phytools (version 0.2-40)

phyl.pairedttest: Phylogenetic paired t-test

Description

This function conducts a phylogenetic paired t-test, roughly following Lindenfors et al. (2010; J. Evol. Biol.).

Usage

phyl.pairedttest(tree, x1, x2=NULL, se1=NULL, se2=NULL, lambda=1.0, h0=0.0,
     fixed=FALSE)

Arguments

tree

a phylogenetic tree in "phylo" format.

x1

data vector for first trait, or matrix with two traits in columns.

x2

data vector for second trait (or null if x1 is a matrix).

se1

standard errors for x1.

se2

standard errors for x2.

lambda

starting value for Pagel's lambda (or fixed value, if fixed=TRUE).

h0

null hypothesis (to be tested) for the mean difference between x1 and x2.

fixed

logical value specifying whether or not to optimize lambda.

Value

• a list with the following components:
• dbar
  phylogenetic mean differenc.
• se
  standard error of dbar.
• sig2
  estimated evolutionary variance (of the difference).
• lambda
  fitted (or fixed) value of lambda.
• logL
  log-likelihood of the fitted model.
• t.dbar
  t-value ((dbar-h0)/se where se is computed from the Hessian).
• P.dbar
  P-value.

Details

Likelihood optimization is performed using optim with method="L-BFGS-B" with box constraints on lambda (0,1).

References

Lindenfors, P., L. J. Revell, and C. L. Nunn. 2010. Sexual dimorphism in primate aerobic capacity: A phylogenetic test. J. Evol. Biol., 23, 1183--1194.