R: Resolve taxonmic names online

taxaResolve {treeman} | R Documentation

## Resolve taxonmic names online

### Description

Resolve taxonomic names via the Global Names Resolver.

### Usage

    taxaResolve(
      nms,
      batch = 100,
      datasource = 4,
      genus = TRUE,
      cache = FALSE,
      parent = NULL
    )

### Arguments

`nms` | vector of names
`batch` | size of the batches to be queried
`datasource` | ID number of the datasource
`genus` | boolean, if true will search against GNR with just the genus name for names that failed to resolve using the full species name
`cache` | T/F, create a local cache of downloaded names?
`parent` | specify parent of all names to prevent false names

### Details

Returns dataframe containing GNR metadata for each name wames that cannot be resolved are returned as NA. Various datasources are available, see http://resolver.globalnames.org/data_sources for a list and IDs. Default is 4 for NCBI. Will raise a warning if connection fails and will return NULL.

### See Also

`searchTxnyms`, `setTxnyms`, `getNdsFrmTxnyms`

### Examples

    my_lovely_names <- c ('Gallus gallus', 'Pongo pingu', 'Homo sapiens',
                          'Arabidopsis thaliana', 'Macaca thibetana', 'Bacillus subtilis')
    res <- taxaResolve (nms=my_lovely_names)
    length(colnames(res))  # 10 different metadata for returned names including original search name
    # let's look at the lineages
    lineages <- strsplit(as.vector(res$lineage), '\\|')
    print(lineages[[6]])  # the bacteria has far fewer taxonomic levels

[Package treeman version 1.1.4 Index]