1db6ab1c4272be48c31f833cb9108b6a *DESCRIPTION
1bac3ec84807ef671a644b963f3d2136 *NAMESPACE
24fb96c8d286e5dc3bc0af5a1ed03236 *R/colorSchemes.R
405fa75f4b371381755b5c7600e8e606 *R/genomeObject.R
b3c8d335763ec4ac20676dadb6887215 *R/mcmcObject.R
783a6a2f7783da0246b6bf65a38c3d02 *R/modelObject.R
2f223172b92d63243e658d123d461e54 *R/onloadPackage.R
14ac00fc5212ce7a368f884df53598a2 *R/parameterObject.R
49cf22e0098544a03600739a179a54f6 *R/plotMCMCAlgorithmObject.R
ae16360c90b10785aac1f36c1ec3bf71 *R/plotModelObject.R
a45d2ba7b9c2ecf8826303bd872deec1 *R/plotParameterObject.R
368b7040b0b3291fccb39888ac15a712 *R/plotTraceObject.R
33713512d7594b9938c694ff8bb71b99 *R/traceObject.R
097190bbf69052f9d7cfe72be07262cb *build/vignette.rds
f07ebe59999e02ec0543c282acc2cea9 *cleanup
1c4f4cf166f927c5f4b601308686baf9 *configure
dc4e7b569ad7318f903461dafc820d6d *configure.ac
f066b88bd90cf521b93e6d7668907f69 *inst/doc/anacoda.R
03bca67d104d4ad4fc0ce6ef85e6f02f *inst/doc/anacoda.Rmd
8922fbc46dfea8b6bdc55083800fb617 *inst/doc/anacoda.html
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
3de44690d03b591996834a5f6588ce79 *man/calculateSCUO.Rd
4384645e2baefaa8050977fd52c9ed1d *man/calculate_marginal_log_likelihood.Rd
4b90de9a475df6456034311ff2575e58 *man/codonToAA.Rd
0b92a19dac9b730b484b597901470bc8 *man/codons.Rd
ac66cd55b6e159ae98809fbe841817e7 *man/convergence.test.Rd
deaa0caceb46fd2530042104048975b5 *man/findOptimalCodon.Rd
e0bf8af18c897ae045e423f512f3bf7d *man/geomMean.Rd
628f59a632761492baf52344363b3c2e *man/getCAI.Rd
24172738ac09207e7c41411c249355cc *man/getCAIweights.Rd
3bacb21e19d9b47e58c924781b2f593a *man/getCSPEstimates.Rd
c04f484a5672e64e2aa3207b2be6de26 *man/getCodonCounts.Rd
6498e0eb58d20f60834dfcfe0e223cbb *man/getCodonCountsForAA.Rd
86badf1bc97017f879fc62be57931bca *man/getExpressionEstimates.Rd
c8f4b5dfe2b56b0036812c94d2a60abc *man/getMixtureAssignmentEstimate.Rd
fa8d83bc6272262664c2337e4eae7f10 *man/getNames.Rd
ca6a091a166d295ff85e75b35ba61c98 *man/getNc.Rd
e4ad3854da0d8cd273654184780758ce *man/getNcAA.Rd
c7cc6c90872c5cf1fdca82a2c3303a1a *man/getObservedSynthesisRateSet.Rd
bc9d108f2c3aee2847f2e3dd80f79ec7 *man/getSelectionCoefficients.Rd
f771ea40511ae9072ff52d14a1f3e3a6 *man/getTrace.Rd
9d0b5c506e8beea0c0f812aa2b200405 *man/initializeCovarianceMatrices.Rd
ae4aa2abccd09a9c6eddc6c66696667f *man/initializeGenomeObject.Rd
359aa6641722302874d9a178c1846e9d *man/initializeMCMCObject.Rd
ab5b649a7145b0adbb99e2a121f2aba3 *man/initializeModelObject.Rd
ba80e8995279c81b712733421614114d *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
de27e105f5ffc63f6e27f893f29bfc0c *man/plot.Rcpp_ROCModel.Rd
7442728a23b8ae34284c3c673715f201 *man/plot.Rcpp_ROCParameter.Rd
03d2c6d45f681e297cac036f22871f2a *man/plot.Rcpp_Trace.Rd
b67e5ad2495636456db11ad3491f0d92 *man/plotCodonSpecificParameters.Rd
974264b611b8167e14b9b0d76ffcc852 *man/runMCMC.Rd
d42867ea01ad0a54a8d8c103a7460269 *man/setRestartSettings.Rd
8d8a06e7fa77a91f3d2fa2fc1750fbff *man/summary.Rcpp_Genome.Rd
4eadaad7d440b4cf1610247cbf2bcc6d *man/writeMCMCObject.Rd
31aa8302c04d5c25075bea87dabea7c3 *man/writeParameterObject.Rd
1e8e0aa7c76275afc985d4168953c6ef *src/CodonTable.cpp
