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Resolve taxonmic names online

Source: R/a.R
taxaResolve.Rd

Resolve taxonomic names via the Global Names Resolver.

Usage

taxaResolve(
  nms,
  batch = 100,
  datasource = 4,
  genus = TRUE,
  cache = FALSE,
  parent = NULL
)

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.

See also

searchTxnyms, setTxnyms, getNdsFrmTxnyms

Examples

my_lovely_names <- c(
  "Gallus gallus", "Pongo pingu", "Homo sapiens",
  "Arabidopsis thaliana", "Macaca thibetana", "Bacillus subtilis"
)
res <- taxaResolve(nms = my_lovely_names)
#> ---- 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.
length(colnames(res)) # 10 different metadata for returned names including original search name
#> [1] 0
# let's look at the lineages
lineages <- strsplit(as.vector(res$lineage), "\\|")
#> Error in strsplit(as.vector(res$lineage), "\\|"): non-character argument
print(lineages[[6]]) # the bacteria has far fewer taxonomic levels
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'lineages' not found