R: Resolve names using Open Tree of Life (OTL) resolver

tol_resolve {taxize} | R Documentation

## Resolve names using Open Tree of Life (OTL) resolver

### Description

Resolve names using Open Tree of Life (OTL) resolver

### Usage

    tol_resolve(names = NULL, context_name = NULL,
      do_approximate_matching = TRUE, ids = NULL, include_suppressed = FALSE,
      ...)

### Arguments

`names` | (character vector) taxon names to be queried
`context_name` | name of the taxonomic context to be searched (length-one character vector). Must match (case sensitive) one of the values returned by `tnrs_contexts`.
`do_approximate_matching` | (logical) A logical indicating whether or not to perform approximate string (a.k.a. “fuzzy”) matching. Using `FALSE` will greatly improve speed. Default: `TRUE`
`ids` | An array of OTL ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length.
`include_suppressed` | (logical) Ordinarily, some quasi-taxa, such as incertae sedis buckets and other non-OTUs, are suppressed from TNRS results. If this parameter is true, these quasi-taxa are allowed as possible TNRS results. Default: `FALSE`
`...` | Curl options passed on to `POST` within `tnrs_match_names`

### Value

A data frame summarizing the results of the query. The original query output is appended as an attribute to the returned object (and can be obtained using `attr(object, "original_response")`).

### Author(s)

Francois Michonneau francois.michonneau@gmail.com Scott Chamberlain myrmecocystus@gmail.com

### References

https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names

### See Also

`gnr_resolve`, `tnrs`

### Examples

    ## Not run:
    tol_resolve(names=c("echinodermata", "xenacoelomorpha",
      "chordata", "hemichordata"))
    tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"))
    tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"),
      context_name = "Animals")

    turducken_spp <- c("Meleagris gallopavo", "Anas platyrhynchos",
      "Gallus gallus")
    tol_resolve(turducken_spp, context_name="Animals")

    ## End(Not run)

[Package taxize version 0.9.0 Index]