phyl.pairedttest {phytools}

Phylogenetic paired t-test

Description

Phylogenetic paired t-test following Lindenfors et al. (2010).

Usage

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

Arguments

tree

a phylogeny as an object of class "phylo".

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 λ (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 λ.

...

optional arguments.

Details

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

This is not a phylogenetic ANOVA, in which we want to compare the means of different sets of species on the tree. Instead, we are interested in the difference between two characters, or two measures of a character within a species, and we want to know if this difference is significantly different from zero controlling for the phylogenetic non-independence of species.

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

Value

An object of class "phyl.pairedttest" with the following elements:

dbar

phylogenetic mean difference.

se

standard error of dbar.

sig2

estimated evolutionary variance (of the difference).

lambda

fitted (or fixed) value of λ.

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.

df

the degrees of freedom.

h0

the null hypothesis that was tested.

Author(s)

Liam Revell [e-mail]

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.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.