Description Usage Arguments Details Value Author(s)

Returns a likelihood function that has been constrained to match an MuSSE model of chromosome evolution yielding essentially the original chromevol model.

1 | ```
constrainMuSSE <- function(data, lik, hyper, s.lambda, s.mu, polyploidy, verbose, constrain)
``` |

`data` |
This is the data matrix created by running |

`lik` |
This is a likelihood function created with make.MuSSE |

`hyper` |
If |

`s.lambda` |
If |

`s.mu` |
If |

`polyploidy` |
If |

`verbose` |
If |

`constrain` |
a list capable of carrying additional model constraints these include see details for specifications. |

If the rate identity matrix is returned rates are indicated by the numbers:

rate1 ascending aneuploidy - diploid or state 1 of hypertrait

rate2 descending aneuploidy - diploid or state 1 of hypertrait

rate3 ascending aneuploidy - polyploid or state 2 of hypertrait

rate4 descending aneuploidy - polyploid or state 2 of hypertrait

rate5 polyploidization of a diploid or state 1 of hypertrait

rate6 polploidization of a polyploid or state 2 of hypertrait

rate7 rediploidization of a polyploid

rate8 transitions from state 1 to 2 of hypertrait

rate9 transitions from state 2 to 1 of hypertrait

The argument `constrain`

can contain any of the items listed below. The default state is shown.

`drop.poly=F`

Sets polyploidy rate to zero

`drop.demi=F`

Sets demiploidy rate to zero

`symmetric=F`

Sets all chromosome change rates to be symmetric

`nometa=F`

Drops metastate from analysis

`meta="ARD"`

Can be set as either `"ARD"`

or `"SYM"`

these have the same meanings as `ace`

in the APE package.

constrained likelihood function is returned

Heath Blackmon

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