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EmpiricalCodonMatrices.R
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##
## Copyright 2009 Botond Sipos
## See the package description for licensing information.
##
## ECMrest
##
##########################################################################/**
#
# @RdocClass ECMrest
#
# @title "The ECMrest empirical codon substitution model"
#
# \description{
#
#
# @classhierarchy
# }
#
# \references{
# Kosiol C., Holmes I., Goldman, N. (2007) An empirical codon model for protein sequence evolution -
# Mol Biol Evol. 24(7):1464-79 DOI: 10.1093/molbev/msm064 \url{http://bit.ly/1ia8gWm}
# }
#
# @synopsis
#
# \arguments{
# \item{equ.dist}{Equilibrium distribution.}
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create substitution model object
# p<-ECMrest()
# # get object summary
# summary(p)
# # display a bubble plot
# plot(p)
#
# # The following code demonstrates how to use
# # the process in a simulation.
#
# # create a sequence, attach process p
# s<-CodonSequence(length=10,processes=list(list(p)) )
# # sample states
# sampleStates(s)
# # make the first three positions invariable
# setRateMultipliers(s,p,0,1:3)
# # get rate multipliers
# getRateMultipliers(s,p)
# # create a simulation object
# sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
# # run simulation
# Simulate(sim)
# # print alignment
# sim$alignment
# }
#
# @author
#
# \seealso{
# CodonSubst GeneralSubstitution CodonUNREST
# }
#
#*/###########################################################################
setConstructorS3(
"ECMrest",
function(
equ.dist=NA,
...
){
this<-CodonSubst$newMatrix(
name="ECMrest",
paml.file="ECMrest.dat",
equ.dist=equ.dist
);
return(this);
},
enforceRCC=FALSE
);
##
## ECMunrest
##
##########################################################################/**
#
# @RdocClass ECMunrest
#
# @title "The ECMunrest empirical codon substitution model"
#
# \description{
#
#
# @classhierarchy
# }
#
# \references{
# Kosiol C., Holmes I., Goldman, N. (2007) An empirical codon model for protein sequence evolution -
# Mol Biol Evol. 24(7):1464-79 DOI: 10.1093/molbev/msm064 \url{http://bit.ly/1ia8gWm}
# }
#
# @synopsis
#
# \arguments{
# \item{equ.dist}{Equilibrium distribution.}
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create substitution model object
# p<-ECMunrest()
# # get object summary
# summary(p)
# # display a bubble plot
# plot(p)
#
# # The following code demonstrates how to use
# # the process in a simulation.
#
# # create a sequence, attach process p
# s<-CodonSequence(length=10,processes=list(list(p)) )
# # sample states
# sampleStates(s)
# # make the first three positions invariable
# setRateMultipliers(s,p,0,1:3)
# # get rate multipliers
# getRateMultipliers(s,p)
# # create a simulation object
# sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
# # run simulation
# Simulate(sim)
# # print alignment
# sim$alignment
# }
#
# @author
#
# \seealso{
# CodonSubst GeneralSubstitution CodonUNREST
# }
#
#*/###########################################################################
setConstructorS3(
"ECMunrest",
function(
equ.dist=NA,
...
){
this<-CodonSubst$newMatrix(
name="ECMunrest",
paml.file="ECMunrest.dat",
equ.dist=equ.dist
);
return(this);
},
enforceRCC=FALSE
);