taxize (version 0.9.4)

ncbi_downstream: Retrieve all taxa names downstream in hierarchy for NCBI

Description

Retrieve all taxa names downstream in hierarchy for NCBI

Usage

ncbi_downstream(id, downto, intermediate = FALSE, ...)

Arguments

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 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

...

Further args passed on to ncbi_children

Value

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.

No Rank

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.

Authentication

See taxize-authentication for help on authentication

Examples

# 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)

## 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")
# }