gbif, class_list = orchid_hier_gbif, low_rank = 'subfamily')
# 
# ## Pass in sci. names
# nms <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea")
# lowest_common(x = nms, db = "ncbi")
# lowest_common(x = nms, db = "gbif")
# # lowest_common(x = nms, db = "itis")
# 
# ## NAs due to taxon not found, stops with error message
# # lowest_common(orchid_itis, db = "itis")
# # lowest_common(get_tsn(cool_orchid))
# ## End(Not run)