setRate.QMatrix: Set an unscaled rate in a QMatrix object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Set an unscaled rate in a QMatrix object.

This method sets the element corresponding to a given event in the unscaled rate matrix. The event can be specified by the inital and target states ("from" and "to" arguments), or by the event name ("from->to"). The event name takes precedence over the "from" and "to" arguments.

Usage

## S3 method for class 'QMatrix'
setRate(this, name=NA, value, from=NA, to=NA, scale=TRUE, diag=TRUE, guess.equ=TRUE, ...)

Arguments

this	A QMatrix object.
name	The name of the event.
value	The new value of the rate.
from	The initial state.
to	Target state.
scale	Call rate rescaling.
diag	Calculate diagonal elements.
guess.equ	Guess equilibrium distribution.
...	Not used.

Value

A Numeric vector of length one.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see QMatrix.

Examples

       # create a QMatrix object
       # provide an Alphabet object and the rates
       m<-QMatrix(alphabet=BinaryAlphabet(), rate.list=list("1->0"=1,"0->1"=1))
       # set the unscaled rate by event name
       setRate(m,"0->1",2)
       # get the unscaled rate of "0->1" by name
       getRate(m,"0->1")     
       # set the unscaled rate by states
       setRate(m,"0->1",0.5)
       # set the unscaled rate of "0->1" by states
       setRate(m,"0->1",0.5)
       # get the unscaled rate of "0->1" by states
       getRate(m,from="0",to="1")
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.