994d240733d175457392ba88b5cd891a *DESCRIPTION
1b507844c343f297f89fbbeb97ba6761 *NAMESPACE
16d3fda3ea70a12b4a10e6da216c65d9 *NEWS.md
24fb96c8d286e5dc3bc0af5a1ed03236 *R/colorSchemes.R
827a59fad346ce8d326e11e172fdb253 *R/genomeObject.R
145902758c5510e9d075e491cce81ddc *R/mcmcObject.R
6edc1a290227d4967b46e2906e641490 *R/modelObject.R
2f223172b92d63243e658d123d461e54 *R/onloadPackage.R
314eab340fde615df51a1c4fc19c3a4c *R/parameterObject.R
49cf22e0098544a03600739a179a54f6 *R/plotMCMCAlgorithmObject.R
ae16360c90b10785aac1f36c1ec3bf71 *R/plotModelObject.R
45fce74bdbaf0ce1d9f8542446f20de3 *R/plotParameterObject.R
df3f6ac67d14065c47af5c6920e424bf *R/plotTraceObject.R
a481c127e9ff891c4e241f48f79583a0 *R/traceObject.R
71e049a5c8fc732e8afa846b17b71576 *README.md
f07ebe59999e02ec0543c282acc2cea9 *cleanup
6986c76bf9d818035bb8ebe8d0a7a75a *configure
c4cb54f8899a57b3d6ec3d2f3c8d2ebd *configure.ac
c893db0a709a6e24401889edf67a2695 *inst/doc/anacoda.Rmd
e588ccf36ac14adaae1420f75c32aa73 *inst/doc/anacoda.bib
6528e79e1bb33d94cc58898118a8dbb2 *inst/doc/anacoda.html
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e4d358e9dc5cee4aa4ae6a5a1717cd71 *inst/doc/selection_trace.png
90a667d38a10111688bc08c3283eb929 *inst/extdata/expression.csv
900de55244acd1f2b532f5cbb395053d *inst/extdata/genome.fasta
7bdce107c67bc387294fb8b7bbcb5d0f *inst/extdata/more_genes.fasta
e20db7363ea194adb2683ca9ebac03e1 *inst/extdata/restart_file.rst
356b16127291012e3396cdc3a4ebab62 *man/AAToCodon.Rd
06f26b2b7273ed22a0bf4e00cc4322c2 *man/acfCSP.Rd
51c7c36ed963f0013c723d4ac954beac *man/acfMCMC.Rd
3ed95f2a9d5d63ed373217a4e1539c83 *man/addObservedSynthesisRateSet.Rd
f9771694a2aad8dc17167e12af605eaa *man/aminoAcids.Rd
4b90de9a475df6456034311ff2575e58 *man/codonToAA.Rd
0b92a19dac9b730b484b597901470bc8 *man/codons.Rd
f7d4328cd08f00c5b6d6b8086bff88be *man/convergence.test.Rd
8f3b61dc7aefaf06ec7987e63c5e8f53 *man/getCAI.Rd
a07bf31e317c13e4cbec64fcc5a32a49 *man/getCAIweights.Rd
83a1a2cd712d54829a3e64e88c9d255f *man/getCSPEstimates.Rd
8529eaa43c539389a638b1a50b92d560 *man/getCodonCountsForAA.Rd
4139152f4d244fc73d88a22559955df3 *man/getExpressionEstimates.Rd
0b53ee2dbef57aafa0afc9cb1b28f2da *man/getMixtureAssignmentEstimate.Rd
fa8d83bc6272262664c2337e4eae7f10 *man/getNames.Rd
ca6a091a166d295ff85e75b35ba61c98 *man/getNc.Rd
e4ad3854da0d8cd273654184780758ce *man/getNcAA.Rd
c7cc6c90872c5cf1fdca82a2c3303a1a *man/getObservedSynthesisRateSet.Rd
bc9d108f2c3aee2847f2e3dd80f79ec7 *man/getSelectionCoefficients.Rd
920fc96f3809762b34c9d9abbe532865 *man/getTrace.Rd
236eb8230f3da44637a6f5d8dade212d *man/initializeCovarianceMatrices.Rd
