975097fe8ae548489f3c37fd5ef6db2b *DESCRIPTION
919712b1b3b8c7f7d1279e0087530fc8 *NAMESPACE
87f6d64d9ff4bd7e2b5db8029306059a *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
266ae8ac2548e1069b8b22760bbe38d3 *R/computeESS.R
1d2bd9029013fd1b6950410c42da0cff *R/continueMCMC.R
364ce47587be4ab9423a08562d70b884 *R/dataset_anoles.R
1b6ca03186aa8d96bc34714b6df3776b *R/dataset_centrarchidae.R
fc91df3020d9b56cf1abcc3fbbdd59d5 *R/estimateTimeMCMC.R
0bdd6eb2f56f1b0851ec153c19ffe320 *R/extractCorrelation.R
1e48af4ee97abec8160608167420ff8e *R/fastSimmap.R
e5988f076da65cc63e0f31f66efa6a08 *R/getEllipseMatrix.R
f2d7f94e27ba6496c4f2ab155d82f191 *R/hastingsDensity.R
21ca9f9439190395c847708aa00b48dd *R/likelihoodFunction.R
f8e462905509e27e3208c8b5b6846920 *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
b48e4c3c7c7cd4c055a6fcd90183bfb9 *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
70ee72d9ef29d7d14fcde9c6e7242d7a *R/mergePosterior.R
0bcade9124c9e49fe4be896c123243a0 *R/mergeSimmap.R
5e97161315e613a10f2892124ec10af5 *R/multRegimeJointMCMC.R
3ce7967a6a446df4937033d6c92eaea7 *R/multRegimeMCMC.R
836d61ed218d03256eb398e4c87a4315 *R/multiplierProposal.R
7779e74c6951621c8663599106737855 *R/mvLogLik.R
c628f089669b756c24b04728c4111bcb *R/plotPrior.R
e2bd9821fadf1df6ff53f50926269c9f *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
82337cba903de277d0289bc26f479b66 *R/ratematrixJointMCMC.R
6fcd343f1a252b5d8ae1c8ec721608a0 *R/ratematrixMCMC.R
da6df3929ebbbdbbb932bd7367c32f31 *R/readMCMC.R
ce85a0c87139b953601f8f752ac96acc *R/readMultRegimeMCMC.R
66692b6bd80a0180f530d29907297ecc *R/readSingleRegimeMCMC.R
9bbde7e5ba955960aba231694a2199c3 *R/riwish.R
1e22b37dd92995fcf79f554526a613e2 *R/samplePrior.R
1be986adb9830d20201ecfacc14aa696 *R/samplePriorSeparationLimits.R
7807a7290c1caa003ce8eb2eeeaa9198 *R/sampleTreeClade.R
c3f516e804a1b4362ea0bcac8ebb0c1b *R/simRatematrix.R
dcb004d9a5c52f1a58f6a395c1610d4a *R/singleRegimeMCMC.R
ba2dfe9ef0c5aaa92574b7460b714819 *R/slideWindow.R
d811df99ad20a6a19a1096d3a5fed570 *R/slideWindowPositive.R
6ff00f15142c5b5f2693d41eedae4073 *R/testRatematrix.R
9b8fdc87873a44b8e5d5461b60ee99cf *R/writeToFile.R
f847b7d3b2167e8def2a2fdafd4b2d40 *R/writeToMultFile.R
113a4fdecca594ce51243d30f87fe853 *README.md
b4295de11e610374e3f9a797e55f78b8 *build/vignette.rds
f04cc9df33bbfea725e7d992c1bc7f6d *data/anoles.RData
ded304dbb8b80774b2fb630a8ed4d455 *data/centrarchidae.RData
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26ec8b12044de6934a8cc680222ec86c *inst/doc/Intro_on_the_package.Rmd
6aabb79b22e022d3b3cd50097ab4ae75 *inst/doc/Intro_on_the_package.html
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5b1d12f409ca6a7c63cf6866c9ef0a60 *inst/doc/Making_prior_on_ratematrix.html
adc719d9817524c688e1c33effb89f77 *inst/doc/Set_custom_starting_point.R
3b71760f98b111eb55c00c0170e7119c *inst/doc/Set_custom_starting_point.Rmd
9bb7253715a00ef85bd6593e15a1f0cf *inst/doc/Set_custom_starting_point.html
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
373e49606effeb9f8806596761423234 *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
df4bc44dee274ca775925059fda20d93 *man/anoles.Rd
7da16939423ec3beac9b40d192a35777 *man/centrarchidae.Rd
bfdd6c05160b8c679628d6233ff16c00 *man/checkConvergence.Rd
e908e24021c220fdb81f1cf780dd4606 *man/computeESS.Rd
f3800fbba6eeb9dbf10b5a554cc96486 *man/continueMCMC.Rd
2c8f4294a332f75b8857d62b24b21246 *man/estimateTimeMCMC.Rd
5629b91a3bd0b3395379a3e2ed751dc1 *man/extractCorrelation.Rd
786c3ff6023454fde8ce767e2ec06c2c *man/fastSimmap.Rd
da1c80c7fee8286848b80ae49a53656d *man/likelihoodFunction.Rd
947b9b2760335d30d920a346764fe30d *man/logAnalyzer.Rd
0887b8daeefac4bed09d5d5c0516b8a1 *man/makePrior.Rd
7c3de1e8d05b33a91297530e9d5a1fbc *man/mergePosterior.Rd
4dd2f9de135958a32e3d84d29bd0ca70 *man/mergeSimmap.Rd
903aa0208474f304b0d6c09c6b658047 *man/plotPrior.Rd
5c659feb4cdc7fbf287083466a65abff *man/plotRatematrix.Rd
b76270f8b5a3dcea0f96d1ff68607324 *man/plotRootValue.Rd
77dbd46abb71cbadd9eecc8d6adca128 *man/print.ratematrix_multi_chain.Rd
228f60e3e86817d09066803c3c97d416 *man/print.ratematrix_multi_mcmc.Rd
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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
02d92b0d52d87e79eeb2e4f90f11023d *man/ratematrixJointMCMC.Rd
1d91ae75a732d6371f6d47b6304c81f7 *man/ratematrixMCMC.Rd
72599aa12a9219055a6334b8ba880aa6 *man/readMCMC.Rd
f63d8b4eae87bfdb8c6ab156da687efd *man/samplePrior.Rd
7a12debc186a918dd0f5a1c253383729 *man/simRatematrix.Rd
f17b32d5358ad06debbf7bcc3d749b7e *man/testRatematrix.Rd
4991ec221c8da7df8cd1aaebec3215e8 *src/Makevars
9a391cb6509f9b6a8201441ff795467a *src/Makevars.win
43c508867ad1181734843df065b25aee *src/MultRegimeMCMC.cpp
97ed58421ed38f68aa1bb8cef1e27aa7 *src/RcppExports.cpp
26ec8b12044de6934a8cc680222ec86c *vignettes/Intro_on_the_package.Rmd
41b0b4914cb80fa86a6d846e68c913b2 *vignettes/Making_prior_on_ratematrix.Rmd
3b71760f98b111eb55c00c0170e7119c *vignettes/Set_custom_starting_point.Rmd
