Rev Language Reference

fnUnitMixture(RateGenerator model, Simplex rootFrequencies, RealPos rate)

model :	RateGenerator (pass by const reference)
	The mixture models to mix.
rootFrequencies :	Simplex (pass by const reference)
	State frequencies at the root.
	Default : NULL
rate :	RealPos (pass by const reference)
	Scale by model by this rate.
	Default : 1

SiteMixtureModel

This function creates a SiteMixtureModel with one component by specifying the rate and root frequencies for a RateGenerator. The rate defaults to 1, leaving the underlying model unchanged. If the site model parameter is a RateMatrix, the root frequencies default to the equilibrium frequencies of the RateMatrix. However, a RateGenerator might not have equilibrium frequencies, in which case the root frequencies must be specified explicitly. In many cases it is not necessary to explicitly call fnUnitMixture(), RevBayes can automatically convert a RateMatrix to a SiteMixtureModel.

M := fnUnitMixture( fnJC(4) )
M := fnJC(4) |> fnUnitMixture()  # nested functions can be expressed using pipes.

# Explicit conversion to SiteMixtureModel
M := fnGTR(er,pi) |> fnUnitMixture() |> fnGammaASRV(alpha) |> fnInvASRV(p_inv)
# Implicit conversion to SiteMixtureModel
M := fnGTR(er,pi) |> fnGammaASRV(alpha) |> fnInvASRV(p_inv)

# Specifying the root frequencies
M := fnDECRateMatrix(dr,er,"Include") |> fnUnitMixture(rootFrequencies=simplex(rep(1,n_states)))