5c2b49bd60b5f6bf6e774e6f255474a6 *man/initializeGenomeObject.Rd
359aa6641722302874d9a178c1846e9d *man/initializeMCMCObject.Rd
4b77de85dc7d2e66bb141a730168cc9e *man/initializeModelObject.Rd
83388251a0d299a29b0a1cfd55c2d1af *man/initializeParameterObject.Rd
daa441e7dc8c681464bba3d3746e4897 *man/length.Rcpp_Genome.Rd
7700a5cf6a01123d70ccd03ae16f60c4 *man/loadMCMCObject.Rd
e9f964f238a4e761d89da8494e1da53d *man/loadParameterObject.Rd
bd40d9d236bd7c32341bd361c9d57de4 *man/plot.Rcpp_FONSEModel.Rd
d4bd5b9210a4edc2837bb5262980e130 *man/plot.Rcpp_FONSEParameter.Rd
31456fd2e539217c69d154ec67a008a1 *man/plot.Rcpp_MCMCAlgorithm.Rd
919fb75f72094253b1a6aebb250ccf6b *man/plot.Rcpp_ROCModel.Rd
7442728a23b8ae34284c3c673715f201 *man/plot.Rcpp_ROCParameter.Rd
03d2c6d45f681e297cac036f22871f2a *man/plot.Rcpp_Trace.Rd
b67e5ad2495636456db11ad3491f0d92 *man/plotCodonSpecificParameters.Rd
2268363b1e295d7b82cf87024613a8fa *man/runMCMC.Rd
d42867ea01ad0a54a8d8c103a7460269 *man/setRestartSettings.Rd
8d8a06e7fa77a91f3d2fa2fc1750fbff *man/summary.Rcpp_Genome.Rd
e10e47b76ff47a2100a6107e09437bbb *man/writeMCMCObject.Rd
a67c2374e4e5ea519bdf6de752845a4c *man/writeParameterObject.Rd
1e8e0aa7c76275afc985d4168953c6ef *src/CodonTable.cpp
5a1066fabb2de6c933aae6117c167007 *src/CovarianceMatrix.cpp
84446033dd5d5bcac8fc4c0006f140c3 *src/FONSEModel.cpp
a776c829b59a6f11a8f5bc4595865cb8 *src/FONSEParameter.cpp
982e2a43dee8c00e538b967203161278 *src/Gene.cpp
920ae04fe66dce41cc649c790b62c5c4 *src/Genome.cpp
bf9f209b8bd30960973a533f054d9d74 *src/MCMCAlgorithm.cpp
09bac362737a8499ea9ef7a4c747c38d *src/Makevars.in
729c2d006145d9bfb9d3d9497cae6815 *src/Makevars.win
c8a8e1e79da9b78b57625a7b31a75668 *src/Model.cpp
33a5b2b7ae4c057cb6623e669e085b87 *src/PAModel.cpp
f56c7ee51a4525d3b7912ebc651f0b7c *src/PANSEModel.cpp
cbc09398aaef64a269d1c56246399c76 *src/PANSEParameter.cpp
3cb0eb2ffda19a19ad451b2f4ed551c6 *src/PAParameter.cpp
557cc9e333a5b3db9d707cb7db5e13f5 *src/Parameter.cpp
d1a8ff780e062b80bb939735d6ea5d69 *src/RCPP_Model.cpp
16937bd81a43ba96f84b52f6ada9b215 *src/RCPP_Parameter.cpp
a44f4305ae7d2db070c42a1ab9b0538d *src/RCPP_Trace.cpp
09374ec7cac5dcdc9bbff125aae43e55 *src/ROCModel.cpp
e9341c59d86b0608254a4fa506194c2a *src/ROCParameter.cpp
346175fd5c017328302d48d09b6db657 *src/SequenceSummary.cpp
42a5d2edccf6372612d955e86021ccb7 *src/Testing.cpp
8472c8243ae9ae426415f7393f02bc82 *src/Trace.cpp
9c596d39e0a9d9d133e4e81ad64360eb *src/include/CodonTable.h
41c3996115eceaf2837b617a0d1a7015 *src/include/CovarianceMatrix.h
4a2ac02ca1dac08e1e3956c7d686b2c1 *src/include/FONSE/FONSEModel.h