ba2eb7cbad9d5b4059c6517b845a47cd *src/CovarianceMatrix.cpp
8279e3fc971b0962160f41935b57d467 *src/FONSEModel.cpp
c1afe2c0eb764f10c0a7d70621eb8de8 *src/FONSEParameter.cpp
18152af5bb6ed3acc1b0ab029fc7f77d *src/Gene.cpp
bc5bb3b5417b0a1e80757cc39f956180 *src/Genome.cpp
f8259c97d8ce5b9f53e8ddc97c9e4393 *src/MCMCAlgorithm.cpp
09bac362737a8499ea9ef7a4c747c38d *src/Makevars.in
729c2d006145d9bfb9d3d9497cae6815 *src/Makevars.win
c8a8e1e79da9b78b57625a7b31a75668 *src/Model.cpp
bc179b0d49967fa6e976509b2ef9b596 *src/PAModel.cpp
dd79ddcc96c511cbfdfb14093e8b9d70 *src/PANSEModel.cpp
dbbaacefdb47b8da78df6834bd5aff1c *src/PANSEParameter.cpp
f46be58addd862b7acb28e866f8449d2 *src/PAParameter.cpp
357400cc3813e1a8265b84168fe1f0b7 *src/Parameter.cpp
d1a8ff780e062b80bb939735d6ea5d69 *src/RCPP_Model.cpp
16937bd81a43ba96f84b52f6ada9b215 *src/RCPP_Parameter.cpp
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f0167c45467027ed7f44f433bc144763 *src/ROCModel.cpp
f895e7ab2269a0bacdfa748d2356e480 *src/ROCParameter.cpp
6738ed3aed50d05faf01c65b51462cde *src/SequenceSummary.cpp
fcb8fa5dd06ef19382094732be09cceb *src/Testing.cpp
4874e4755e1a96ca7cc6ca7192cc352d *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
629d9d1e580337f447a1a9f51842ac9d *src/include/Genome.h
658745f666ba54f8e85e1ac4443e01a1 *src/include/MCMCAlgorithm.h
1d89d9249be661ed131b2c990133707f *src/include/PA/PAModel.h
bae7122f55ee95c3001793b3cdf5176e *src/include/PA/PAParameter.h
0fe72ea1dda8308f64302bcd486c8964 *src/include/PANSE/PANSEModel.h
27f34802e957082d38c87bb77df7454e *src/include/PANSE/PANSEParameter.h
39e3cb02051a13f069ff610fa1dd66cb *src/include/ROC/ROCModel.h
2502b75edc2ae8a3d77abfb6af9f42f9 *src/include/ROC/ROCParameter.h
efacc70159b948fa3fa3bff616f7fb5a *src/include/SequenceSummary.h
c84c46da5391c8b1970d9311d945f3ca *src/include/Testing.h
7144e4b43fc0209daa915278efb66330 *src/include/Utility.h
848775cafca8eb6bcaa116d4de5b0e2d *src/include/base/Model.h
4bedde80ecf50bbd4c9c0f7287cef019 *src/include/base/Parameter.h
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1bcc8cbc533563304aa15cf835e26bbd *src/include/mixtureDefinition.h
326a3d5c35e3192c62c3df20b9df42e2 *src/main.cpp
ef410cf82c1181af37835113f3d24c24 *src/registerDynamicSymbol.c
1e66a5316e88eaa8823dfeacf072ed3b *tests/testthat.R
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a8b3f440a45055fe508ceafe29476a13 *tests/testthat/UnitTestingData/readSimulatedGenome.csv
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a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/writeFasta.fasta
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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
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ed9b60f4ca8ecbc7566e362931641650 *tests/testthat/testPAModel.R
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17e7d9eec58a8845136c183cb6547806 *tests/testthat/testSequenceSummary.R
69853ca5442764d0034eb82ea6b199e9 *tests/testthat/testutility.R
03bca67d104d4ad4fc0ce6ef85e6f02f *vignettes/anacoda.Rmd
e588ccf36ac14adaae1420f75c32aa73 *vignettes/anacoda.bib
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e4d358e9dc5cee4aa4ae6a5a1717cd71 *vignettes/selection_trace.png
