phylo.toBackbone {phytools}

Converts tree to backbone or vice versa

Description

Converts between "phylo" and "backbonePhylo".

Usage

phylo.toBackbone(x, trans, ...)
backbone.toPhylo(x)

Arguments

x

an object of class "phylo" (for the function phylo.toBackbone), or an object of the special class "backbonePhylo" (for backbone.toPhylo).

trans

data frame containing the attributes necessary to translate a backbone tree to an object of class "backbonePhylo". The data frame should contain the following variables: tip.label: the tip labels in the input tree (not all need be included); clade.label: labels for the unobserved subtrees; N: number of species in each subtree; and depth: desired depth of each subtree. depth for each terminal taxon in x cannot be greater than the terminal edge length for that taxon.

...

optional arguments.

Value

Either an object of class "phylo" or an object of class "backbonePhylo", depending on the method.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

plot.backbonePhylo