taxaResolve {treeman} | R Documentation |
Resolve taxonomic names via the Global Names Resolver.
taxaResolve(nms, batch = 100, datasource = 4, genus = TRUE, cache = FALSE, parent = NULL)
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 |
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.
searchTxnyms
, setTxnyms
, getNdsFrmTxnyms
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