phylosim (version 3.0.5)

plusInvGamma.Sequence: Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object

Description

Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object.

The gamma distribution is discretized by calculating the means of the portions corresponding to the categories having equal probabilities. If the ncat argument is not numeric, the rates are sampled from the continuous gamma distribution.

Usage

# S3 method for Sequence
plusInvGamma(this, process, pinv, shape, index, ncat=4, ...)

Arguments

this

A Sequence object.

process

A Process object.

pinv

The proportion of invariant sites.

shape

The shape parameter of the gamma distribution.

index

A vector of positions.

ncat

Numer of categories in the discretized gamma distribution (4 by default).

...

Not used.

Value

The Sequence object (invisible);

References

Gu X, Fu, YX, Li, WH (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites - Mol. Biol. Evol. 12(4):546-57 http://bit.ly/aE6xF0

Yang, Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods - Journal of Molecular Evolution 39:306-314 http://dx.doi.org/10.1007/BF00160154

See Also

For more information see Sequence.

Examples

# NOT RUN {
	# create a sequence
	s<-NucleotideSequence(length=20)
	# attach a process
	p<-JC69()
	attachProcess(s,p)
	# get rate multipliers
	getRateMultipliers(s,p)	# the default value is 1.0
	# sample rate multipliers in range 1:5 from I+discrete Gamma
	plusInvGamma(s,p,pinv=0.5,shape=0.5,1:5)
	# get rate multipliers
	getRateMultipliers(s,p)	# the default value is 1.0
	# sample rates from an I+continuos Gamma model
	plusInvGamma(s,p,pinv=0.5,shape=0.5,1:5,ncat="cont")
	# get rate multipliers
	getRateMultipliers(s,p)
 
# }