6085dc4b1275a9e6e87b52051cbeaa53 *DESCRIPTION
ab19fd7502b33bb39e08429d4998e710 *NAMESPACE
943d8a8d8d0a11d7cf41885b1d01d570 *NEWS.md
24fb96c8d286e5dc3bc0af5a1ed03236 *R/colorSchemes.R
f66707fc37409c84a93a8d2c52baf37a *R/genomeObject.R
145902758c5510e9d075e491cce81ddc *R/mcmcObject.R
6edc1a290227d4967b46e2906e641490 *R/modelObject.R
2f223172b92d63243e658d123d461e54 *R/onloadPackage.R
8e1750f365b26ff19a84f7e5abd2e769 *R/parameterObject.R
49cf22e0098544a03600739a179a54f6 *R/plotMCMCAlgorithmObject.R
ae16360c90b10785aac1f36c1ec3bf71 *R/plotModelObject.R
a3ffedfb91c969849dbdb41219a6b01d *R/plotParameterObject.R
37cdedc0faea4543fd28fb47bd6bb322 *R/plotTraceObject.R
a481c127e9ff891c4e241f48f79583a0 *R/traceObject.R
eefb18e0732051c5b4cb609ae8f926e1 *README.md
eec6e1c864f69f0e2873d8692798d550 *build/vignette.rds
f07ebe59999e02ec0543c282acc2cea9 *cleanup
6986c76bf9d818035bb8ebe8d0a7a75a *configure
c4cb54f8899a57b3d6ec3d2f3c8d2ebd *configure.ac
f066b88bd90cf521b93e6d7668907f69 *inst/doc/anacoda.R
c893db0a709a6e24401889edf67a2695 *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
d7434bdca1337e1f43841765bdae9731 *man/calculateSCUO.Rd
4b90de9a475df6456034311ff2575e58 *man/codonToAA.Rd
0b92a19dac9b730b484b597901470bc8 *man/codons.Rd
f7d4328cd08f00c5b6d6b8086bff88be *man/convergence.test.Rd
deaa0caceb46fd2530042104048975b5 *man/findOptimalCodon.Rd
e0bf8af18c897ae045e423f512f3bf7d *man/geomMean.Rd
628f59a632761492baf52344363b3c2e *man/getCAI.Rd
24172738ac09207e7c41411c249355cc *man/getCAIweights.Rd
1ef98a9871079a67dff61b230e2f391e *man/getCSPEstimates.Rd
c04f484a5672e64e2aa3207b2be6de26 *man/getCodonCounts.Rd
6498e0eb58d20f60834dfcfe0e223cbb *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
918baff412f79d74cc8777de566ac4e8 *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
70666b53b46884eacfa5ad7b432a04a2 *man/plotCodonSpecificHyperParameters.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
58d1e1ac8678c9c503d8e90c186d511b *src/Default/makefile
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8c50276b78cb19eb180987ac547b8b67 *src/Default/sources.mk
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84446033dd5d5bcac8fc4c0006f140c3 *src/FONSEModel.cpp
c1afe2c0eb764f10c0a7d70621eb8de8 *src/FONSEParameter.cpp
18152af5bb6ed3acc1b0ab029fc7f77d *src/Gene.cpp
1ea82fe5e1ddcd45b19152f39d7059c8 *src/Genome.cpp
817527095c6a653f2a5cf7a71fb9c327 *src/MCMCAlgorithm.cpp
09bac362737a8499ea9ef7a4c747c38d *src/Makevars.in
729c2d006145d9bfb9d3d9497cae6815 *src/Makevars.win
c8a8e1e79da9b78b57625a7b31a75668 *src/Model.cpp
acf7e7a7114b764d1c7409e78406d0c8 *src/PAModel.cpp
4a124ee440525e381f6216401a53547e *src/PANSEModel.cpp
cbc09398aaef64a269d1c56246399c76 *src/PANSEParameter.cpp
cd5aa8cb19132d06ff3d4323a6d81296 *src/PAParameter.cpp
c339f091f924d5ce48b131f8bf991743 *src/Parameter.cpp
d1a8ff780e062b80bb939735d6ea5d69 *src/RCPP_Model.cpp
16937bd81a43ba96f84b52f6ada9b215 *src/RCPP_Parameter.cpp
a44f4305ae7d2db070c42a1ab9b0538d *src/RCPP_Trace.cpp
f0167c45467027ed7f44f433bc144763 *src/ROCModel.cpp
f895e7ab2269a0bacdfa748d2356e480 *src/ROCParameter.cpp
862f6646a1115202284c284b75ba5230 *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
e4fd38b72cc6a79f86f0f7d20f766f53 *src/include/base/Trace.h
1bcc8cbc533563304aa15cf835e26bbd *src/include/mixtureDefinition.h
326a3d5c35e3192c62c3df20b9df42e2 *src/main.cpp
aba5805ccce6d803e6eca2b13b214276 *src/registerDynamicSymbol.c
13fb3b681cd259175623b3252bc07818 *tests/testthat.R
a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/readFasta.fasta
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a8b3f440a45055fe508ceafe29476a13 *tests/testthat/UnitTestingData/readSimulatedGenome.csv
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a2e71f490d59da1fbe935e5183cb1a1c *tests/testthat/UnitTestingData/writeFasta.fasta
c2df03454d13c60497749f59e7aec069 *tests/testthat/UnitTestingData/writeRFPData.csv
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d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPAlphaValues.csv
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/UnitTestingOut/RFPLambdaPrimeValues.csv
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7c007529abf00b6d03d5e2587a5443f1 *tests/testthat/UnitTestingOut/testMCMCROCLogPhi.txt
4d178b339d02dae8ffeb204fa2b0e116 *tests/testthat/UnitTestingOut/testMCMCROCLogWithoutPhi.txt
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
c893db0a709a6e24401889edf67a2695 *vignettes/anacoda.Rmd
e588ccf36ac14adaae1420f75c32aa73 *vignettes/anacoda.bib
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7229bd99f42b53e3df233b8f07dc5078 *vignettes/model_fit.png
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2b01fbf39fc30667ab6caa6cfcd17beb *vignettes/sel_cai_comp.png
e4d358e9dc5cee4aa4ae6a5a1717cd71 *vignettes/selection_trace.png
