phylosim (version 3.0.5)

sampleStates.Sequence: Sample the states for a collection of Site objects aggregated by a Sequence object

Description

Sample the states for a collection of Site objects aggregated by a Sequence object. This method samples new states from the equlibrium distribution of the attched process(es) for sites having undefined states (NA). If a site has more than one substitution process attached, then the method samples the new state from the mixture of equlibrium distributions. The weight of each equlibrium distribution is proportional to the site-process specific rate multiplier of the corresponding process at the given site.

Sites having defined states are not touched. All sites with undefined states must have at least one substitution process (object inheriting from GeneralSubstitution) attached.

Usage

# S3 method for Sequence
sampleStates(this, index, ...)

Arguments

this

A Sequence object.

index

An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.

...

Not used.

Value

The Sequence object (invisible).

See Also

sampleState.GeneralSubstitution GeneralSubstitution

Examples

# NOT RUN {
	# create a nucleotide sequence
	s<-NucleotideSequence(length=80)
	# create some processes
	jc69<-JC69(); 				# Jukes-Cantor
	hky<-HKY(base.freqs=c(0.1,0.4,0.1,0.4)) # "GC-rich" HKY
	# attach the processes
	s$processes<-list(list(jc69)) # jc is attached to all sites
	attachProcess(s,hky,60:80)  # hky is attached to range 60:80
	# tweak rate multiplier for hky
	setRateMultipliers(s,hky,10,60:80)
	# set states in range 1:20
	setStates(s,"A",1:20)
	# sample remaining states
	sampleStates(s)
	# print sequence
	s
 
# }