494979ba69efb2a9f5d1c8acee5a6ef0 *DESCRIPTION
e7f906a0389e59e91f058f76df14b4fa *NAMESPACE
322b84f09fc7e10b2f88a9f4e980d784 *NEWS.md
aeb66fcff7df5b7e3ecd3e1bf280621f *R/AutoGeneratedModelTypes.R
315eb75a546e39ef7a944c5d80a85de9 *R/BM.R
901c975feb65960d77279e1180aa81da *R/BMdrift.R
4b1931a4e84577e9ccba0cb4ff82c8bc *R/DOU.R
a6ccd43ebefd8b0e67d1e0fd7ed20cf4 *R/DefaultModelTypes.R
bb5dc6c67af15e6ac337335b1f57e6c6 *R/GaussianPCM.R
7af2bcc2123768f87cfee19b2266ea90 *R/JOU.R
5e07bcf5d06566d93f5ee039e6dc3c1e *R/LatexTools.R
d10b4a559017d751d3009a0888ac9b77 *R/MixedGaussian.R
e81684643769040c2b6234286737cfc6 *R/OU.R
7a8c5c0efefe56ff54c5fe67ce352082 *R/PCM.R
01573fac7b4e22dbf3f2f57f8018b035 *R/PCMBaseTestObjects.R
776ce66fbd0841e3d4c3c94e40023483 *R/PCMParam.R
65a4a9b4c1907ed951f69e1089e483e8 *R/PCMTable.R
e050fd742d41e4b4f0d9449331517a69 *R/PCMTree.R
61adbab82cfe3ae9c86da3cd52543316 *R/Utilities.R
5dacb3fd27055ccb0a63434e260f2244 *R/White.R
929d01b971bfccfa9d02a975f7cda1de *R/matrixparametrizations.R
f4b59cc6a137b66dde4b620b042f6b31 *R/zzz.R
619f5bf1f26a1b9d83f9403a8ddd1324 *README.md
1d99676d5aa6c1a0fdd0e3f88d666d4f *build/vignette.rds
466f3d064aad6748c2b857d4c7b226cf *data/PCMBaseTestObjects.rda
d5fef50df80327ded737bd53a241bd33 *data/dataFig3.rda
1c41d97ee15b5bbc6457bb07327eda71 *inst/CITATION
bdf458981bdc1d56b35d29bb43b40d15 *inst/doc/PCMBase.R
e5dc347762a51b4c5449f6a8e9478838 *inst/doc/PCMBase.Rmd
5e91f1288381a6564a50341c1e228adb *inst/doc/PCMBase.html
8a0081ccd2f591d3c6716d9f595b5c2c *inst/doc/PCMCreateModel.R
f9b8ea50c910fa18e315ace1bfa93356 *inst/doc/PCMCreateModel.Rmd
39c09de1efcfe2ca4bf735fc7d1edec7 *inst/doc/PCMCreateModel.html
550ed11d9332044eccba886124787456 *inst/doc/PCMParam.R
f2a3acc05ea12560cf40c72ee8784fa7 *inst/doc/PCMParam.Rmd
4c59ccce90bea73bac9f2b39636a7948 *inst/doc/PCMParam.html
ce1c408c7c4db48aac79ff7bd3777612 *inst/doc/PCMTracePruning.R
a350d900cdf5f8bad7ad7c1c9280958a *inst/doc/PCMTracePruning.Rmd
2af6592bcaecfc787c4422f9a88d51d1 *inst/doc/PCMTracePruning.html
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fc36a6901817f41f5efcfc23dac3f9b7 *man/Args_MixedGaussian_MGPMScalarOUType.Rd
7ae0f0d6c8271cd8fad97015bbcb6945 *man/Args_MixedGaussian_MGPMSurfaceOUType.Rd
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898075f9aacde88cb64e4a62686e7e95 *man/MGPMScalarOUType.Rd
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7689d864504dad47d07f40752bfb3a24 *man/MatchListMembers.Rd
07f3ee0192c7ba71b77b4b5b12a73b3c *man/MixedGaussian.Rd
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8d03b7bbc61ad52c4cf5d829e385f87e *man/PCM.Rd
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ee4a557a5484d70e4f706f8bf4621c81 *man/PCMBaseIsADevRelease.Rd
c7f76097e2bfd79ca1d78fac3afc3542 *man/PCMBaseTestObjects.Rd
24b04311c2974651d7650d15cde0300e *man/PCMColorPalette.Rd
0ce00a386d6022797bb9414ecda28609 *man/PCMCombineListAttribute.Rd
e3784cf2ca76cf7b927dec0a2cd706c6 *man/PCMCond.GaussianPCM.Rd
66a7525be04536223238bbfcba033fbd *man/PCMCond.Rd
