Convert phylo with attached simmap to nexml object

Convert phylo with attached simmap to nexml object

Convert nexml object with simmap to phylo

Usage

simmap_to_nexml(phy, state_ids = NULL)

nexml_to_simmap(nexml)

Arguments

phy

a phylo object containing simmap phy$maps element, from the phytools package

state_ids

a named character vector giving the state names corresponding to the ids used to refer to each state in nexml. If null ids will be generated and states taken from the phy$states names.

nexml

a nexml object

Value

a nexml representation of the simmap

a simmap object (phylo object with a $maps element for use in phytools functions).

Functions

• nexml_to_simmap(): Convert nexml object with simmap to phylo

Examples

simmap_ex <- read.nexml(system.file("examples","simmap_ex.xml", package="RNeXML"))
phy <- nexml_to_simmap(simmap_ex)
nex <- simmap_to_nexml(phy)