AAToCodon	AAToCodon
acfCSP	acfCSP
acfMCMC	acfMCMC
addObservedSynthesisRateSet	addObservedSynthesisRateSet
aminoAcids	aminoAcids
calculateMarginalLogLikelihood	calculateMarginalLogLikelihood
calculateSCUO	calculateSCUO
codons	codons
codonToAA	codonToAA
convergence.test	convergence.test
findOptimalCodon	findOptimalCodon
fixDEta	fixDEta
fixDM	fixDM
fixSphi	fixSphi
geomMean	geomMean
getAdaptiveWidth	getAdaptiveWidth
getCAI	getCAI
getCAIweights	getCAIweights
getCodonCounts	getCodonCounts
getCodonCountsForAA	getCodonCountsForAA
getCodonSpecificPosteriorMeanForCodon	getCodonSpecificPosteriorMeanForCodon
getCodonSpecificPosteriorVarianceForCodon	getCodonSpecificPosteriorVarianceForCodon
getCodonSpecificQuantilesForCodon	getCodonSpecificQuantilesForCodon
getCSPEstimates	getCSPEstimates
getEstimatedMixtureAssignmentForGene	getEstimatedMixtureAssignmentForGene
getEstimatedMixtureAssignmentProbabilitiesForGene	getEstimatedMixtureAssignmentProbabilitiesForGene
getExpressionEstimates	getExpressionEstimates
getGroupList	getGroupList
getLogLikelihoodTrace	getLogLikelihoodTrace
getLogPosteriorMean	getLogPosteriorMean
getLogPosteriorTrace	getLogPosteriorTrace
getMixtureAssignmentEstimate	getMixtureAssignmentEstimate
getNames	getNames
getNc	getNc
getNcAA	getNcAA
getNoiseOffsetPosteriorMean	getNoiseOffsetPosteriorMean
getNoiseOffsetVariance	getNoiseOffsetVariance
getObservedSynthesisRateSet	getObservedSynthesisRateSet
getSamples	getSamples
getSelectionCoefficients	getSelectionCoefficients
getStdDevSynthesisRatePosteriorMean	getStdDevSynthesisRatePosteriorMean
getStdDevSynthesisRateVariance	getStdDevSynthesisRateVariance
getStepsToAdapt	getStepsToAdapt
getSynthesisRate	getSynthesisRate
getSynthesisRatePosteriorMeanForGene	getSynthesisRatePosteriorMeanForGene
getSynthesisRatePosteriorVarianceForGene	getSynthesisRatePosteriorVarianceForGene
getThinning	getThinning
getTrace	getTrace
getTraceObject	getTraceObject
initializeCovarianceMatrices	initializeCovarianceMatrices
initializeGenomeObject	initializeGenomeObject
initializeMCMCObject	initializeMCMCObject
initializeModelObject	initializeModelObject
initializeParameterObject	initializeParameterObject
initializeSynthesisRateByGenome	initializeSynthesisRateByGenome
initializeSynthesisRateByList	initializeSynthesisRateByList
initializeSynthesisRateByRandom	initializeSynthesisRateByRandom
initMutationCategories	initMutationCategories
initSelectionCategories	initSelectionCategories
length.Rcpp_Genome	length.Rcpp_Genome
loadMCMCObject	loadMCMCObject
loadParameterObject	loadParameterObject
plot.Rcpp_FONSEModel	plot.Rcpp_FONSEModel
plot.Rcpp_FONSEParameter	plot.Rcpp_FONSEParameter
plot.Rcpp_MCMCAlgorithm	plot.Rcpp_MCMCAlgorithm
plot.Rcpp_ROCModel	plot.Rcpp_ROCModel
plot.Rcpp_ROCParameter	plot.Rcpp_ROCParameter
plot.Rcpp_Trace	plot.Rcpp_Trace
plotAcceptanceRatios	plotAcceptanceRatios
plotCodonSpecificParameters	plotCodonSpecificParameters
readPhiValue	readPhiValue
runMCMC	runMCMC
setAdaptiveWidth	setAdaptiveWidth
setGroupList	setGroupList
setRestartFileSettings	setRestartFileSettings
setRestartSettings	setRestartSettings
setSamples	setSamples
setStepsToAdapt	setStepsToAdapt
setThinning	setThinning
simulateGenome	simulateGenome
summary.Rcpp_Genome	summary.Rcpp_Genome
writeMCMCObject	writeMCMCObject
writeParameterObject	writeParameterObject
