Estimation of phylogenetic signal using 2 methods.
phylosig(): this function computes phylogenetic signal using the lambda and K methods.
Input
result<-phylosig(tree,x,method="K",test=FALSE,nsim=1000)
"tree" is an object of class "phylo";
"x" is a labeled vector of trait values for a continuous trait - labels in "x" can be missing from "tree" but not vice-versa;
"method" is the method - can be "K" or "lambda";
"test" indicates whether or not to conduct the null hypothesis tests of no signal - test for K is by randomization, test for lambda is likelihood-ratio test;
"nsim" (only applicable to method="K") indicates the number of randomizations to conduct.
Function requires the "ape" package.
Output
phylosig() returns:
"K" the value of K statistic and (optionally) "P" the P-value for the randomization test; or
"lambda" the value of lambda, "logL" the log-likelihood, and (optionally) "P" the P-value of the likelihood ratio test.
Citation
Function written by Liam J. Revell 2011.
Based on:
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.
Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.
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Last modified Mar. 17, 2011.