c71fe1d5489cda797c27275a9649e097 *DESCRIPTION
00a11aaaaed0ccdc33bcdf7dffc0353e *NAMESPACE
522216538391216c2990cd10044f63a6 *R/RcppExports.R
267386f960fca80df6835e5f40870175 *R/calcNodeToNode.R
8d5ab38b998bebe26b3e8c9854c50322 *R/calcNodeToTip.R
b56a6d69c0b62a069189e8ae74ef9ad4 *R/calcNodeToTipNode.R
1a1ce5d88a3c930ad09463480a0c22c8 *R/checkConvergence.R
9d733da4aca081c6943144d7add6833a *R/checkHPD.R
d31bb4dfe1f144157695999020f6b458 *R/checkHeidelTest.R
886b2b90d8c847a2b07a09d6b63ed866 *R/check_phy_list.R
f276f52a271a13958c3ab26733b02a13 *R/computeESS.R
1d2bd9029013fd1b6950410c42da0cff *R/continueMCMC.R
364ce47587be4ab9423a08562d70b884 *R/dataset_anoles.R
1b6ca03186aa8d96bc34714b6df3776b *R/dataset_centrarchidae.R
277fd4b231cda9e528dfe47510fdba34 *R/estimateTimeMCMC.R
8a760b90d5fdb20f83561a4a21a9b2e1 *R/extractCorrelation.R
407f65c8be68dd85cad6866ed2c804f9 *R/fastSimmap.R
e5988f076da65cc63e0f31f66efa6a08 *R/getEllipseMatrix.R
ccf81c0f05056ab939f79aa87a2b899d *R/getStartPointFromPosterior.R
f2d7f94e27ba6496c4f2ab155d82f191 *R/hastingsDensity.R
9fac7da6b284db16fe275db97daf2a5b *R/likelihoodFunction.R
6e89c6deb50b0b469a7e192b38c6bf37 *R/logAnalyzer.R
5e2481afdea10e984e13184e4b25c977 *R/logDensityIWish.R
dd51ff662a9699e5cd9a42b4d5cdd4f7 *R/logDensityMvNorm.R
3363829749456e205ef4e99635202d18 *R/logLikNode.R
4666aa5833e896963e57cfee08c3b8a7 *R/logLikPrunningMCMC.R
ddacc8058f93985872f91968af2d8ee3 *R/logLikSingleRegime.R
0f0026b9b5e7952affeb7578b555401d *R/makeDataTips.R
419d12d5a08a547ad75236b956ab4cc4 *R/makePrior.R
5e506e022fb4ab36328772c43bf283a5 *R/makePriorIWish.R
1fe25736123d1113737c0d10f2b148e5 *R/makePropIWish.R
3f93edb178d3991a51561480af0289c1 *R/makePropMean.R
b6c6e152c23f04e73c9307a6f53842b4 *R/makePropMeanForMult.R
893069fe346d8255e2e577a54a1462bf *R/makePropMeanForMultList.R
a5535464303dfbbf366742315485e524 *R/makePropMeanList.R
7546a773e1fe76f3eb52fa037d551589 *R/makePropMultSigma.R
d89b21f892e75a1ed9b5c34097de7289 *R/makePropMultSigmaList.R
963f76d7d2790130757ad8bbaaa8ba98 *R/makePropSingleSigma.R
698959d12a95541a10d4a68235ea16c2 *R/makePropSingleSigmaList.R
95557f83f38817130727b9ad9ca77cf6 *R/mergePosterior.R
0bcade9124c9e49fe4be896c123243a0 *R/mergeSimmap.R
3fb583a1e6bdd7bbb6628eb67f948406 *R/multRegimeJointMCMC.R
ac08a123771fae8b04886fb5f8d47067 *R/multRegimeMCMC.R
836d61ed218d03256eb398e4c87a4315 *R/multiplierProposal.R
7779e74c6951621c8663599106737855 *R/mvLogLik.R
b504ea72789da9f1cc6ddd07db6db785 *R/plotPrior.R
bdeaf05660339adf0ef7ede811ddbbc6 *R/plotRatematrix.R
493516ee5355afd6d0ddc392d5f13120 *R/plotRootValue.R
a1c1004db824ff3c675ed293f7d47066 *R/print.ratematrix_multi_chain.R
bf29afc3b5305255f50eff45e1730afd *R/print.ratematrix_multi_mcmc.R
63bd8e4c7a1ec72c3155b7c852a21f3c *R/print.ratematrix_prior_function.R
e625dff04d252e542db71ba4bffacb05 *R/print.ratematrix_prior_sample.R
eb027eabc64eb83a83f9946ac636d333 *R/print.ratematrix_single_chain.R
5171e33d823cfb3c03aea8699c8d9616 *R/print.ratematrix_single_mcmc.R
dccb69a18690db648024442d833c42e0 *R/priorDensityVcvBarnard.R
c4a0a924777dc17e3cb475be3dce4b92 *R/ratematrix-package.R
73ca4261d57135b504606e5fc997579c *R/ratematrixJointMCMC.R
be07ca3765e4a115fc3c940d1903eae0 *R/ratematrixMCMC.R
8db66a29e3686739503502d33cb9d48c *R/readMCMC.R
ce85a0c87139b953601f8f752ac96acc *R/readMultRegimeMCMC.R
66692b6bd80a0180f530d29907297ecc *R/readSingleRegimeMCMC.R
9bbde7e5ba955960aba231694a2199c3 *R/riwish.R
4a2f5c4a9a1e276b9c2ed69ecc3b228d *R/samplePrior.R
1be986adb9830d20201ecfacc14aa696 *R/samplePriorSeparationLimits.R
7807a7290c1caa003ce8eb2eeeaa9198 *R/sampleTreeClade.R
