61c1c10bec519a0d94ce593cee6d09f2 *DESCRIPTION
043dd82a26aa49634fcb57318344418f *NAMESPACE
b30b9ea40c73042a276037ab75a57868 *R/RcppExports.R
24fb96c8d286e5dc3bc0af5a1ed03236 *R/colorSchemes.R
37bc62d1cf475675a6e4a1404650343e *R/genomeObject.R
c046dab51ed918d626760e64e0124a56 *R/mcmcObject.R
88d081c9f8741754e13383d95186a218 *R/modelObject.R
2f223172b92d63243e658d123d461e54 *R/onloadPackage.R
2bdea8e120e79dc0d3f12ece3c7b6e0f *R/parameterObject.R
49cf22e0098544a03600739a179a54f6 *R/plotMCMCAlgorithmObject.R
0b1e0d4f491892bdb27325b397793a6f *R/plotModelObject.R
28a8fcb87af9ca0f55ff4f4ab23f4c13 *R/plotParameterObject.R
e3d36d7ed440a095dc747fa7c4b0012f *R/plotTraceObject.R
5fe0d547b82eef9453e73b7e2af3deed *R/traceObject.R
aaa5023668652855506f07325b0360d3 *build/vignette.rds
f07ebe59999e02ec0543c282acc2cea9 *cleanup
1c4f4cf166f927c5f4b601308686baf9 *configure
dc4e7b569ad7318f903461dafc820d6d *configure.ac
cda0710a9400168b1bfd2f7fe372102c *inst/doc/anacoda.R
4bfb7de36426af0462f6c0385a2f54f7 *inst/doc/anacoda.Rmd
b8de37a542ca3beb7a9cbbf9916b57f7 *inst/doc/anacoda.html
6d7a2df4fdde8675ae00776e7e43cbc1 *inst/extdata/expression.csv
900de55244acd1f2b532f5cbb395053d *inst/extdata/genome.fasta
7bdce107c67bc387294fb8b7bbcb5d0f *inst/extdata/more_genes.fasta
e20db7363ea194adb2683ca9ebac03e1 *inst/extdata/restart_file.rst
41710961f05e6b33a7d811d45a3a3302 *man/AAToCodon.Rd
00ba2a500f298998f2ad44bde4428e94 *man/acfCSP.Rd
103b0bfb96db7c6d9eff1914f05460c5 *man/acfMCMC.Rd
2940420bcb058681ebca0513cf3db973 *man/addObservedSynthesisRateSet.Rd
f9771694a2aad8dc17167e12af605eaa *man/aminoAcids.Rd
6682c42ba46b74d6d1a241c3d171f1a3 *man/calculateMarginalLogLikelihood.Rd
3de44690d03b591996834a5f6588ce79 *man/calculateSCUO.Rd
4b90de9a475df6456034311ff2575e58 *man/codonToAA.Rd
0b92a19dac9b730b484b597901470bc8 *man/codons.Rd
20032b7afb63688aec2abe94a8f8d82d *man/convergence.test.Rd
deaa0caceb46fd2530042104048975b5 *man/findOptimalCodon.Rd
9527044b8890fc124c956aa0a0f5190f *man/fixDEta.Rd
d7a92e801782dbfb20cbcb3c99d65962 *man/fixDM.Rd
3b0e77f81d02351a703a420ab6b11c00 *man/fixSphi.Rd
e0bf8af18c897ae045e423f512f3bf7d *man/geomMean.Rd
1fa0eed23f20813a10abb8c3d1aad7a0 *man/getAdaptiveWidth.Rd
628f59a632761492baf52344363b3c2e *man/getCAI.Rd
24172738ac09207e7c41411c249355cc *man/getCAIweights.Rd
eec394b34738bfaf1abbc9dfe2344b75 *man/getCSPEstimates.Rd
87d69f41aec08de3b81e4138900bd82f *man/getCodonCounts.Rd
6498e0eb58d20f60834dfcfe0e223cbb *man/getCodonCountsForAA.Rd
b05e48fcc5f433003e4aa87fc4c4d408 *man/getCodonSpecificPosteriorMeanForCodon.Rd
bcbfbeeec5cae06f764cc7907a37094f *man/getCodonSpecificPosteriorVarianceForCodon.Rd
c8c44f15394f19bfef3c049ce66da40b *man/getCodonSpecificQuantilesForCodon.Rd
f4c4fdcb069806990f2226f8618ec911 *man/getEstimatedMixtureAssignmentForGene.Rd
