Resolve taxonomic names via the Global Names Resolver.
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.
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
#> [1] 10
# let's look at the lineages
lineages <- strsplit(as.vector(res$lineage), "\\|")
print(lineages[[6]]) # the bacteria has far fewer taxonomic levels
#> [1] "" "Bacteria" "Terrabacteria"
#> [4] "Bacillota" "Bacilli" "Bacillales"
#> [7] "Bacillaceae" "Bacillus" "Bacillus subtilis"
#> [10] "Bacillus subtilis"