Gets a taxonomic tree from a vector of taxa — tree_from

This uses the taxize package's wrapper of the Global Names Resolver to get taxonomic paths for the vector of taxa you pass in. Sources is a vector of source labels in order (though it works best if everything uses the same taxonomy, so we recommend doing just one source). You can see options by doing taxize::gnr_datasources(). Our default is Catalogue of Life. The output is a phylo object (typically with many singleton nodes if collapse_singles is FALSE: nodes with only one descendant (like "Homo" having "Homo sapiens" as its only descendant) but these singletons typically have node.labels

Usage

tree_from_taxonomy(
  taxa,
  sources = "Catalogue of Life",
  collapse_singles = TRUE
)

Arguments

taxa: Vector of taxon names
sources: Vector of names of preferred sources; see taxize::gnr_datasources(). Currently supports 100 taxonomic resources, see details.
collapse_singles: If true, collapses singleton nodes

Value

A list containing a phylo object with resolved names and a vector with unresolved names

Examples

if (FALSE)  # This is a flag for package development. You are welcome to run the example.

taxa <- c(
  "Homo sapiens", "Ursus arctos", "Pan paniscus", "Tyrannosaurus rex",
  "Ginkgo biloba", "Vulcan", "Klingon"
)
results <- tree_from_taxonomy(taxa)
#> Error in lapply(x, f): object 'taxa' not found
print(results$unresolved) # The taxa that do not match
#> Error in print(results$unresolved): object 'results' not found
ape::plot.phylo(results$phy) # may generate warnings due to problems with singletons
#> Error in ape::plot.phylo(results$phy): object 'results' not found
ape::plot.phylo(ape::collapse.singles(results$phy), show.node.label = TRUE)
#> Error in ape::collapse.singles(results$phy): object 'results' not found
# got rid of singles, but this also removes a lot of the node.labels
 # end dontrun