Retrieve all taxa names downstream in hierarchy for NCBI
Retrieve all taxa names downstream in hierarchy for NCBI
ncbi_downstream(id, downto, intermediate = FALSE, ...)
id |
(numeric/integer) An NCBI taxonomic identifier |
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 |
... |
Further args passed on to |
Data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediate=TRUE, list of length two,
with target taxon rank names, and intermediate names.
A sticky point with NCBI is that they can have designation for taxonomic rank of "No Rank". So we have no way of programatically knowing what to do with that taxon. Of course one can manually look at a name and perhaps know what it is, or look it up on the web - but we can't do anything programatically. So, no rank things will sometimes be missing.
See taxize-authentication() for help on authentication.
We strongly recommend getting an API key
Scott Chamberlain
## Not run:
## genus Apis
ncbi_downstream(id = 7459, downto="species")
## get intermediate taxa as a separate object
ncbi_downstream(id = 7459, downto="species", intermediate = TRUE)
## Lepidoptera
ncbi_downstream(id = 7088, downto="superfamily")
## families in the ferns (Moniliformopses)
(id <- get_uid("Moniliformopses"))
ncbi_downstream(id = id, downto = "order")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.