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

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

Usage

lowest_common(...)

# Default S3 method
lowest_common(
  sci_id,
  db = NULL,
  rows = NA,
  class_list = NULL,
  low_rank = NULL,
  x = NULL,
  ...
)

# S3 method for class 'uid'
lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)

# S3 method for class 'tsn'
lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)

# S3 method for class 'gbifid'
lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)

# S3 method for class 'tolid'
lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)

Arguments

...

Other arguments passed to get_tsn(), get_uid(), get_gbifid(), get_tolid()

sci_id

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

db

character; database to query. either ncbi, itis, gbif, tol. If using ncbi, we recommend getting an API key; see taxize-authentication

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, gbifid, tolid. 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

x

Deprecated, see sci_id

Value

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

• name

• rank

• id

Authentication

See taxize-authentication for help on authentication

Author

Jimmy O'Donnell jodonnellbio@gmail.com Scott Chamberlain

Examples

if (FALSE) { # \dontrun{
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')

# TOL
taxa <- c("Angraecum sesquipedale", "Dracula vampira",
  "Masdevallia coccinea")
(cls <- classification(taxa, db = "tol"))
lowest_common(taxa, db = "tol", class_list = cls)
lowest_common(get_tolid(taxa), class_list = cls)
xx <- get_tolid(taxa)
lowest_common(xx, class_list = cls)

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)

cool_orchids2 <- c("Domingoa haematochila", "Gymnadenia conopsea",
  "Masdevallia coccinea")
orchid_itis <- get_tsn(cool_orchids2)

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')

lowest_common(orchid_itis, class_list = orchid_hier_itis,
  low_rank = 'class')

## 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))
} # }