Calculate the weight matrix of a set of regimes on a phylogeny


These functions calculate weight matrices from regimes specified by a bayou formatted parameter list parmap.W calculates the weight matrix for a set of regimes from a phylogeny with a stored regime history. .parmap.W calculates the same matrix, but without checks and is generally run internally.


parmap.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.


.parmap.W is more computationally efficient within a mcmc and is used internally.

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