phylosim (version 3.0.5)

getOmegaScalingFactor.GY94: Get the omega scaling factor

Description

Get the omega scaling factor.

The rate matrix of the GY94 model is scaled in a way that the expected number of potential substiutions per site is equal to one at equlibrium. The codeml program from the PAML package scales the rate matrix in order to have the expected number of accepted substiutions per site equal to one.

This method calculates the branch length multiplier needed for switching to PAML-style scaling given a fixed omega.

Usage

# S3 method for GY94
getOmegaScalingFactor(this, omega, ...)

Arguments

this

A GY94 object.

omega

The value of omega.

...

Not used.

Value

A numeric vector of length one.

See Also

For more information see GY94.

Examples

# NOT RUN {
	# construct a GY94 process object
	p<-GY94(kappa=4)
	# Calculate scaling factor for omega=2
	getOmegaScalingFactor(p,omega=2)
 
# }