taxize (version 0.7.6)

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(...)
## S3 method for class 'default':
lowest_common(x, db = NULL, rows = NA,
  class_list = NULL, low_rank = NULL, ...)
## S3 method for class 'uid':
lowest_common(x, class_list = NULL, low_rank = NULL, ...)
## S3 method for class 'tsn':
lowest_common(x, class_list = NULL, low_rank = NULL, ...)
## S3 method for class 'gbifid':
lowest_common(x, class_list = NULL, low_rank = NULL, ...)

Arguments

...

Other arguments passed to get_tsn, get_uid, get_eolid,

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 inifity. 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

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))