Prepares a phylogeny for use in the insitu pipeline

Handles non-ultrametricity and incomplete taxon sampling. The tree must be fully bifurcating.

Usage

prep_phylo(phy, force_ultrametric = TRUE, sampling_fraction = 1)

Arguments

phy

A phylo object.

force_ultrametric

Logical. If TRUE and the tree is not ultrametric, it is forced ultrametric using phytools::force.ultrametric. Default: TRUE.

sampling_fraction

The proportion of extant species included in the phylogeny (between 0 and 1). Used to correct branch length-based rate estimates. Default: 1 (complete sampling assumed).

Value

The prepared phylo object, with sampling_fraction stored as an attribute.