# Analysis of Codon Data under Stationarity using a Bayesian Framework

## Documentation for package ‘AnaCoDa’ version 0.1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
calculateSCUO | calculates the synonymous codon usage order (SCUO)
calculate_marginal_log_likelihood | Calculates the marginal log-likelihood for a set of parameters
codons | Codons
codonToAA | translates codon to amino acid
convergence.test | Convergence Test
findOptimalCodon | Find and return list of optimal codons
geomMean | Take the geometric mean of a vector
getCAI | Calculate the Codon Adaptation Index
getCAIweights | Calculate the CAI codon weigths for a reference genome
getCodonCounts | Get Codon Counts For all Amino Acids
getCodonCountsForAA | Get Codon Counts For a specific Amino Acid
getCSPEstimates | Return Codon Specific Paramters (or write to csv) estimates as data.frame
getExpressionEstimates | Returns the estimated phi posterior for a gene
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
getObservedSynthesisRateSet | Get gene observed synthesis rates
getSelectionCoefficients | Calculate Selection coefficients
getTrace | extracts an object of traces from a parameter object.
initializeCovarianceMatrices | Initialize Covariance Matrices
initializeGenomeObject | Genome Initialization
initializeMCMCObject | Initialize MCMC
initializeModelObject | Model Initialization
initializeParameterObject | Initialize Parameter
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
plotCodonSpecificParameters | Plot Codon Specific Parameter
runMCMC | Run MCMC
setRestartSettings | Set Restart Settings
summary.Rcpp_Genome | Summary of Genome
writeMCMCObject | Write MCMC Object
writeParameterObject | Write Parameter Object to a File