mvMORPH (version 1.2.1)

halflife: 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)

Value

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

Arguments

object

Object fitted with the "mvOU" function.

Author

Julien Clavel

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).

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.

See Also

mvMORPH mvOU stationary

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)