getTotalRatesFromRange.Sequence: Get the vector of total site rates for a collection of Site...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object.

Usage

## S3 method for class 'Sequence'
getTotalRatesFromRange(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

A numeric vector.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see Sequence.

Examples

	# create a sequence with some processes attached
	s<-Sequence(
               string="ATGC",
               alphabets=list(NucleotideAlphabet()),
               processes=list(list(JC69()),list(JC69(),GTR()))
               )
	# get total rates for positions 1 and 3
	getTotalRatesFromRange(s,c(1,3))
	# get all total rates via virtual field
	s$totalRates	# via the "getTotalRates.Sequence" method
 

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