464f3b0a2eb5e0280fd3d49ec7cf7c0c *src/include/FONSE/FONSEParameter.h
499ce5425551df811f148ac41812d5a9 *src/include/Gene.h
c3ae1d141e7756a98c1d0d2f07b28356 *src/include/Genome.h
658745f666ba54f8e85e1ac4443e01a1 *src/include/MCMCAlgorithm.h
3c3123ed161419f887fe72284c9a4d66 *src/include/PA/PAModel.h
7110d5a2499972b7d173522129e2fc56 *src/include/PA/PAParameter.h
0fe72ea1dda8308f64302bcd486c8964 *src/include/PANSE/PANSEModel.h
27f34802e957082d38c87bb77df7454e *src/include/PANSE/PANSEParameter.h
39e3cb02051a13f069ff610fa1dd66cb *src/include/ROC/ROCModel.h
24df4d78272bb02d02f6ec7be92b5907 *src/include/ROC/ROCParameter.h
a2e138582d6629fe6c87130f57d82157 *src/include/SequenceSummary.h
c84c46da5391c8b1970d9311d945f3ca *src/include/Testing.h
7144e4b43fc0209daa915278efb66330 *src/include/Utility.h
848775cafca8eb6bcaa116d4de5b0e2d *src/include/base/Model.h
fd860753b7a4c5237cd8a8ce070ae9f5 *src/include/base/Parameter.h
245cbaef2f899fb2fe2a8d2b2a2c34fa *src/include/base/Trace.h
1bcc8cbc533563304aa15cf835e26bbd *src/include/mixtureDefinition.h
081b0a4cb93450636266e5ea9b461f14 *src/main.cpp
aba5805ccce6d803e6eca2b13b214276 *src/registerDynamicSymbol.c
13fb3b681cd259175623b3252bc07818 *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
82e726df5ce0e373c4f98692afcd4388 *tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR.fasta
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a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/writeFasta.fasta
c2df03454d13c60497749f59e7aec069 *tests/testthat/UnitTestingData/writeRFPData.csv
7097d9c7e9738452f997f4c1af7512be *tests/testthat/UnitTestingData/writeSimulatedGenome.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPAlphaValues.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPLambdaPrimeValues.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPPsiValues.csv
15d88e868a7dd0d538e0c936fa389183 *tests/testthat/UnitTestingOut/testMCMCROCLogPhi.txt
4d178b339d02dae8ffeb204fa2b0e116 *tests/testthat/UnitTestingOut/testMCMCROCLogWithoutPhi.txt
ae43ce9c016bae1b0d514fbd6892468c *tests/testthat/testCovarianceMatrix.R
af0bf8cf914be672c16174d51cbf7854 *tests/testthat/testGene.R
3d0504ecb5444fad5286039ecc17d808 *tests/testthat/testGenome.R
a881098e5b6abe7e662a21fcedb04f6b *tests/testthat/testMCMCAlgorithm.R
54a96871ea29bd94a918c5c7684db146 *tests/testthat/testMCMCROC.R
5dbf9a9d59add7b5c1063044d116b2e6 *tests/testthat/testPAModel.R
f6036bc8edaf269b0ba9118ef5e6817a *tests/testthat/testParameter.R
17e7d9eec58a8845136c183cb6547806 *tests/testthat/testSequenceSummary.R
69853ca5442764d0034eb82ea6b199e9 *tests/testthat/testutility.R
