gbif_downstream: Retrieve all taxonomic names downstream in hierarchy for GBIF

In taxize: Taxonomic Information from Around the Web

Retrieve all taxonomic names downstream in hierarchy for GBIF

Description

Retrieve all taxonomic names downstream in hierarchy for GBIF

Usage

gbif_downstream(
  id,
  downto,
  intermediate = FALSE,
  limit = 100,
  start = NULL,
  key = NULL,
  ...
)

Arguments

id	A taxonomic serial number.
downto	The taxonomic level you want to go down to. See examples below. The taxonomic level IS case sensitive, and you do have to spell it correctly. See data(rank_ref) for spelling.
intermediate	(logical) If TRUE, return a list of length two with target taxon rank names, with additional list of data.frame's of intermediate taxonomic groups. Default: FALSE
limit	Number of records to return. default: 100. max: 1000. use in combination with the start parameter
start	Record number to start at. default: 0. use in combination with the limit parameter
key	Deprecated, see id
...	Further args passed on to gbif_name_usage()

Details

Sometimes records don't have a canonicalName entry which is what we look for. In that case we grab the scientificName entry. You can see the type of name colleceted in the column name_type

Value

data.frame of taxonomic information downstream to family from e.g., Order, Class, etc., or if intermediated=TRUE, list of length two, with target taxon rank names, and intermediate names.

Author(s)

Scott Chamberlain

Examples

## Not run: 
## the plant class Bangiophyceae
gbif_downstream(id = 198, downto="genus")
gbif_downstream(id = 198, downto="genus", intermediate=TRUE)

# families downstream from the family Strepsiptera (twisted wing parasites)
gbif_downstream(id = 1227, "family")
## here, intermediate leads to the same result as the target
gbif_downstream(id = 1227, "family", intermediate=TRUE)

if (interactive()) {
# Lepidoptera
gbif_downstream(id = 797, "family")

# get species downstream from the genus Ursus
gbif_downstream(id = 2433406, "species")

# get tribes down from the family Apidae
gbif_downstream(id = 7799978, downto="species")
gbif_downstream(id = 7799978, downto="species", intermediate=TRUE)

# names that don't have canonicalname entries for some results
# Myosotis: key 2925668
key <- 2925668
res <- gbif_downstream(key, downto = "species")
res2 <- downstream(key, db = "gbif", downto = "species")

# Pagination
# GBIF limits queries to a maximum of 1000 records per request, so if
# there's more than 1000, use the start parameter
# Piper, taxonKey = 3075433
x1 <- gbif_downstream(id = 3075433, downto = "species", limit=1000)
x2 <- gbif_downstream(id = 3075433, downto = "species", limit=1000,
  start=1000)
x3 <- gbif_downstream(id = 3075433, downto = "species", limit=1000,
  start=2000)
x4 <- gbif_downstream(id = 3075433, downto = "species", limit=1000,
  start=3000)
rbind(x1, x2, x3, x4)
}

## End(Not run)

taxize documentation built on Sept. 11, 2024, 6:13 p.m.