simmap.W: Calculate the weight matrix of a set of regimes on a...
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description
Usage
Arguments
Details
Description
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.
Usage
1
simmap.W(tree, pars)
Arguments
tree
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.
pars
a list of the parameters used to calculate the weight matrix. Only pars$alpha is
necessary to calculate the matrix, but others can be present.
Details
.simmap.W is more computationally efficient within a mcmc and is used internally. The value
of TotExp is supplied to speed computation and reduce redundancy, and cache objects must be supplied as
the phylogeny, and the parameter ntheta must be present in the list pars.
bayou documentation built on May 2, 2019, 2:46 a.m.
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Description Usage Arguments Details
Description
These functions calculate weight matrices from regimes specified in phytools' simmap format.
simmap.W calculates the weight matrix for a set of regimes from a phylogeny
with a stored regime history. .simmap.W calculates the same matrix, but without checks and is
generally run internally.
Usage
1 | simmap.W(tree, pars)
|
Arguments
tree |
either a tree of class "phylo" or a cache object produced by bayOU's internal functions. Must include list element 'maps' which is a simmap reconstruction of regime history. |
pars |
a list of the parameters used to calculate the weight matrix. Only pars$alpha is necessary to calculate the matrix, but others can be present. |
Details
.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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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