R: Get node labels based on online taxonomic database

searchTxnyms {treeman} | R Documentation

## Get node labels based on online taxonomic database

### Description

Return names of each node in tree based on searching tip labels through Global Names Resolver http://resolver.globalnames.org/ in NCBI.

### Usage

    searchTxnyms(tree, cache = FALSE, parent = NULL, clean = TRUE, infer = TRUE)

### Arguments

`tree` | TreeMan object
`cache` | T/F, create a local cache of downloaded names?
`parent` | specify parent of all names to prevent false names
`clean` | T/F, ensure returned names contain no special characters?
`infer` | T/F, infer taxonyms for unfound nodes?

### Details

For each node, all the descendants are searched, the taxonomic lineages returned and then searched to find the lowest shared name. All the tip labels are searched against a specified taxonomic database through the GNR and NCBI. (So far only tested with NCBI database.) Use the infer argument to ensure a taxonym is returned for all nodes. If infer is true, all nodes without an identifed taxonym adopt the taxonym of their parent. Will raise a warning if connection fails and will return NULL.

### See Also

`taxaResolve`, `setTxnyms`, `getNdsFrmTxnyms`

### Examples

    tree <- randTree(8)
    new_tids <- c("Gallus_gallus", "Aileuropoda_melanoleucha", "Ailurus_fulgens",
    "Rattus_rattus", "Mus_musculus", "Gorilla_gorilla", "Pan_trogoldytes", "Homo_sapiens")
    tree <- setNdsID(tree, tree['tips'], new_tids)
    nd_labels <- searchTxnyms(tree)
    print(nd_labels)

[Package treeman version 1.1.4 Index]