274856053495d149792fed5c0e44aba9 *DESCRIPTION
d0eb85e3a67c4e485da79b80816f2c50 *NAMESPACE
0c683e5b70db6eab31e84793c354a19f *NEWS.md
c08f772f25035c2e40a930707637a455 *R/BM.R
a32ce544e53f37aebe23a6ba501278ec *R/DOU.R
03cbbc9982a043bb82591173ced03a93 *R/GaussianPCM.R
335cb2e3beb2bc5a01e0ff289d85c455 *R/JOU.R
a97d34fab61cb51d7ed26fcfbfe5cdd8 *R/MixedGaussian.R
cc105294d6276deb7c5f2495441f88c7 *R/OU.R
b8826b5bab71e6261666375dda30207f *R/PCM.R
7123ba9104e75d3b7d9cd5768c502801 *R/PCMParam.R
1c5817651c360ee081e40513bca33947 *R/PCMTree.R
1bfd2bc0037c2eeb40e98d95ddf7562a *R/Utilities.R
594fe7fc0509d98e3835c43a4e594903 *R/White.R
6fea370a4925caca89b50cc2fdd12a1e *R/matrixparametrizations.R
2862410386180b12415729bdf9f34e9c *README.md
31ddd877f7d216c37d73396a002f8998 *build/vignette.rds
a78794bc0ded37f0029cd7d9e62352a6 *inst/CITATION
1fa943eec86d042084c8d064379a6d56 *inst/doc/PCMBase.R
9c8b0c08a3c307c3905898b4d8fc6337 *inst/doc/PCMBase.Rmd
eeac7672d428e0495a82de671598a3da *inst/doc/PCMBase.html
82a2e93ad4efbb4df26fb9881e72edbb *inst/doc/PCMParam.R
1d1824db0f88efeedcdf19ee18ea4c36 *inst/doc/PCMParam.Rmd
8360cef0e30699aa240a017814cb578c *inst/doc/PCMParam.html
83e150fb9e8c6fded54e5846d198973a *man/MixedGaussian.Rd
04d225c67019cb85f7d69912014b0f0b *man/PCM.Rd
9f49fbebed634051b55eb63276e0a9bb *man/PCMAbCdEf.Rd
b0bd49ac9a139fa11387556a07b9c5b4 *man/PCMApplyTransformation.Rd
e85e13943006ecdcce78d71f2dc17b12 *man/PCMBaseIsADevRelease.Rd
39b08ef48406308c6bba54f56175218a *man/PCMColorPalette.Rd
e14b6b491a8d597fd7961a0673f3613c *man/PCMCond.GaussianPCM.Rd
6157ee839917a39d8a2fc07bcbcfc3f6 *man/PCMCond.Rd
f3987f61f3f8007d4f2cd6a2429a1dc8 *man/PCMCondVOU.Rd
bb09817de40dbe0a8b0e3d5504cf660f *man/PCMCreateLikelihood.Rd
890f88b6a41197f74be32a3d2fb98137 *man/PCMDefaultObject.Rd
a089c175e744a7eabe995dd4c8d5fbe3 *man/PCMDescribe.Rd
a13f3f7a1413ad494fd06d747c41270e *man/PCMDescribeParameters.Rd
bcc1e2c5c2e00e365508eee9eaacd9a0 *man/PCMFixParameter.Rd
ff1057fc0e76e0ad40589cc5073fd173 *man/PCMGenerateParameterizations.Rd
867399e0642eab0cb5e367356afcd2a6 *man/PCMGetVecParamsRegimesAndModels.Rd
600f6cbcaad799a03ad654aa684a5753 *man/PCMInfo.Rd
bfb4dc6455f14730286a39d07ffb1aaf *man/PCMLik.Rd
1610367b5b31ee3338f04ed6cc0e6bb1 *man/PCMListParameterizations.Rd
9f85e8fec9e2f9d91dddda367fa6d279 *man/PCMLmr.Rd