f85c69bb954295575a5861f25859aa79 *man/getEstimatedMixtureAssignmentProbabilitiesForGene.Rd
5446bba2dd706fedb282d4d43f385ee4 *man/getExpressionEstimates.Rd
cac96a6193efcc955d50bad8f685e885 *man/getGroupList.Rd
bb95ad59b1bdcbe861b9d29993cb6976 *man/getLogLikelihoodTrace.Rd
5e72ecfc47efa1fc9a1cc6aed81b9af2 *man/getLogPosteriorMean.Rd
a9413b0c244dcdec0bd7c7acb92749ae *man/getLogPosteriorTrace.Rd
c8f4b5dfe2b56b0036812c94d2a60abc *man/getMixtureAssignmentEstimate.Rd
fa8d83bc6272262664c2337e4eae7f10 *man/getNames.Rd
ca6a091a166d295ff85e75b35ba61c98 *man/getNc.Rd
e4ad3854da0d8cd273654184780758ce *man/getNcAA.Rd
57b13156c7276ec30b48b7c0d946ae51 *man/getNoiseOffsetPosteriorMean.Rd
afb24ba0d08a9c03f8eb4e4a52d92007 *man/getNoiseOffsetVariance.Rd
c7cc6c90872c5cf1fdca82a2c3303a1a *man/getObservedSynthesisRateSet.Rd
26d5f3195b145c9f1648f6962f0faedc *man/getSamples.Rd
bc9d108f2c3aee2847f2e3dd80f79ec7 *man/getSelectionCoefficients.Rd
ef4e7aa27aa4edcadd5a62daf536fbed *man/getStdDevSynthesisRatePosteriorMean.Rd
c9d3297ea483b008941f22cecdce319a *man/getStdDevSynthesisRateVariance.Rd
a1d8074f2b92eca538bd18ff93631335 *man/getStepsToAdapt.Rd
322940ecfd585f95cdffdf0651df6fbb *man/getSynthesisRate.Rd
e77c8af6990beca40faa7d09076ebe45 *man/getSynthesisRatePosteriorMeanForGene.Rd
48ae6abf3ad358205d6f0a7f80ba7635 *man/getSynthesisRatePosteriorVarianceForGene.Rd
d4d386cd45848ac7228e6c663d0d7281 *man/getThinning.Rd
f771ea40511ae9072ff52d14a1f3e3a6 *man/getTrace.Rd
18b007ee2cedae03cce1ac2388092ed1 *man/getTraceObject.Rd
0ca2c780c07f60ad69eadb8efe3200f9 *man/initMutationCategories.Rd
c15a8c942e936e1ce5d4cb5ae14937f4 *man/initSelectionCategories.Rd
ace93da4ea2c69a76c607452bdba0cfa *man/initializeCovarianceMatrices.Rd
b79f5af51270c282986a84b736c95ee7 *man/initializeGenomeObject.Rd
08303f1ce4045621751922d769f5aaeb *man/initializeMCMCObject.Rd
337cdb9035e125396bc23c371ce9203c *man/initializeModelObject.Rd
28048c40e10e81dce63f0af60f8c220b *man/initializeParameterObject.Rd
29d438ef3de67af5bf969bf6e611fd93 *man/initializeSynthesisRateByGenome.Rd
515c381b54a92ccb7a5ff646f5969550 *man/initializeSynthesisRateByList.Rd
c8d69d1e66b532f8f7061733dd5aef8c *man/initializeSynthesisRateByRandom.Rd
daa441e7dc8c681464bba3d3746e4897 *man/length.Rcpp_Genome.Rd
7700a5cf6a01123d70ccd03ae16f60c4 *man/loadMCMCObject.Rd
e9f964f238a4e761d89da8494e1da53d *man/loadParameterObject.Rd
98605f927f539a52a7a6cf73e27b805f *man/plot.Rcpp_FONSEModel.Rd
abb42caf41f0881d9db8f2c15baad687 *man/plot.Rcpp_FONSEParameter.Rd
85859dcf992df4a3a2332cc0bb132b5c *man/plot.Rcpp_MCMCAlgorithm.Rd
5df5d95d249d9d99d24c98b28f9f841f *man/plot.Rcpp_ROCModel.Rd
e01960d8028ef91ccec177389bb96b6c *man/plot.Rcpp_ROCParameter.Rd
f4fb7ee1838dc96fbde40735cf21e49c *man/plot.Rcpp_Trace.Rd
