setTxnyms: Set the txnym slots in a tree

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Set the txnym slots in a tree

Description

Return a tree with txnyms added to specified nodes

Usage

setTxnyms(tree, txnyms)

Arguments

tree	TreeMan object
txnyms	named vector or list

Details

Returns a tree. Specify the taxonomic groups for nodes in a tree by providing a vector or list named by node IDs. Takes output from searchTxnyms. Only letters, numbers and underscores allowed. To remove special characters use regular expressions, e.g. gsub(['a-zA-Z0-9_'], '', txnym)

See Also

taxaResolve, searchTxnyms, getNdsLng, getNdLng, https://github.com/DomBennett/treeman/wiki/set-methods

Examples

data(mammals)
# let's change the txnym for humans
# what's its summary before we change anything?
summary(mammals[["Homo_sapiens"]])
# now let's add Hominini
new_txnym <- list("Homo_sapiens" = c("Hominini", "Homo"))
mammals <- setTxnyms(mammals, new_txnym)
summary(mammals[["Homo_sapiens"]])

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.