constrainMuSSE: Constrain a diversitree MuSSE model

Description Usage Arguments Details Value Author(s)

Description

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

Usage

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

s.lambda

If TRUE a single value of lambda is assumed across metastates

s.mu

If TRUE a single value of mu is assumed across metastates

polyploidy

If TRUE then polyploidy is assumed to be the metastate

verbose

If TRUE then a list is returned with the first element containing the likelihood function and the second containing the rate identity matrix.

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.

Value

constrained likelihood function is returned

Author(s)

Heath Blackmon


coleoguy/chromePlus documentation built on June 10, 2019, 8:06 a.m.