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 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.

1 | ```
simmap.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. |

`.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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