phytools (version 0.1-0)

phylosig: Compute phylogenetic signal with two methods

Description

This function computes phylogenetic signal using two different methods. It can also conduct the hypothesis tests for significant phylogenetic signal.

Usage

phylosig(tree,x,method="K",test=FALSE,nsim=1000)

Arguments

tree

a phylogenetic tree in "phylo" format.

x

vector containing values for a single continuously distributed trait.

method

method to compute signal: can be "K" or "lambda".

test

logical indicating whether or not to conduct a hypothesis test of "K" or "lambda".

nsim

for method="K", number of simulations in randomization test.

Value

• if (method="K"), a list with the following components:
• K
  value of the K-statistic.
• P
  optionally, the P-value from the randomization test.
• if (method="lambda"), a list with the following components:
• lambda
  fitted value of lambda.
• logL
  log-likelihood.
• P
  P-value of the likelihood ratio test.

Details

Lambda optimization is performed using optimize with the range of lambda set between 0 and the theoretical upper limit of lambda (determined by the relative height of the most recent internal node on the tree).

References

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature, 401, 877--884. Blomberg, S. P., T. Garland Jr., A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57, 717--745.

Examples

tree<-rbdtree(1,0,Tmax=4)
  x<-fastBM(tree)
  phylosig(tree,x,method="lambda",test=TRUE)