Description Usage Arguments Details

View source: R/bayou-weight_matrix.R View source: R/bayou-weight_matrix.R

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.

1 | ```
parmap.W(tree, pars)
``` |

`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. |

`.parmap.W`

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

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