halflife: The phylogenetic half-life for an Ornstein-Uhlenbeck process
In mvMORPH: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

halflife

R Documentation

The phylogenetic half-life for an Ornstein-Uhlenbeck process

Description

This function returns the phylogenetic half-life for an Ornstein-Uhlenbeck process (object of class "ou").

Usage

halflife(object)

Arguments

object

Object fitted with the "mvOU" function.

Details

The phylogenetic half-life describes the time to move halfway from the ancestral state to the primary optimum (Hansen, 1997). The multivariate counterpart is computed on the eigenvalues of the "selection" matrix (Bartoszek et al. 2012).

Value

The phylogenetic half-life computed from each eigenvalues (or alpha for the univariate case)

Author(s)

Julien Clavel

References

Bartoszek K., Pienaar J., Mostad P., Andersson S., Hansen T.F. 2012. A phylogenetic comparative method for studying multivariate adaptation. J. Theor. Biol. 314:204-215.

Hansen T.F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution. 51:1341-1351.

Examples

# Simulated dataset
set.seed(14)
# Generating a random tree
tree<-pbtree(n=50)

# Setting the regime states of tip species
sta<-as.vector(c(rep("Forest",20),rep("Savannah",30))); names(sta)<-tree$tip.label

# Making the simmap tree with mapped states
tree<-make.simmap(tree,sta , model="ER", nsim=1)
col<-c("blue","orange"); names(col)<-c("Forest","Savannah")

# Plot of the phylogeny for illustration
plotSimmap(tree,col,fsize=0.6,node.numbers=FALSE,lwd=3, pts=FALSE)

# Simulate the traits
alpha<-matrix(c(2,0.5,0.5,1),2)
sigma<-matrix(c(0.1,0.05,0.05,0.1),2)
theta<-c(2,3,1,1.3)
data<-mvSIM(tree, param=list(sigma=sigma, alpha=alpha, ntraits=2, theta=theta,
            names_traits=c("head.size","mouth.size")), model="OUM", nsim=1)

## Fitting the models
# OUM - Analysis with multiple optima
result<-mvOU(tree, data)

halflife(result)

mvMORPH documentation built on March 31, 2023, 6:25 p.m.