simmap.W: Calculate the weight matrix of a set of regimes on a...

Description Usage Arguments Details


These functions calculate weight matrices from regimes specified in phytools' simmap format. simmap.W calculates the weight matrix for a set of regimes from a phylogeny with a stored regime history. .simmap.W calculates the same matrix, but without checks and is generally run internally.


simmap.W(tree, pars)



either a tree of class "phylo" or a cache object produced by bayOU's internal functions. Must include list element 'maps' which is a simmap reconstruction of regime history.


a list of the parameters used to calculate the weight matrix. Only pars$alpha is necessary to calculate the matrix, but others can be present.


.simmap.W is more computationally efficient within a mcmc and is used internally. The value of TotExp is supplied to speed computation and reduce redundancy, and cache objects must be supplied as the phylogeny, and the parameter ntheta must be present in the list pars.

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