4eea96b227c189af91e37dea011d33fe *man/PCMCondVOU.Rd
5c25ac1b09ff2343ed240875b1296dd1 *man/PCMCreateLikelihood.Rd
ea9726412aa6aa13aeb4c3847b2b70e9 *man/PCMDefaultModelTypes.Rd
e9688ee48df9131239e177cb1acb2b95 *man/PCMDefaultObject.Rd
305ec7a091914642ef98c57ebc1d8b56 *man/PCMDescribe.Rd
4b0587d2716368d43b298367794999e2 *man/PCMDescribeParameters.Rd
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9f0a098603cd098c3715a659209e9cb2 *man/PCMGetVecParamsRegimesAndModels.Rd
629f6d4c8de58ee1d49bf1d53a92e21a *man/PCMInfo.Rd
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8c782275e3ab1d9173a12be6c4cc9bc0 *man/PCMListParameterizations.Rd
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252fee5abe86cb19bf8198c85acb1b7e *man/PCMMapModelTypesToRegimes.Rd
54e5803c1d8b3b224efb0338bbc2d4af *man/PCMMean.Rd
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1a4dd49228fe82e6a8452c863071a5c7 *man/PCMModelTypes.Rd
221d716c07853a7b72d26499c780de5a *man/PCMModels.Rd
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a9d2f6463ca04f8acff1dd3a4d347573 *man/PCMOptions.Rd
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bd7b97dd94c125d0a1915d68e84c3f81 *man/PCMParam.Rd
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2973d5cfe02f43df5b15aacda952d1b6 *man/PCMParamLocateInShortVector.Rd
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869d3b0af8ed8383f7e45c4b27f9d472 *man/PCMParamRandomVecParams.Rd
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4ad12150fcfbb9687cc9bcc2bc6ebaf9 *man/PCMParamType.Rd
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b53a52404c63be160b0063b12260daea *man/PCMPlotGaussianDensityGrid2D.Rd
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9f0923e3850e99ae65476dfdb5b96e31 *man/PCMPlotMath.Rd
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032ae477fd26e0ecf0255cecf3d890cf *man/PCMSim.Rd
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83299d29eb3b87d0d9037b49dc17a45c *man/PCMTable.Rd
6c59b513e17fd680795a537740faef0f *man/PCMTableParameterizations.Rd
37b7d6589cbfccb50ba77105609fe417 *man/PCMTrajectory.Rd
0ddea496891ee31385e2bf79242b6e39 *man/PCMTree.Rd
58b68e899dbdb3daefb25e200660d099 *man/PCMTreeBackbonePartition.Rd
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74449a3dcce3b78ef027f8e9c52751ce *man/PCMTreeExtractClade.Rd
308fd3ac374ce75dcd949e7cdcd6c463 *man/PCMTreeGetBranchLength.Rd
9100a30adf25501adb0c88437b25db40 *man/PCMTreeGetDaughters.Rd
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140395271bb0b0443353e49982944dc9 *man/PCMTreeGetPartRegimes.Rd
8a7dffa480c52d70aac3481870f5373e *man/PCMTreeGetPartition.Rd
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b3e6de6665772a5a474ac561d55d0eed *man/PCMTreeGetRegimesForNodes.Rd
1ede318e42cbb7b1c3ac7311e13ccfba *man/PCMTreeGetTipsInPart.Rd
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4657fbef1549a6f194bf09ef1436313b *man/PCMTreeInsertSingletons.Rd
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1f87db2d3d8c92d73138815ad4fbfd67 *man/PCMTreeListAllPartitions.Rd
