setAlphabet.GeneralSubstitution: Set the Alphabet object aggregated by a GeneralSubstitution...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Set the Alphabet object aggregated by a GeneralSubstitution object.

This method also sets the alphabet for the associated QMatrix object, which will set all rates to NA. This method will also re-initialize the equlibrium distribution by setting all frequencies to NA.

Usage

## S3 method for class 'GeneralSubstitution'
setAlphabet(this, value, ...)

Arguments

this	A GeneralSubstitution object.
value	An Alphabet object.
...	Not used.

Value

The Alphabet object.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see GeneralSubstitution.

Examples

	# create a GeneralSubstitution object with an attached BinaryAlphabet object
	p<-GeneralSubstitution(alphabet=BinaryAlphabet())
	# get object summary
	summary(p)
	# get alphabet
	getAlphabet(p)
	# get alphabet via virtual field
	p$alphabet
	# set a new alphabet
	setAlphabet(p,NucleotideAlphabet())
	summary(p)
	# set alphabet via virtual field
	p$alphabet<-BinaryAlphabet()
	p$alphabet
 

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