Files in AnaCoDa
Analysis of Codon Data under Stationarity using a Bayesian Framework
MD5
NAMESPACE
cleanup
configure.ac
DESCRIPTION
configure
tests/testthat.R
tests/testthat/testParameter.R
tests/testthat/testPAModel.R
tests/testthat/testGene.R
tests/testthat/testutility.R
tests/testthat/testSequenceSummary.R
tests/testthat/testMCMCAlgorithm.R
tests/testthat/testMCMCROC.R
tests/testthat/testCovarianceMatrix.R
tests/testthat/testGenome.R
tests/testthat/UnitTestingData/readObservedPhiValues.csv
tests/testthat/UnitTestingData/readSimulatedGenome.csv
tests/testthat/UnitTestingData/readRFPData.csv
tests/testthat/UnitTestingData/writeSimulatedGenome.csv
tests/testthat/UnitTestingData/writeFasta.fasta
tests/testthat/UnitTestingData/writeRFPData.csv
tests/testthat/UnitTestingData/readObservedPhiValuesError.csv
tests/testthat/UnitTestingData/readFasta.fasta
tests/testthat/UnitTestingData/testPAModelFiles/codonTranslationRates.csv
tests/testthat/UnitTestingData/testPAModelFiles/testPAModel.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR.fasta
tests/testthat/UnitTestingData/testMCMCROCFiles/mutation_1.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/selection_2.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR_phi_withPhiSet.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/selection_1.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/mutation_2.csv
tests/testthat/UnitTestingOut/RFPAlphaValues.csv
tests/testthat/UnitTestingOut/RFPLambdaPrimeValues.csv
tests/testthat/UnitTestingOut/RFPPsiValues.csv
src/Model.cpp
src/RCPP_Trace.cpp
src/SequenceSummary.cpp
src/ROCParameter.cpp
src/Parameter.cpp
src/CodonTable.cpp
src/Trace.cpp
src/CovarianceMatrix.cpp
src/Makevars.win
src/PANSEModel.cpp
src/MCMCAlgorithm.cpp
src/PANSEParameter.cpp
src/FONSEModel.cpp
src/Genome.cpp
src/Makevars.in
src/main.cpp
src/ROCModel.cpp
src/PAParameter.cpp
src/RCPP_Model.cpp
src/FONSEParameter.cpp
src/registerDynamicSymbol.c
src/Testing.cpp
src/PAModel.cpp
src/Gene.cpp
src/RCPP_Parameter.cpp
src/include/Utility.h
src/include/Gene.h
src/include/Testing.h
src/include/MCMCAlgorithm.h
src/include/CodonTable.h
src/include/CovarianceMatrix.h
src/include/SequenceSummary.h
src/include/Genome.h
src/include/mixtureDefinition.h
src/include/PANSE/PANSEModel.h
src/include/PANSE/PANSEParameter.h
src/include/base/Model.h
src/include/base/Parameter.h
src/include/base/Trace.h
src/include/FONSE/FONSEParameter.h
src/include/FONSE/FONSEModel.h
src/include/PA/PAParameter.h
src/include/PA/PAModel.h
src/include/ROC/ROCParameter.h
src/include/ROC/ROCModel.h
R/mcmcObject.R
R/RcppExports.R
R/traceObject.R
R/modelObject.R
R/plotParameterObject.R
R/genomeObject.R
R/plotMCMCAlgorithmObject.R
R/onloadPackage.R
R/plotTraceObject.R
R/colorSchemes.R
R/parameterObject.R
R/plotModelObject.R
man/setStepsToAdapt.Rd
man/summary.Rcpp_Genome.Rd
man/getCSPEstimates.Rd
man/acfCSP.Rd
man/setRestartSettings.Rd
man/getCAIweights.Rd
man/fixSphi.Rd
man/getLogPosteriorTrace.Rd
man/initializeSynthesisRateByRandom.Rd
man/convergence.test.Rd
man/getObservedSynthesisRateSet.Rd
man/getEstimatedMixtureAssignmentForGene.Rd
man/initSelectionCategories.Rd
man/plotCodonSpecificParameters.Rd
man/readPhiValue.Rd
man/getSynthesisRatePosteriorMeanForGene.Rd
man/runMCMC.Rd
man/initializeSynthesisRateByList.Rd
man/getCodonSpecificPosteriorVarianceForCodon.Rd
man/getStdDevSynthesisRatePosteriorMean.Rd
man/getMixtureAssignmentEstimate.Rd
man/getCodonCountsForAA.Rd
man/calculateSCUO.Rd
man/getStdDevSynthesisRateVariance.Rd
man/geomMean.Rd
man/plot.Rcpp_MCMCAlgorithm.Rd
man/getNcAA.Rd
man/getExpressionEstimates.Rd
man/getStepsToAdapt.Rd
man/simulateGenome.Rd
man/getCodonCounts.Rd
man/writeMCMCObject.Rd
man/length.Rcpp_Genome.Rd
man/initializeModelObject.Rd
man/loadParameterObject.Rd
man/findOptimalCodon.Rd
man/getCAI.Rd
man/setSamples.Rd
man/calculateMarginalLogLikelihood.Rd
man/getThinning.Rd
man/acfMCMC.Rd
man/setThinning.Rd
man/setRestartFileSettings.Rd
man/initializeSynthesisRateByGenome.Rd
man/getTraceObject.Rd
man/initializeCovarianceMatrices.Rd
man/plot.Rcpp_Trace.Rd
man/initializeMCMCObject.Rd
man/getNoiseOffsetPosteriorMean.Rd
man/addObservedSynthesisRateSet.Rd
man/loadMCMCObject.Rd
man/getSamples.Rd
man/fixDEta.Rd
man/getNc.Rd
man/getCodonSpecificQuantilesForCodon.Rd
man/plot.Rcpp_FONSEModel.Rd
man/getGroupList.Rd
man/plot.Rcpp_ROCModel.Rd
man/getSelectionCoefficients.Rd
man/plotAcceptanceRatios.Rd
man/initializeGenomeObject.Rd
man/getAdaptiveWidth.Rd
man/getTrace.Rd
man/AAToCodon.Rd
man/codonToAA.Rd
man/setAdaptiveWidth.Rd
man/getLogPosteriorMean.Rd
man/initMutationCategories.Rd
man/getSynthesisRatePosteriorVarianceForGene.Rd
man/fixDM.Rd
man/getEstimatedMixtureAssignmentProbabilitiesForGene.Rd
man/getCodonSpecificPosteriorMeanForCodon.Rd
man/getNames.Rd
man/initializeParameterObject.Rd
man/getLogLikelihoodTrace.Rd
man/getNoiseOffsetVariance.Rd
man/codons.Rd
man/aminoAcids.Rd
man/getSynthesisRate.Rd
man/plot.Rcpp_FONSEParameter.Rd
man/plot.Rcpp_ROCParameter.Rd
man/writeParameterObject.Rd
man/setGroupList.Rd
inst/extdata/more_genes.fasta
inst/extdata/restart_file.rst
inst/extdata/genome.fasta
inst/extdata/expression.csv
inst/doc/anacoda.R
inst/doc/anacoda.Rmd
inst/doc/anacoda.html
build/vignette.rds
vignettes/param_comp.png
vignettes/sel_cai_comp.png
vignettes/expression_trace.png
vignettes/logpost_trace.png
vignettes/selection_trace.png
vignettes/model_fit.png
vignettes/anacoda.Rmd
vignettes/anacoda.bib
