09016f663074a7273523e56601a945d3 *DESCRIPTION
17961634b8b19ecabdb438327ed896e5 *NAMESPACE
33e89c638cc488f0d1a0c68af5f42143 *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
e4bee2381872c7fbf1abfeaafb71d4f6 *R/fastSimmap.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
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
77f17979a02e9d604389b9949eba0f20 *R/mergePosterior.R
0bcade9124c9e49fe4be896c123243a0 *R/mergeSimmap.R
6ee52a385de549825c6c0cfdea3ac48d *R/multRegimeJointMCMC.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
18b4c24025c9ca2c1395c947bf248723 *R/ratematrixJointMCMC.R
8f4053b8aa3dea5f8795c8d976195d18 *R/ratematrixMCMC.R
ed7b6aa00eb93fc4a27f747d3989179a *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
601fdf9ad17b43a7fc9c6ce8299192a4 *R/singleRegimeMCMC.R
ba2dfe9ef0c5aaa92574b7460b714819 *R/slideWindow.R
d811df99ad20a6a19a1096d3a5fed570 *R/slideWindowPositive.R
704dc9298f3e88a808bb44a692c7c4f5 *R/testRatematrix.R
9b8fdc87873a44b8e5d5461b60ee99cf *R/writeToFile.R
f847b7d3b2167e8def2a2fdafd4b2d40 *R/writeToMultFile.R
accc2f090dac20ae12adfb9b814bc294 *README.md
7a162dab07d3b86f652436dbc7386cd4 *build/vignette.rds
7792e1b26bc4699c1ea7b0afcd7881f9 *data/anoles.RData
7820fec1786632d2e77560c20e6b5e1c *data/centrarchidae.RData
f29d78b4db337e6ee708c4a4d765fae0 *inst/doc/Intro_on_the_package.R
d0cc8aed87b3295bacc955fb05978b64 *inst/doc/Intro_on_the_package.Rmd
1bd15e9b506a16cb5cfb630700e2b401 *inst/doc/Intro_on_the_package.pdf
0e8f34c48ee80dc014658a1a65102eae *inst/doc/Making_prior_on_ratematrix.R
bea35c2f21efe91f8e6546f70f6f64dc *inst/doc/Making_prior_on_ratematrix.Rmd
09218b2bc35b08ff8bdbc40b5726bb6f *inst/doc/Making_prior_on_ratematrix.pdf
4c1fcb4299be04a571807e506e0f3743 *inst/doc/Set_custom_starting_point.R
b3cf07a6b28e036fadb8f4b5939fa0fd *inst/doc/Set_custom_starting_point.Rmd
758496990a4a6a461a115630372664ab *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
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
7265767897f446f24d4da929a971eccf *man/fastSimmap.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
17ebd7a1a61e533a450c38de22910292 *man/ratematrixJointMCMC.Rd
6b5ceeafe8c4a95a9be91c497b2abf12 *man/ratematrixMCMC.Rd
f6fe50f0819b936ed6d27c683d0d0341 *man/readMCMC.Rd
f63d8b4eae87bfdb8c6ab156da687efd *man/samplePrior.Rd
7a12debc186a918dd0f5a1c253383729 *man/simRatematrix.Rd
fda6821d73ff93c7dca2de69ad0cb9a1 *man/testRatematrix.Rd
afe1990f43bde8ab9e65249cb2519208 *src/Makevars
61059660eb073d93e00e8ee054237071 *src/Makevars.win
a150ca83f04102d42fceb1047a6825be *src/MultRegimeMCMC.cpp
29b3f7faeb35cae07d62153949610535 *src/RcppExports.cpp
d0cc8aed87b3295bacc955fb05978b64 *vignettes/Intro_on_the_package.Rmd
bea35c2f21efe91f8e6546f70f6f64dc *vignettes/Making_prior_on_ratematrix.Rmd
b3cf07a6b28e036fadb8f4b5939fa0fd *vignettes/Set_custom_starting_point.Rmd
