Files in AnaCoDa
Analysis of Codon Data under Stationarity using a Bayesian Framework

NAMESPACE
NEWS.md
configure.ac
cleanup
DESCRIPTION
README.md
configure
MD5
tests/testthat.R tests/testthat/testPAModel.R tests/testthat/testSequenceSummary.R tests/testthat/testGenome.R tests/testthat/testMCMCAlgorithm.R tests/testthat/testMCMCROC.R tests/testthat/testGene.R tests/testthat/testParameter.R tests/testthat/testutility.R tests/testthat/testCovarianceMatrix.R
tests/testthat/UnitTestingData/readObservedPhiValues.csv
tests/testthat/UnitTestingData/writeSimulatedGenome.csv
tests/testthat/UnitTestingData/readObservedPhiValuesError.csv
tests/testthat/UnitTestingData/writeFasta.fasta
tests/testthat/UnitTestingData/readFasta.fasta
tests/testthat/UnitTestingData/readRFPData.csv
tests/testthat/UnitTestingData/writeRFPData.csv
tests/testthat/UnitTestingData/readSimulatedGenome.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR_phi_withPhiSet.csv
tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR.fasta
tests/testthat/UnitTestingData/testPAModelFiles/testPAModel.csv
tests/testthat/UnitTestingData/testPAModelFiles/codonTranslationRates.csv
tests/testthat/UnitTestingOut/RFPPsiValues.csv
tests/testthat/UnitTestingOut/RFPLambdaPrimeValues.csv
tests/testthat/UnitTestingOut/testMCMCROCLogPhi.txt
tests/testthat/UnitTestingOut/RFPAlphaValues.csv
tests/testthat/UnitTestingOut/testMCMCROCLogWithoutPhi.txt
man/plot.Rcpp_FONSEParameter.Rd man/codons.Rd man/initializeGenomeObject.Rd man/getExpressionEstimates.Rd man/plot.Rcpp_MCMCAlgorithm.Rd man/convergence.test.Rd man/initializeParameterObject.Rd man/loadMCMCObject.Rd man/setRestartSettings.Rd man/codonToAA.Rd man/getTrace.Rd man/getCSPEstimates.Rd man/length.Rcpp_Genome.Rd man/acfMCMC.Rd man/loadParameterObject.Rd man/summary.Rcpp_Genome.Rd man/initializeMCMCObject.Rd man/AAToCodon.Rd man/aminoAcids.Rd man/getObservedSynthesisRateSet.Rd man/writeMCMCObject.Rd man/initializeModelObject.Rd man/plot.Rcpp_FONSEModel.Rd man/initializeCovarianceMatrices.Rd man/addObservedSynthesisRateSet.Rd man/runMCMC.Rd man/plotCodonSpecificParameters.Rd man/getMixtureAssignmentEstimate.Rd man/getNames.Rd man/plot.Rcpp_Trace.Rd man/getCodonCountsForAA.Rd man/plot.Rcpp_ROCParameter.Rd man/writeParameterObject.Rd man/plot.Rcpp_ROCModel.Rd man/acfCSP.Rd R/genomeObject.R R/plotModelObject.R R/parameterObject.R R/modelObject.R R/plotTraceObject.R R/plotParameterObject.R R/colorSchemes.R R/onloadPackage.R R/plotMCMCAlgorithmObject.R R/mcmcObject.R R/traceObject.R
inst/doc/anacoda.html
inst/doc/anacoda.Rmd
inst/doc/model_fit.png
inst/doc/logpost_trace.png
inst/doc/selection_trace.png
inst/doc/anacoda.bib
inst/doc/expression_trace.png
inst/doc/param_comp.png
inst/extdata/genome.fasta
inst/extdata/more_genes.fasta
inst/extdata/restart_file.rst
inst/extdata/expression.csv
src/ROCModel.cpp
src/Trace.cpp
src/SequenceSummary.cpp
src/Makevars.in
src/RCPP_Trace.cpp
src/RCPP_Parameter.cpp
src/Makevars.win
src/CodonTable.cpp
src/CovarianceMatrix.cpp
src/registerDynamicSymbol.c
src/PANSEParameter.cpp
src/Gene.cpp
src/Genome.cpp
src/MCMCAlgorithm.cpp
src/RCPP_Model.cpp
src/PAParameter.cpp
src/main.cpp
src/PAModel.cpp
src/Model.cpp
src/Parameter.cpp
src/FONSEParameter.cpp
src/ROCParameter.cpp
src/FONSEModel.cpp
src/PANSEModel.cpp
src/Testing.cpp
src/include/CovarianceMatrix.h
src/include/CodonTable.h
src/include/Testing.h
src/include/SequenceSummary.h
src/include/Gene.h
src/include/MCMCAlgorithm.h
src/include/Genome.h
src/include/mixtureDefinition.h
src/include/Utility.h
src/include/ROC/ROCModel.h
src/include/ROC/ROCParameter.h
src/include/FONSE/FONSEParameter.h
src/include/FONSE/FONSEModel.h
src/include/base/Trace.h
src/include/base/Parameter.h
src/include/base/Model.h
src/include/PANSE/PANSEParameter.h
src/include/PANSE/PANSEModel.h
src/include/PA/PAModel.h
src/include/PA/PAParameter.h
AnaCoDa documentation built on Jan. 11, 2018, 5:04 p.m.