constrainMuSSE: Constrain a diversitree MuSSE model
In coleoguy/chromevolR: Analysis of chromosome number evolution and binary traits

View source: R/constrainMuSSE.R

constrainMuSSE

R Documentation

Constrain a diversitree MuSSE model

Description

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

Usage

constrainMuSSE(data, lik, hyper = T, 
               polyploidy = F, s.lambda = T, s.mu = T,
               verbose = F, constrain)

Arguments

`data`	This is the data matrix created by running `dataMatrx`
`lik`	This is a likelihood function created with make.MuSSE
`hyper`	If `TRUE` then a binary metastate is assumed. Defaults to `TRUE`
`polyploidy`	If `TRUE` then polyploidy is assumed to be the metastate. Defaults to `FALSE`
`s.lambda`	If `TRUE` a single value of lambda is assumed across metastates. Defaults to `TRUE`
`s.mu`	If `TRUE` a single value of mu is assumed across metastates. Defaults to `TRUE`
`verbose`	If `TRUE` then a list is returned with the first element containing the likelihood function and the second containing the rate identity matrix. Defaults to `FALSE`
`constrain`	a list capable of carrying additional model constraints these include see details for specifications.

Details

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.