This function uses a while loop to continually collect children taxa down
to the taxonomic rank that you specify in the downto parameter. You
can get data from ITIS (itis), GBIF (gbif), NCBI (ncbi), WORMS (worms),
or BOLD (bold). There is no method exposed by these four
services for getting taxa at a specific taxonomic rank, so we do it
ourselves here.
downstream(...)
# S3 method for default
downstream(
sci_id,
db = NULL,
downto = NULL,
intermediate = FALSE,
rows = NA,
x = NULL,
...
)
# S3 method for tsn
downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
# S3 method for gbifid
downstream(
sci_id,
db = NULL,
downto = NULL,
intermediate = FALSE,
limit = 100,
start = NULL,
...
)
# S3 method for uid
downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
# S3 method for wormsid
downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
# S3 method for boldid
downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
# S3 method for ids
downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)Further args passed on to itis_downstream(),
gbif_downstream(), ncbi_downstream(),
worms_downstream(), or bold_downstream()
Vector of taxa names (character) or IDs (character or numeric) to query.
character; database to query. One or more of itis, gbif,
ncbi, worms, or bold. Note that each taxonomic data source has
their own identifiers, so that if you provide the wrong db value for
the identifier
you could get a result, but it will likely be wrong (not what you were
expecting). If using ncbi, we recommend getting an API key; see
taxize-authentication
What taxonomic rank to go down to. One of: 'superkingdom', 'kingdom', 'subkingdom','infrakingdom','phylum','division','subphylum', 'subdivision','infradivision', 'superclass','class','subclass','infraclass', 'superorder','order','suborder','infraorder','superfamily','family', 'subfamily','tribe','subtribe','genus','subgenus','section','subsection', 'species group','species','subspecies','variety','form','subvariety','race', 'stirp', 'morph','aberration','subform', 'unspecified', 'no rank'
(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
(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.
Deprecated, see sci_id
Number of records to return. Applies to gbif only.
default: 100. max: 1000. use in combination with the start parameter
Record number to start at. Applies to gbif only. default: 0.
use in combination with the limit parameter
A named list of data.frames with the downstream names of every supplied taxa. You get an NA if there was no match in the database.
See taxize-authentication for help on authentication
BEWARE: db="bold" scrapes the BOLD website, so may be unstable. That is,
one day it may work, and the next it may fail. Open an issue if you
encounter an error: https://github.com/ropensci/taxize/issues
if (FALSE) {
# Plug in taxon IDs
downstream(125732, db = 'worms', downto = 'species')
downstream(3451, db = 'bold', downto = 'species')
if (interactive()) {
# Plug in taxon names
downstream("Apis", db = 'ncbi', downto = 'species')
downstream("Apis", db = 'itis', downto = 'species')
downstream("Apis", db = 'bold', downto = 'species')
downstream("Gadus", db = 'worms', downto = 'species')
downstream(c("Apis","Epeoloides"), db = 'itis', downto = 'species')
downstream("Ursus", db = 'gbif', downto = 'species')
downstream(get_gbifid("Ursus"), db = 'gbif', downto = 'species')
# Many taxa
sp <- names_list("genus", 3)
downstream(sp, db = 'itis', downto = 'species')
downstream(sp, db = 'gbif', downto = 'species')
# Both data sources
ids <- get_ids("Apis", db = c('gbif','itis'))
downstream(ids, downto = 'species')
## same result
downstream(get_ids("Apis", db = c('gbif','itis')), downto = 'species')
# Collect intermediate names
## itis
downstream('Bangiophyceae', db="itis", downto="genus")
downstream('Bangiophyceae', db="itis", downto="genus", intermediate=TRUE)
downstream(get_tsn('Bangiophyceae'), downto="genus")
downstream(get_tsn('Bangiophyceae'), downto="genus", intermediate=TRUE)
# Use the rows parameter
## note how in the second function call you don't get the prompt
downstream("Poa", db = 'gbif', downto="species")
downstream("Poa", db = 'gbif', downto="species", rows=1)
# use curl options
res <- downstream("Apis", db = 'gbif', downto = 'species', verbose = TRUE)
# 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
z1 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000)
z2 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000,
start=1000)
z3 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000,
start=2000)
z4 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000,
start=3000)
NROW(rbind(z1[[1]], z2[[1]], z3[[1]], z4[[1]]))
}}