AAToCodon               Amino Acid to codon set
acfCSP                  Plots ACF for codon specific parameter traces
acfMCMC                 Autocorrelation function for the likelihood or
                        posterior trace
addObservedSynthesisRateSet
                        Add gene observed synthesis rates
aminoAcids              Amino acids
calculateMarginalLogLikelihood
                        Calculates the marginal log-likelihood for a
                        set of parameters
calculateSCUO           calculates the synonymous codon usage order
                        (SCUO)
codonToAA               translates codon to amino acid
codons                  Codons
convergence.test        Convergence Test
findOptimalCodon        Find and return list of optimal codons
fixDEta                 fixDEta
fixDM                   fixDM
fixSphi                 fixSphi
geomMean                Take the geometric mean of a vector
getAdaptiveWidth        getAdaptiveWidth
getCAI                  Calculate the Codon Adaptation Index
getCAIweights           Calculate the CAI codon weigths for a reference
                        genome
getCSPEstimates         Return Codon Specific Paramters (or write to
                        csv) estimates as data.frame
getCodonCounts          Get Codon Counts For all Amino Acids
getCodonCountsForAA     Get Codon Counts For a specific Amino Acid
getCodonSpecificPosteriorMeanForCodon
                        getCodonSpecificPosteriorMeanForCodon
getCodonSpecificPosteriorVarianceForCodon
                        getCodonSpecificPosteriorVarianceForCodon
getCodonSpecificQuantilesForCodon
                        getCodonSpecificQuantilesForCodon
getEstimatedMixtureAssignmentForGene
                        getEstimatedMixtureAssignmentForGene
getEstimatedMixtureAssignmentProbabilitiesForGene
                        getEstimatedMixtureAssignmentProbabilitiesForGene
getExpressionEstimates
                        Returns the estimated phi posterior for a gene
getGroupList            getGroupList
getLogLikelihoodTrace   getLogLikelihoodTrace
getLogPosteriorMean     getLogPosteriorMean
getLogPosteriorTrace    getLogPosteriorTrace
getMixtureAssignmentEstimate
                        Returns mixture assignment estimates for each
                        gene
getNames                Gene Names of Genome
getNc                   Calculate the Effective Number of Codons
getNcAA                 Calculate the Effective Number of Codons for
                        each Amino Acid
getNoiseOffsetPosteriorMean
                        getNoiseOffsetPosteriorMean
getNoiseOffsetVariance
                        getNoiseOffsetVariance
getObservedSynthesisRateSet
                        Get gene observed synthesis rates
getSamples              getSamples
getSelectionCoefficients
                        Calculate Selection coefficients
getStdDevSynthesisRatePosteriorMean
                        getStdDevSynthesisRatePosteriorMean
getStdDevSynthesisRateVariance
                        getStdDevSynthesisRateVariance
getStepsToAdapt         getStepsToAdapt
getSynthesisRate        getSynthesisRate
getSynthesisRatePosteriorMeanForGene
                        getSynthesisRatePosteriorMeanForGene
getSynthesisRatePosteriorVarianceForGene
                        getSynthesisRatePosteriorVarianceForGene
getThinning             getThinning
getTrace                extracts an object of traces from a parameter
                        object.
getTraceObject          getTraceObject
initMutationCategories
                        initMutationCategories
initSelectionCategories
                        initSelectionCategories
initializeCovarianceMatrices
                        Initialize Covariance Matrices
initializeGenomeObject
                        Genome Initialization
initializeMCMCObject    Initialize MCMC
initializeModelObject   Model Initialization
initializeParameterObject
                        Initialize Parameter
initializeSynthesisRateByGenome
                        initializeSynthesisRateByGenome
initializeSynthesisRateByList
                        initializeSynthesisRateByList
initializeSynthesisRateByRandom
                        initializeSynthesisRateByRandom
length.Rcpp_Genome      Length of Genome
loadMCMCObject          Load MCMC Object
loadParameterObject     Load Parameter Object
plot.Rcpp_FONSEModel    Plot Model Object
plot.Rcpp_FONSEParameter
                        Plot Parameter
plot.Rcpp_MCMCAlgorithm
                        Plot MCMC algorithm
plot.Rcpp_ROCModel      Plot Model Object
plot.Rcpp_ROCParameter
                        Plot Parameter
plot.Rcpp_Trace         Plot Trace Object
plotAcceptanceRatios    Plot Acceptance ratios
plotCodonSpecificParameters
                        Plot Codon Specific Parameter
readPhiValue            readPhiValue
runMCMC                 Run MCMC
setAdaptiveWidth        setAdaptiveWidth
setGroupList            setGroupList
setRestartFileSettings
                        setRestartFileSettings
setRestartSettings      Set Restart Settings
setSamples              setSamples
setStepsToAdapt         setStepsToAdapt
setThinning             setThinning
simulateGenome          simulateGenome
summary.Rcpp_Genome     Summary of Genome
writeMCMCObject         Write MCMC Object
writeParameterObject    Write Parameter Object to a File
