Retrieve all taxonomic names downstream in hierarchy for GBIF
Retrieve all taxonomic names downstream in hierarchy for GBIF
gbif_downstream( id, downto, intermediate = FALSE, limit = 100, start = NULL, key = NULL, ... )
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 |
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 |
Record number to start at. default: 0. use in combination
with the |
key |
Deprecated, see |
... |
Further args passed on to |
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
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.
Scott Chamberlain
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.