R: Get scientific names from common names.

comm2sci {taxize} | R Documentation

## Get scientific names from common names.

### Description

Get scientific names from common names.

### Usage

    comm2sci(commnames, db = "eol", itisby = "search", simplify = TRUE, ...)

### Arguments

`commnames` | One or more common names or partial names.
`db` | Data source, one of "eol" (default), "itis", "tropicos", "ncbi", or "worms".
`itisby` | Search for common names across entire names (search, default), at beginning of names (begin), or at end of names (end).
`simplify` | (logical) If `TRUE`, simplify output to a vector of names. If `FALSE`, return variable formats from different sources, usually a data.frame.
`...` | Further arguments passed on to internal methods.

### Details

For data sources ITIS and NCBI you can pass in common names directly, and use `get_uid` or `get_tsn` to get ids first, then pass in to this fxn.

For the other data sources, you can only pass in common names directly.

### Value

If `simplify=TRUE`, a list of scientific names, with list labeled by your input names. If `simplify=FALSE`, a data.frame with columns that vary by data source

### Author(s)

Scott Chamberlain

### See Also

`sci2comm`

### Examples

    ## Not run:
    comm2sci(commnames='black bear')
    comm2sci(commnames='black bear', simplify = FALSE)
    comm2sci(commnames='black bear', db='itis')
    comm2sci(commnames='annual blue grass', db='tropicos')
    comm2sci(commnames=c('annual blue grass','tree of heaven'), db='tropicos')
    comm2sci(commnames=c('black bear', 'roe deer'))
    comm2sci('blue whale', db = "worms")
    comm2sci(c('blue whale', 'dwarf surfclam'), db = "worms")

    # Output easily converts to a data.frame with plyr::ldply
    library(plyr)
    ldply(comm2sci(commnames=c('annual blue grass','tree of heaven'),
      db='tropicos'))

    # ncbi: pass in uid's from get_uid() directly
    x <- get_uid("western capercaillie", modifier = "Common Name")
    comm2sci(x)
    # itis: pass in tsn's from get_tsn() directly
    x <- get_tsn(c("Louisiana black bear", "american crow"),
      searchtype = "common")
    comm2sci(x)

    ## End(Not run)

[Package taxize version 0.9.0 Index]