ae2a195ae254da9868bf75c07f0b1ab9 *man/PCMTreeListCladePartitions.Rd
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3b803a740064eb1254806191a5231e07 *man/PCMTreeListRootPaths.Rd
1ac2a38a7f2c53fe58cbb7daefd8c499 *man/PCMTreeLocateEpochOnBranches.Rd
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793b7df507a9a45b3ce1ca5d39d8c855 *man/PCMTreeMatchLabels.Rd
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21ffc0d9036d9a25dc2869aa2b0e8d29 *man/PCMTreeNearestNodesToEpoch.Rd
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993641f178d18de1c8716845a823ea81 *man/PCMTreePostorder.Rd
24edb93b6cdb382d7ff6192eecf36275 *man/PCMTreePreorder.Rd
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50e66b6e5424eea2ed8e340a6c290024 *man/PCMTreeSetPartRegimes.Rd
2a9df192957103e46ccaf126dcaefa79 *man/PCMTreeSetPartition.Rd
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4f3077fbfa5b4a68cd7860265bdaeab8 *man/PCMTreeTableAncestors.Rd
da69f6871932d2a92b9e229facb456dc *man/PCMTreeToString.Rd
182cefb0cb9a88ec55e471dc473df127 *man/PCMTreeVCV.Rd
2cd869b5c4aae08b815b2fbf36f6ecb6 *man/PCMUnfixParameter.Rd
390bfc5b057d9f5236da8dfb9886283d *man/PCMVar.Rd
707a3a070ef2466604f3c372b23e6261 *man/PCMVarAtTime.Rd
1dbd50dd8c95e8d2c550a5daf701fa79 *man/TruePositiveRate.Rd
8f6e54c242d7a57049cea024053bbce4 *man/UpperTriFactor.Rd
83f9bb2af278d631754a21962a2492f0 *man/White.Rd
4a9d2857889f2eb72862b11a3a58ec26 *man/as.MixedGaussian.Rd
bef0f43f7968fd5a9074b92c6225852e *man/dataFig3.Rd
6947aa06f9f549141159cc37f3227872 *man/is.GaussianPCM.Rd
2a5ed97b1ec62a1000c89d056586670c *man/is.MixedGaussian.Rd
f1273be1676fb6dda206162c88143936 *man/is.PCM.Rd
c8e3e28858249da609c38ce95d54509a *man/is.PCMTree.Rd
17e57b20a891d69b2462415a68e9602e *tests/README.txt
57601ce23a6e081155f13be6b100c03b *tests/testthat.R
b2d314646243466e92fd0c391c532d39 *tests/testthat/test-MixedGaussian.R
aeccd25550d38beddbf6fa48960ac2d3 *tests/testthat/test-PCM.R
95f6d7a6395b1f5df477e893e9c8a327 *tests/testthat/test-PCMLik-BM.R
79bb4b1f49dd51045ed93f4fc9b47fa1 *tests/testthat/test-PCMLik-BMdrift.R
e12759249ebbc08547744866d6c4994d *tests/testthat/test-PCMLik-DOU.R
363d381b3763cf61b3df275d99469dcf *tests/testthat/test-PCMLik-OU.R
d93f3b6c825b6d1af4560bfe67e11d6c *tests/testthat/test-PCMParam.R
0285cbfab0b7d44deb77d9566f38d198 *tests/testthat/test-PCMSim.R
4e2fc8d0174bb2f2431f73925e9d22c7 *tests/testthat/test-PCMTree.R
99e753f25e214f47cb9e7d01fa7d2cef *tests/testthat/test-Transformations.R
32e9c1a6bd68ff370306c4bbb9d6224a *vignettes/Fig1.pdf
3625539c3f025ebfe5fefcaa58eb9abf *vignettes/PCMBMkappa.zip
e5dc347762a51b4c5449f6a8e9478838 *vignettes/PCMBase.Rmd
f9b8ea50c910fa18e315ace1bfa93356 *vignettes/PCMCreateModel.Rmd
f2a3acc05ea12560cf40c72ee8784fa7 *vignettes/PCMParam.Rmd
a350d900cdf5f8bad7ad7c1c9280958a *vignettes/PCMTracePruning.Rmd
57c1a89f5d5439f5c5418a55fa91859b *vignettes/REFERENCES-R.bib
8d8793fb59047e11ac28df3d3fcb3312 *vignettes/REFERENCES.bib