b60b827fb04ef724d9880b49079c1c04 *man/plotAcceptanceRatios.Rd
db57776a9e46387754ff79edfd973a4e *man/plotCodonSpecificParameters.Rd
ee4a8ff9536622b10c28b854e8b04cde *man/readPhiValue.Rd
974264b611b8167e14b9b0d76ffcc852 *man/runMCMC.Rd
b4f1b94e2ba64425df042cb7cab04a92 *man/setAdaptiveWidth.Rd
d425501d632faf2e2a0b9fd93d366428 *man/setGroupList.Rd
f951c1c07876470d8595c9ad716ca990 *man/setRestartFileSettings.Rd
d42867ea01ad0a54a8d8c103a7460269 *man/setRestartSettings.Rd
38fc11467d29b3f96f44d3070abbcc25 *man/setSamples.Rd
9c1ef1aead2e69de7ef91c97c92cd031 *man/setStepsToAdapt.Rd
004fbcd739a37158896d6a4639582c09 *man/setThinning.Rd
dfb7e6b36477677d8e85e98a7e942775 *man/simulateGenome.Rd
8d8a06e7fa77a91f3d2fa2fc1750fbff *man/summary.Rcpp_Genome.Rd
4eadaad7d440b4cf1610247cbf2bcc6d *man/writeMCMCObject.Rd
31aa8302c04d5c25075bea87dabea7c3 *man/writeParameterObject.Rd
1e8e0aa7c76275afc985d4168953c6ef *src/CodonTable.cpp
2feef718ea8d437d1e8addde7d9ee4bc *src/CovarianceMatrix.cpp
ffd38395a3b384e66258ac9bb3c574ae *src/FONSEModel.cpp
daf492e1c8d48d9f0488b87f2a5bbec6 *src/FONSEParameter.cpp
4709aa0b88887a9d848d821a51abbfe9 *src/Gene.cpp
1b0f060662228e013fdd5b988a04917c *src/Genome.cpp
f36f0293ae60dd882d66678e5f1639d0 *src/MCMCAlgorithm.cpp
09bac362737a8499ea9ef7a4c747c38d *src/Makevars.in
729c2d006145d9bfb9d3d9497cae6815 *src/Makevars.win
dcce90eccd0b0d2cc1f4c7d6427595fc *src/Model.cpp
c48bf5367795a8776fe86166b101bcda *src/PAModel.cpp
94188429996c78d17f666f5f4a36275f *src/PANSEModel.cpp
a6ec153c4e4013afb29bf147180fe1db *src/PANSEParameter.cpp
11a5b030e9b715bc52169faa27d3c3b1 *src/PAParameter.cpp
b68bccf1034150b11a7336a76ff34898 *src/Parameter.cpp
19874812151a504935995c1b981e663d *src/RCPP_Model.cpp
3a51495440f1e135d622af951e892b6c *src/RCPP_Parameter.cpp
26078807c2849afb1f49d9402dfb13ff *src/RCPP_Trace.cpp
d301394191508d949307828b1a20f3ed *src/ROCModel.cpp
e2fe5ea1014e49516be05b3c507cec64 *src/ROCParameter.cpp
db9398aad3b806dec2b514a89ab9975e *src/SequenceSummary.cpp
4dbca5ddda0aaff96269f44164568ebd *src/Testing.cpp
cdd060d546e54a04211c07dec524787f *src/Trace.cpp
9c596d39e0a9d9d133e4e81ad64360eb *src/include/CodonTable.h
fcb8f275de127f7f288efa15017a87b1 *src/include/CovarianceMatrix.h
c40d273b9eef33d7179be9fe10f8498f *src/include/FONSE/FONSEModel.h
75789ba0324c379c8c8c724641deadae *src/include/FONSE/FONSEParameter.h
0a641247df70be27a918f1e72e590c8b *src/include/Gene.h
8ed481750c5fe5fc55050130c0890fce *src/include/Genome.h
070e9db62c3a818b812aecd3bd4fe02c *src/include/MCMCAlgorithm.h
8f9ce0d929fbeeaf01265ab465cbd1ea *src/include/PA/PAModel.h
fd3374e65f44215beb5d370e79fef6dc *src/include/PA/PAParameter.h
4e237856834cc34f32dc6d783b1adb6f *src/include/PANSE/PANSEModel.h
d59f013e1836dfaf0bbba7fbed2f7109 *src/include/PANSE/PANSEParameter.h
