df031f68a7796189addd68edf2b9008e *DESCRIPTION
c59b59559db15ef1aafb24d9887be723 *NAMESPACE
010d238a85ab30f3fc130d130ec8d12d *R/RcppExports.R
267386f960fca80df6835e5f40870175 *R/calcNodeToNode.R
8d5ab38b998bebe26b3e8c9854c50322 *R/calcNodeToTip.R
b56a6d69c0b62a069189e8ae74ef9ad4 *R/calcNodeToTipNode.R
3676cfc5f0306596997fed347567fdbc *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
0d0b250e080b19d26416e69bb3001459 *R/fastSimmap.R
e5988f076da65cc63e0f31f66efa6a08 *R/getEllipseMatrix.R
ccf81c0f05056ab939f79aa87a2b899d *R/getStartPointFromPosterior.R
f2d7f94e27ba6496c4f2ab155d82f191 *R/hastingsDensity.R
ab4dc21f1a6138ea5856c69c53f51a7b *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
28391c6f486ed8d642a923ce0dd51166 *R/ratematrix-package.R
db25c687a6d588ad6baa039c5095fbcc *R/ratematrixJointMCMC.R
ee0b0179663331fd9632d220d958ac64 *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
0de37ca1205c0bd01774a038eb6dd6d3 *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
e9b348e472d831e198437e800e6413fa *build/vignette.rds
b4dd6af74a22405006333e859841ed5b *data/anoles.RData
f9b5760549e18c10a043c2987294fbf8 *data/centrarchidae.RData
63cb1b19ddd615941330313988de77ab *inst/doc/Intro_on_the_package.R
3c31f3da2ccbea2fb9dd7a0239bb9650 *inst/doc/Intro_on_the_package.Rmd
9254d07602c986c8d932164753140cbf *inst/doc/Intro_on_the_package.pdf
3cc2d599a38975f93944cea095a8dd17 *inst/doc/Making_prior_on_ratematrix.R
2138f066d7bfbc628ef80a497e4064a5 *inst/doc/Making_prior_on_ratematrix.Rmd
d2f34b68601a19fd55db45723389e952 *inst/doc/Making_prior_on_ratematrix.pdf
13523d77a3f362551c406052e27f070c *inst/doc/Set_custom_starting_point.R
b0dd6d065bee35716d30907253a67367 *inst/doc/Set_custom_starting_point.Rmd
32909e9a2bd637b6e2f50f9939b071e2 *inst/doc/Set_custom_starting_point.pdf
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
2749a8fe1862aea0d0ad81f1306fbab9 *inst/include/stochastic_mapping.h
3eca2d58bb98d90a8434ece7e046029b *man/anoles.Rd
284af5ee9be4d04e67c7f7c833c71e34 *man/centrarchidae.Rd
4c260dab0fb90cea0b08ecb96ea20580 *man/checkConvergence.Rd
ebd6a648c64e9318f7e7eb0be0139383 *man/computeESS.Rd
f3800fbba6eeb9dbf10b5a554cc96486 *man/continueMCMC.Rd
73dfd107eb94d9f26a506083c89fca15 *man/estimateTimeMCMC.Rd
cde6ea0beda03d166f6214150ed6ce2b *man/extractCorrelation.Rd
bea5c758331cbddc927df4654838d683 *man/fastSimmap.Rd
3a0c4d1f16f9de706752539bbbfffa0e *man/getStartPointFromPosterior.Rd
d5b518402b67a061d1180a13ab86dfec *man/likelihoodFunction.Rd
947b9b2760335d30d920a346764fe30d *man/logAnalyzer.Rd
27bee2f87b5ee6e1eb7175b3e0a662be *man/makePrior.Rd
38f740a1674d1b457613b0571bd8297c *man/mergePosterior.Rd
4dd2f9de135958a32e3d84d29bd0ca70 *man/mergeSimmap.Rd
757d0501fb865d746fe2d1cb2c98c1c7 *man/plotPrior.Rd
34f0cf047b2cc375167d2705a4ab8798 *man/plotRatematrix.Rd
b76270f8b5a3dcea0f96d1ff68607324 *man/plotRootValue.Rd
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
ad099a5d11f53a1abde68e85fd3a952e *man/ratematrix.Rd
c02cdc77bc6a63c990d4ede42afbee20 *man/ratematrixJointMCMC.Rd
666601eeb1a5dd8401b29ed343d4a88e *man/ratematrixMCMC.Rd
91afebaa136ab93cf521574c706c2426 *man/readMCMC.Rd
59b240e54f239e643e4fd3f819223c58 *man/readMCMC_Mk.Rd
716b942b29cff1de9f2987ae1c0101ae *man/samplePrior.Rd
4925512f11bbf7f47b79e082108d1fb5 *man/simRatematrix.Rd
61b62dc7153e09f3a589d624f97be74e *man/testRatematrix.Rd
70b3398e4446f91a0086209a7decf7db *src/Makevars
a01b62de2348aa7878f7b17652a3ca0b *src/Makevars.win
4064ed09a2b35948e9776f17e1229255 *src/MultRegimeMCMC.cpp
f5c205af8eca1c2f7c684ca3c33cfcab *src/RcppExports.cpp
3c31f3da2ccbea2fb9dd7a0239bb9650 *vignettes/Intro_on_the_package.Rmd
2138f066d7bfbc628ef80a497e4064a5 *vignettes/Making_prior_on_ratematrix.Rmd
b0dd6d065bee35716d30907253a67367 *vignettes/Set_custom_starting_point.Rmd
