clade.freq: Returns clade names and frequencies

In rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Returns clade names and frequencies

Description

Uses ape functionality to get the frequencies and names of clades in an MCMC chain or subset thereof.

Usage

clade.freq(x, start, end, rooted = FALSE, ...)

Arguments

x	A multiPhylo or rwty.chain object
start	The index of the first tree to consider in calcuating frequencies
end	The index of the last tree to consider in calculating frequencies
rooted	(TRUE/FALSE). Tells RWTY whether your trees are rooted or not.
...	Arguments to be passed to ape's prop.part function

Value

clade.df A data froma containing clade names and frequencies

Examples

## Not run: 
data(fungus)
clade.freq(fungus$Fungus.Run1, start=10, end=100)

## End(Not run)

rwty documentation built on April 3, 2025, 9:20 p.m.