c3f516e804a1b4362ea0bcac8ebb0c1b *R/simRatematrix.R
a57d66fc896fc731fd0ab32e9129f196 *R/singleRegimeMCMC.R
ba2dfe9ef0c5aaa92574b7460b714819 *R/slideWindow.R
d811df99ad20a6a19a1096d3a5fed570 *R/slideWindowPositive.R
301a03bfdd7db33deea173a1ab177e6c *R/testRatematrix.R
9b8fdc87873a44b8e5d5461b60ee99cf *R/writeToFile.R
f847b7d3b2167e8def2a2fdafd4b2d40 *R/writeToMultFile.R
292194ddc8437d406023b3c07601fbb2 *build/vignette.rds
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f9b5760549e18c10a043c2987294fbf8 *data/centrarchidae.RData
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26ec8b12044de6934a8cc680222ec86c *inst/doc/Intro_on_the_package.Rmd
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154a71390f5c1b9dd8f1307f645f562f *inst/extdata/corr.zero.RData
28d1f6115560642174294f04c128741f *inst/extdata/handle.start.point.tutorial.RData
63aefc385b95367885e35ee6913bae37 *inst/extdata/intro_vignette.RData
2ce6a0262fe5dd33cf7ea00462730c74 *inst/extdata/mcmc.start.point.tutorial.RData
25c8bb61c549e0ce55be30b0d0873a4f *inst/extdata/norm.root.RData
a5cdf02206aacd0b0250c69d7f357ff1 *inst/extdata/unif.root.RData
b770e68a9e35a080dfa76983233d908d *inst/include/distributions_and_helpers.h
8f5bbd856f84f11e1ab6d5374a5ddf37 *inst/include/likelihood_pruning.h
b453ae758767ef668a2e386aadf45a93 *inst/include/log_functions.h
1726fc521eb34b13c65850352d705e02 *inst/include/priors.h
f4354178f1c44fa84b370c88b8a76d18 *inst/include/proposals.h
32e63c84d6709c462ba98e5435e64398 *inst/include/stochastic_mapping.h
3eca2d58bb98d90a8434ece7e046029b *man/anoles.Rd
284af5ee9be4d04e67c7f7c833c71e34 *man/centrarchidae.Rd
bfdd6c05160b8c679628d6233ff16c00 *man/checkConvergence.Rd
ebd6a648c64e9318f7e7eb0be0139383 *man/computeESS.Rd
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73dfd107eb94d9f26a506083c89fca15 *man/estimateTimeMCMC.Rd
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5c03b54ca5f60c881dfb6f0c607791f3 *man/fastSimmap.Rd
3a0c4d1f16f9de706752539bbbfffa0e *man/getStartPointFromPosterior.Rd
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947b9b2760335d30d920a346764fe30d *man/logAnalyzer.Rd
27bee2f87b5ee6e1eb7175b3e0a662be *man/makePrior.Rd
38f740a1674d1b457613b0571bd8297c *man/mergePosterior.Rd
4dd2f9de135958a32e3d84d29bd0ca70 *man/mergeSimmap.Rd
757d0501fb865d746fe2d1cb2c98c1c7 *man/plotPrior.Rd
34f0cf047b2cc375167d2705a4ab8798 *man/plotRatematrix.Rd
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77dbd46abb71cbadd9eecc8d6adca128 *man/print.ratematrix_multi_chain.Rd
228f60e3e86817d09066803c3c97d416 *man/print.ratematrix_multi_mcmc.Rd
75ba1b8d8022ee78632e4269c618587d *man/print.ratematrix_prior_function.Rd
1e816c5234dc7651012973f48b924139 *man/print.ratematrix_prior_sample.Rd
2f741d1c410ea2947e9211b25082788f *man/print.ratematrix_single_chain.Rd
a2ebc4c5247a009745c58e2567585c40 *man/print.ratematrix_single_mcmc.Rd
edf41d8cbda0892ad229835e8e1e331e *man/ratematrix.Rd
5dd23ab09612dd88437eee833481e6bd *man/ratematrixJointMCMC.Rd
666601eeb1a5dd8401b29ed343d4a88e *man/ratematrixMCMC.Rd
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7a12debc186a918dd0f5a1c253383729 *man/simRatematrix.Rd
61b62dc7153e09f3a589d624f97be74e *man/testRatematrix.Rd
4991ec221c8da7df8cd1aaebec3215e8 *src/Makevars
9a391cb6509f9b6a8201441ff795467a *src/Makevars.win
698034ce131caf7a331b4198cdc80858 *src/MultRegimeMCMC.cpp
cd17be15e43400ac4dd3536cfcf9b0fb *src/RcppExports.cpp
26ec8b12044de6934a8cc680222ec86c *vignettes/Intro_on_the_package.Rmd
41b0b4914cb80fa86a6d846e68c913b2 *vignettes/Making_prior_on_ratematrix.Rmd
3b71760f98b111eb55c00c0170e7119c *vignettes/Set_custom_starting_point.Rmd
