2a7a3130a1276b3e669044f3861a5027 *DESCRIPTION
0a5cceed103f937b9bfa9d5363afe259 *NAMESPACE
d41d8cd98f00b204e9800998ecf8427e *NEWS.md
24fb96c8d286e5dc3bc0af5a1ed03236 *R/colorSchemes.R
1b8ac7e671696332990cb1862710881f *R/genomeObject.R
145902758c5510e9d075e491cce81ddc *R/mcmcObject.R
6edc1a290227d4967b46e2906e641490 *R/modelObject.R
2f223172b92d63243e658d123d461e54 *R/onloadPackage.R
410c37526a1956eb31821c143af02dc4 *R/parameterObject.R
49cf22e0098544a03600739a179a54f6 *R/plotMCMCAlgorithmObject.R
a9bc38ea4713eba3a6148b0f2d9ed60d *R/plotModelObject.R
d7762c98c612e8bd84703f3ac6a7cfd2 *R/plotParameterObject.R
df3f6ac67d14065c47af5c6920e424bf *R/plotTraceObject.R
a481c127e9ff891c4e241f48f79583a0 *R/traceObject.R
71e049a5c8fc732e8afa846b17b71576 *README.md
f07ebe59999e02ec0543c282acc2cea9 *cleanup
6986c76bf9d818035bb8ebe8d0a7a75a *configure
c4cb54f8899a57b3d6ec3d2f3c8d2ebd *configure.ac
bec2ef51080b86bbe1e593c61f9bec9a *inst/doc/anacoda.Rmd
5e6f4052b0bc4bbe5ef254efe38c258c *inst/doc/anacoda.bib
75d5abea9bc393831b225ee8415c3f9a *inst/doc/anacoda.html
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fb8350e653082f5030793e5048724654 *inst/doc/logpost_trace.png
7229bd99f42b53e3df233b8f07dc5078 *inst/doc/model_fit.png
668576d9af92c119f43b23fa03120fb7 *inst/doc/param_comp.png
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
98fe9f9610bd70b26732f4c3167ba767 *man/acfCSP.Rd
51c7c36ed963f0013c723d4ac954beac *man/acfMCMC.Rd
d561928177dd5bbaf142a080355d9aab *man/addObservedSynthesisRateSet.Rd
f9771694a2aad8dc17167e12af605eaa *man/aminoAcids.Rd
4b90de9a475df6456034311ff2575e58 *man/codonToAA.Rd
0b92a19dac9b730b484b597901470bc8 *man/codons.Rd
f7d4328cd08f00c5b6d6b8086bff88be *man/convergence.test.Rd
a94df456ab374eb066abd4b9501aa529 *man/getCSPEstimates.Rd
731cf325727d8cac908a77a7f7f73712 *man/getCodonCountsForAA.Rd
4139152f4d244fc73d88a22559955df3 *man/getExpressionEstimates.Rd
0b53ee2dbef57aafa0afc9cb1b28f2da *man/getMixtureAssignmentEstimate.Rd
fa8d83bc6272262664c2337e4eae7f10 *man/getNames.Rd
7fcf1b8cb401396b94e044198f4e1d6e *man/getObservedSynthesisRateSet.Rd
920fc96f3809762b34c9d9abbe532865 *man/getTrace.Rd
236eb8230f3da44637a6f5d8dade212d *man/initializeCovarianceMatrices.Rd
5c2b49bd60b5f6bf6e774e6f255474a6 *man/initializeGenomeObject.Rd
359aa6641722302874d9a178c1846e9d *man/initializeMCMCObject.Rd
4b77de85dc7d2e66bb141a730168cc9e *man/initializeModelObject.Rd
0ef30b88d32ebc9a09f8ebf0981620ab *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
f2f51ece9e7d009468b95c024435bf7a *src/Gene.cpp
6968133393fbc58e41b2ed7234171e3a *src/Genome.cpp
bf9f209b8bd30960973a533f054d9d74 *src/MCMCAlgorithm.cpp
09bac362737a8499ea9ef7a4c747c38d *src/Makevars.in
729c2d006145d9bfb9d3d9497cae6815 *src/Makevars.win
c8a8e1e79da9b78b57625a7b31a75668 *src/Model.cpp
796f01312e5406cab84778d46ee3a9a6 *src/PAModel.cpp
f56c7ee51a4525d3b7912ebc651f0b7c *src/PANSEModel.cpp
cbc09398aaef64a269d1c56246399c76 *src/PANSEParameter.cpp
10b8687e5a31c6bd6cdf7ec74db67d0c *src/PAParameter.cpp
e8c2c553bcb914f77d241d68d89c5c39 *src/Parameter.cpp
d1a8ff780e062b80bb939735d6ea5d69 *src/RCPP_Model.cpp
288bf7fd32bb6f909dbf37fb22cc578d *src/RCPP_Parameter.cpp
a44f4305ae7d2db070c42a1ab9b0538d *src/RCPP_Trace.cpp
09374ec7cac5dcdc9bbff125aae43e55 *src/ROCModel.cpp
e9341c59d86b0608254a4fa506194c2a *src/ROCParameter.cpp
346175fd5c017328302d48d09b6db657 *src/SequenceSummary.cpp
5997a5e96876f813d69e45dfab25a168 *src/Testing.cpp
c355c7a9cc88f718e1dc39bf75593d81 *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
b71beea5733d32281bd218c8c1957ba8 *src/include/Gene.h
7e9511571f6b09822e719a35824abef4 *src/include/Genome.h
658745f666ba54f8e85e1ac4443e01a1 *src/include/MCMCAlgorithm.h
3c3123ed161419f887fe72284c9a4d66 *src/include/PA/PAModel.h
24df45a3aa50328d58ddff47a3680176 *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
23eae7affaeba6c3359f668e330154cb *src/include/Testing.h
7144e4b43fc0209daa915278efb66330 *src/include/Utility.h
848775cafca8eb6bcaa116d4de5b0e2d *src/include/base/Model.h
947a161f64e832f00d1a1c9d5b21798e *src/include/base/Parameter.h
959db7429147200d6a099e4f0ee7f2fb *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
1871e7398e9d22e819e18d16341cf6ec *tests/testthat/UnitTestingData/readRFPData.csv
a8b3f440a45055fe508ceafe29476a13 *tests/testthat/UnitTestingData/readSimulatedGenome.csv
82e726df5ce0e373c4f98692afcd4388 *tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR.fasta
2e3201facbee9b14b0b8b4db8e1b32cf *tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR_phi_withPhiSet.csv
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c81ae06f450c689d106907d59906f5fb *tests/testthat/UnitTestingData/testPAModelFiles/testPAModel.csv
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
7aa7e2a2b05d4acbdee974ff29ead751 *tests/testthat/testParameter.R
17e7d9eec58a8845136c183cb6547806 *tests/testthat/testSequenceSummary.R
69853ca5442764d0034eb82ea6b199e9 *tests/testthat/testutility.R
