3f41f1674275cce7d247b6e760d902b7 *DESCRIPTION
6ea2ed96cc9bc544aea6f15286eb3645 *NAMESPACE
3a46420e6488eafce7eef923cb090ebf *R/RcppExports.R
267386f960fca80df6835e5f40870175 *R/calcNodeToNode.R
8d5ab38b998bebe26b3e8c9854c50322 *R/calcNodeToTip.R
b56a6d69c0b62a069189e8ae74ef9ad4 *R/calcNodeToTipNode.R
9cbdce841cefa0546a5c8771491c1b88 *R/checkConvergence.R
9d733da4aca081c6943144d7add6833a *R/checkHPD.R
d31bb4dfe1f144157695999020f6b458 *R/checkHeidelTest.R
266ae8ac2548e1069b8b22760bbe38d3 *R/computeESS.R
07bf8713bc6efae7a6a56156f5269911 *R/continueMCMC.R
364ce47587be4ab9423a08562d70b884 *R/dataset_anoles.R
1b6ca03186aa8d96bc34714b6df3776b *R/dataset_centrarchidae.R
921e8db4a8d1536c0449e926b3d02868 *R/estimateTimeMCMC.R
e52ebe4a6f2b62f8699a66bf8af4d1b4 *R/extractCorrelation.R
e5988f076da65cc63e0f31f66efa6a08 *R/getEllipseMatrix.R
f2d7f94e27ba6496c4f2ab155d82f191 *R/hastingsDensity.R
21ca9f9439190395c847708aa00b48dd *R/likelihoodFunction.R
7b81406a89a162019d025bef1887eda7 *R/logAnalyzer.R
5e2481afdea10e984e13184e4b25c977 *R/logDensityIWish.R
dd51ff662a9699e5cd9a42b4d5cdd4f7 *R/logDensityMvNorm.R
3363829749456e205ef4e99635202d18 *R/logLikNode.R
4666aa5833e896963e57cfee08c3b8a7 *R/logLikPrunningMCMC.R
ddacc8058f93985872f91968af2d8ee3 *R/logLikSingleRegime.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
77f17979a02e9d604389b9949eba0f20 *R/mergePosterior.R
0bcade9124c9e49fe4be896c123243a0 *R/mergeSimmap.R
9f99c930b6f0307e37d98280d9f9130c *R/multRegimeMCMC.R
5f9fa709cea4668d1586561f6f937c22 *R/multiplierProposal.R
7779e74c6951621c8663599106737855 *R/mvLogLik.R
c628f089669b756c24b04728c4111bcb *R/plotPrior.R
0887531d73891f5a6ee68aa40cfb0cba *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
a9b291b7a4283a79830fb049d8658a07 *R/ratematrixMCMC.R
ed7b6aa00eb93fc4a27f747d3989179a *R/readMCMC.R
37d1d7c8db09575e30cf0b7ae4a5ddee *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
601fdf9ad17b43a7fc9c6ce8299192a4 *R/singleRegimeMCMC.R
ba2dfe9ef0c5aaa92574b7460b714819 *R/slideWindow.R
d811df99ad20a6a19a1096d3a5fed570 *R/slideWindowPositive.R
79726154440f4762366bb3b9ef270896 *R/testRatematrix.R
9b8fdc87873a44b8e5d5461b60ee99cf *R/writeToFile.R
f847b7d3b2167e8def2a2fdafd4b2d40 *R/writeToMultFile.R
ed09c8381c2aa55ce1633abc59697ea2 *README.md
095ce134a2b3838a2a443f2775f4b135 *build/vignette.rds
2ac532068c08bd745abd9252277243c3 *cleanup
527e84f7ff1cbaf339f315f8d26e5492 *configure
da213b013707fccd793da1138791da31 *configure.ac
7792e1b26bc4699c1ea7b0afcd7881f9 *data/anoles.RData
2d9d50c0cd65a61a1a442ef65bc66b9e *data/centrarchidae.RData
e52ae4040dea9822b2f747d68fa5823d *inst/doc/Making_prior_on_ratematrix.R
7300df517e18f4814c412fe6a81f22e0 *inst/doc/Making_prior_on_ratematrix.Rmd
7f432a9fb3e05e39e3b35593ccf569b8 *inst/doc/Making_prior_on_ratematrix.html
b75ae5e1da1cff55425c48f1174f09a9 *inst/doc/Set_custom_starting_point.R
a7cd2cd4a11f759739a76677a6b399fe *inst/doc/Set_custom_starting_point.Rmd
1ed0589f996581d0e3dbd052b56302b5 *inst/doc/Set_custom_starting_point.html
9d99308e7642d8589ceebccdf3f8a3c3 *inst/extdata/corr.zero.RData
28d1f6115560642174294f04c128741f *inst/extdata/handle.start.point.tutorial.RData
265e2cf0efc7aba17b5af3c34ba4ea7d *inst/extdata/mcmc.start.point.tutorial.RData
2f8f96ebd0221478a76efb9c1c18f1c6 *inst/extdata/norm.root.RData
b4e78e92eddfceecff12990ad9747f31 *inst/extdata/unif.root.RData
df4bc44dee274ca775925059fda20d93 *man/anoles.Rd
7da16939423ec3beac9b40d192a35777 *man/centrarchidae.Rd
bfdd6c05160b8c679628d6233ff16c00 *man/checkConvergence.Rd
e908e24021c220fdb81f1cf780dd4606 *man/computeESS.Rd
f3800fbba6eeb9dbf10b5a554cc96486 *man/continueMCMC.Rd
2c8f4294a332f75b8857d62b24b21246 *man/estimateTimeMCMC.Rd
c0ae7d9d059eb4b8fa24742c53085a3f *man/extractCorrelation.Rd
da1c80c7fee8286848b80ae49a53656d *man/likelihoodFunction.Rd
1105f710c943b9468571c8ae7e6d4728 *man/logAnalyzer.Rd
7506c906a223a110253c3760ae9d99e0 *man/makePrior.Rd
7c3de1e8d05b33a91297530e9d5a1fbc *man/mergePosterior.Rd
6e2ad475cd2250d5630dd3c1ee5e75bf *man/mergeSimmap.Rd
903aa0208474f304b0d6c09c6b658047 *man/plotPrior.Rd
f74f6b845768fd9ab3ae07984dbb80e6 *man/plotRatematrix.Rd
878e51e9f75780ac1e838fd66269f555 *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
5539c4120971ff0870761efeb9df747c *man/ratematrix.Rd
6b5ceeafe8c4a95a9be91c497b2abf12 *man/ratematrixMCMC.Rd
f6fe50f0819b936ed6d27c683d0d0341 *man/readMCMC.Rd
f63d8b4eae87bfdb8c6ab156da687efd *man/samplePrior.Rd
7a12debc186a918dd0f5a1c253383729 *man/simRatematrix.Rd
79e79ad0057cbc7c37ba3c7d9c574e82 *man/testRatematrix.Rd
561cb3ea034715836d09bc124fe2df7b *src/Makevars.in
661f394ccbe8c6b76109df1fa806b490 *src/Makevars.win
4fd64d9a75eae28ae2d41750bc51d373 *src/MultRegimeMCMC.cpp
b77e6f5bc1208de322f4908ed4b11e04 *src/RcppExports.cpp
7300df517e18f4814c412fe6a81f22e0 *vignettes/Making_prior_on_ratematrix.Rmd
a7cd2cd4a11f759739a76677a6b399fe *vignettes/Set_custom_starting_point.Rmd