86c087876936929439a29f1024f8ce1b *src/include/ROC/ROCModel.h
d85836db7b6d8888ef2c9b18748a6ec9 *src/include/ROC/ROCParameter.h
17e99257c08af149e074e3c0d35025ea *src/include/SequenceSummary.h
c84c46da5391c8b1970d9311d945f3ca *src/include/Testing.h
7144e4b43fc0209daa915278efb66330 *src/include/Utility.h
514b68492824cd930469ca7fbee2fd04 *src/include/base/Model.h
0b6a91974c75f155c4e63decbee6b7c2 *src/include/base/Parameter.h
b4ee5f90d7c40dfca6fe73b8de4ad88b *src/include/base/Trace.h
1bcc8cbc533563304aa15cf835e26bbd *src/include/mixtureDefinition.h
55fc44799dedec9550984d3f7f83240e *src/main.cpp
ef410cf82c1181af37835113f3d24c24 *src/registerDynamicSymbol.c
1e66a5316e88eaa8823dfeacf072ed3b *tests/testthat.R
a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/readFasta.fasta
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4bd9fcbd2b8a9beebafbf43930474c67 *tests/testthat/UnitTestingData/readObservedPhiValuesError.csv
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a8b3f440a45055fe508ceafe29476a13 *tests/testthat/UnitTestingData/readSimulatedGenome.csv
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5c8e3cfa00cf48442731cfa31e1d4dde *tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR_phi_withPhiSet.csv
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a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/writeFasta.fasta
c2df03454d13c60497749f59e7aec069 *tests/testthat/UnitTestingData/writeRFPData.csv
fa50a4f15b7088f9e9a23fa5aade6b58 *tests/testthat/UnitTestingData/writeSimulatedGenome.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPAlphaValues.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPLambdaPrimeValues.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPPsiValues.csv
ae43ce9c016bae1b0d514fbd6892468c *tests/testthat/testCovarianceMatrix.R
1fd678de6b111facca99d2fbf26bf876 *tests/testthat/testGene.R
d150b50df2fa9d9df960d2dd550755e4 *tests/testthat/testGenome.R
a881098e5b6abe7e662a21fcedb04f6b *tests/testthat/testMCMCAlgorithm.R
420fa51ffab8fd534c4c6ae48faa2810 *tests/testthat/testMCMCROC.R
ed9b60f4ca8ecbc7566e362931641650 *tests/testthat/testPAModel.R
f6036bc8edaf269b0ba9118ef5e6817a *tests/testthat/testParameter.R
17e7d9eec58a8845136c183cb6547806 *tests/testthat/testSequenceSummary.R
69853ca5442764d0034eb82ea6b199e9 *tests/testthat/testutility.R
4bfb7de36426af0462f6c0385a2f54f7 *vignettes/anacoda.Rmd
e588ccf36ac14adaae1420f75c32aa73 *vignettes/anacoda.bib
e5c766dfd7c4ede809520f4fe0de2e04 *vignettes/expression_trace.png
fb8350e653082f5030793e5048724654 *vignettes/logpost_trace.png
7229bd99f42b53e3df233b8f07dc5078 *vignettes/model_fit.png
668576d9af92c119f43b23fa03120fb7 *vignettes/param_comp.png
2b01fbf39fc30667ab6caa6cfcd17beb *vignettes/sel_cai_comp.png
e4d358e9dc5cee4aa4ae6a5a1717cd71 *vignettes/selection_trace.png
