Get node labels based on online taxonomic database

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)
#> ---- Connection failed: trying again in [2s]----
#> ---- Connection failed: trying again in [4s]----
#> ---- Connection failed: trying again in [8s]----
#> ---- Connection failed: trying again in [16s]----
#> ---- Connection failed: trying again in [32s]----
#> Warning: Failed to connect, server may be down.
print(nd_labels)
#> NULL