hOUwie.recon: Reconstruct the marginal probability of discrete node states...

In thej022214/OUwie: Analysis of Evolutionary Rates in an OU Framework

Reconstruct the marginal probability of discrete node states under the hOUwie model.

Description

Uses the output object from hOUwie to conduct an ancestral state reconstruction of the discrete regime states.

Usage

hOUwie.recon(houwie_obj, 
             nodes      = "all")

Arguments

houwie_obj	A list of class "houwie".
nodes	One of "internal", "external", or "all" to represent reconstructing internal nodes, external (tips) nodes, or all nodes. "External" is only useful if the model has hidden states or there is uncertainty in the tip states.

Details

Reconstructs the marginal probability of a particular state at a given node. To do this, all possible states at the given node are fixed and the joint likelihoods are evaluated for each possibility. Those joint probabilities are then normalized by the total likelihood so that the probability sums to one.

Value

recon_matrix

a data.frame containing the marginal probabilities of each state (given by the column).

Author(s)

James D. Boyko

References

Yang Z. 2006. Computational molecular evolution. Oxford University Press Oxford.

thej022214/OUwie documentation built on April 13, 2025, 9:36 a.m.