phytools (version 0.0-8)

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.

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.