taxaResolve: Resolve taxonmic names online
In DomBennett/treemantools: Extended methods for treeman

Description Usage Arguments Details Examples

Resolve taxonomic names via the Global Names Resolver.

1	taxaResolve(names, batch = 100, datasource = 4, genus = TRUE)

`names`	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

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.biodinfo.org/data_sources for a list and IDs. Default is 4 for NCBI.

my_lovely_names <- c('Gallus gallus', 'Pongo pingu', 'Homo sapiens',
                      'Arabidopsis thaliana', 'Macaca thibetana', 'Bacillus subtilis')
res <- taxaResolve(names=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