Description Usage Arguments Details Value Author(s) References
View source: R/likTraitPhylo.R
This function calculates the log-likelihood and Brownian (co)variance for a trait(s) and a phylogeny using phylogenetically independent contrasts.
1 | likTraitPhylo(y, phy, meserr=NULL)
|
y |
A matrix of trait data. Rownames must be included and match the taxon names in the phylogeny. Can accept single traits (calculates variance) or multiple traits (calculates variance-covariance matrix). |
phy |
An object of class "phylo" (see ape package). |
meserr |
A vector (or matrix) of measurement error for each tip. This is only applicable to univariate analyses. |
The "phylo" object must be rooted and fully dichotomous.
brownianVariance |
Brownian variance (or covariance for multiple traits) given the data and phylogeny |
logLikelihood |
The log-likelihood of the model and data |
Gavin Thomas, Rob Freckleton
Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25, 471-492.
Felsenstein J. 1985. Phylogenies and the comparative method. American Naturalist 125, 1-15.
Freckleton RP & Jetz W. 2009. Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proc. Roy. Soc. B 276, 21-30.
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