AAToCodon	AAToCodon
acfCSP	acfCSP
acfMCMC	acfMCMC
addObservedSynthesisRateSet	addObservedSynthesisRateSet
aminoAcids	aminoAcids
calculateSCUO	calculateSCUO
calculate_marginal_log_likelihood	calculate_marginal_log_likelihood
codons	codons
codonToAA	codonToAA
convergence.test	convergence.test
findOptimalCodon	findOptimalCodon
geomMean	geomMean
getCAI	getCAI
getCAIweights	getCAIweights
getCodonCounts	getCodonCounts
getCodonCountsForAA	getCodonCountsForAA
getCSPEstimates	getCSPEstimates
getExpressionEstimates	getExpressionEstimates
getMixtureAssignmentEstimate	getMixtureAssignmentEstimate
getNames	getNames
getNc	getNc
getNcAA	getNcAA
getObservedSynthesisRateSet	getObservedSynthesisRateSet
getSelectionCoefficients	getSelectionCoefficients
getTrace	getTrace
initializeCovarianceMatrices	initializeCovarianceMatrices
initializeGenomeObject	initializeGenomeObject
initializeMCMCObject	initializeMCMCObject
initializeModelObject	initializeModelObject
initializeParameterObject	initializeParameterObject
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
plotCodonSpecificParameters	plotCodonSpecificParameters
runMCMC	runMCMC
setRestartSettings	setRestartSettings
summary.Rcpp_Genome	summary.Rcpp_Genome
writeMCMCObject	writeMCMCObject
writeParameterObject	writeParameterObject
