test.subtrees: Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model


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).


test.subtrees(phy, dat, norm = 1)



an ape format phylogeny


a matrix of gene expression data. Rows of dat correspond to species and columns of dat correspond to genes


the species by which data should be normalized


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).

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