test.subtrees: Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model
Description
This function will find the maximum likelihood estimate of
the parameters of every single rate shift model that is
compatible with the phylogeny phy, as well as the
likelihood and wAIC for each model. The procedure is
described in Schraiber et al (2013).
Usage
test.subtrees(phy, dat, norm = 1)
Arguments
phy
an ape format phylogeny
dat
a matrix of gene expression data. Rows of dat
correspond to species and columns of dat correspond to
genes
norm
the species by which data should be
normalized
Value
A list of several elements: res is the full output of the
optim runs used maximize the likelihood, branches are lists
of the branches that have a rate shift for each model, LL
is the log likelihood for each model, wAIC is the Akaike
information criterion weight for each model, alpha are
maximum likelihood estimates of the shape parameter of the
inverse gamma distribution for each model, beta are maximum
likelihood estimates of the scale paramter for each model
and shift are maximum likelihood estimates of the rate
shift parameter for each model (except for
Ornstein-Uhlenbeck, in which shift is an estimate of the
constraint parameter of the OU process).