bcaa728795e891b1ed4b57c3ef1ce40b *man/PCMMapModelTypesToRegimes.Rd
2f15992d1fd4e186a89da9bd694dc233 *man/PCMMean.Rd
fbc77f5e756e3c9270b0af1d3bdd9cb2 *man/PCMMeanAtTime.Rd
b9c9218251549237888a3b3f369026bc *man/PCMModels.Rd
2805cdcafdffc13bc338e7d24fd4cc0c *man/PCMNumRegimes.Rd
4b2b14987b686b0da6e6bc9397307696 *man/PCMNumTraits.Rd
7e7a1ace58a597efd87537496d5d67e0 *man/PCMOptions.Rd
6766293bb5b6e5c11f7d4566a1c6ab0c *man/PCMPExpxMeanExp.Rd
6853e9a4a297f00a49a028f1a6dca1a6 *man/PCMPLambdaP_1.Rd
117b514bd0ae9a913105d933ab48b824 *man/PCMPairSums.Rd
bb18822ac477c0d75304292561189448 *man/PCMParam.Rd
3e8764967b9c5c40a881402965241916 *man/PCMParamCount.Rd
72e2f13f5c965fb42af01858784e01cc *man/PCMParamGetShortVector.Rd
4564fa741dc725989cd1ec291bc129bf *man/PCMParamLoadOrStore.Rd
8623f0ac08368ee37eb716d9f4a75b89 *man/PCMParamLowerLimit.Rd
2f2fe78db51d8c7937fb63a2951ad1b4 *man/PCMParamRandomVecParams.Rd
d03dfde3ac78d5d74dd62de5a51f89ee *man/PCMParamSetByName.Rd
dd57f022cb5cfa6ad21a61a2d5885ae7 *man/PCMParamType.Rd
33880c1550ebc228be86d3e7e8b33df1 *man/PCMParamUpperLimit.Rd
ce7e8c7fd1c23f360f49cef2cd4188ce *man/PCMParentClasses.Rd
b930af2e9e4c5dd13298cea6a0a52cb4 *man/PCMParseErrorMessage.Rd
9b235647944ed37230faf8fb3907acd7 *man/PCMPlotGaussianDensityGrid2D.Rd
9c1c5fd7ac14127927f4b392bb3999f3 *man/PCMPlotGaussianSample2D.Rd
eb765b4a92cfe071476bc5c55d65728e *man/PCMPlotMath.Rd
d06bb82c74435a4ca75fcd6b4e4962da *man/PCMPlotTraitData2D.Rd
0b3a871b3f718f226f9550ed86c33095 *man/PCMPresentCoordinates.Rd
2bafe9370b118ebe94385bf374536d2c *man/PCMRegimes.Rd
0dfa55bf827a241e3a1035ca784a1e53 *man/PCMSim.Rd
20f8dc305adbd913d74f1eeffeebcb9e *man/PCMSpecify.Rd
f5582c1a4d5f100660d5c7227d543e5a *man/PCMTableParameterizations.Rd
69607cf2cb04e611f6ad18da008e1950 *man/PCMTreeDropClade.Rd
78a92ea60ff962a33b205a8668050cc2 *man/PCMTreeDtNodeRegimes.Rd
4630200a73c657b0fe9511db9befd5fb *man/PCMTreeEdgeTimes.Rd
5e79b4d8e757a73a3ca77be990b2dd09 *man/PCMTreeEvalNestedEDxOnTree.Rd
118225e6e80313cf2de6e6af8e986c40 *man/PCMTreeExtractBackboneRegimes.Rd
b72c452b22a2337786cc0d703533ea33 *man/PCMTreeExtractClade.Rd
d2ef15d3c3db7edb12cff391437a4d3d *man/PCMTreeGetBranchLength.Rd
d35816b075d6cbef1bab25b3e9bfa7d5 *man/PCMTreeGetDaughters.Rd
d84361a998d13597e8c7d7b1cbdbd237 *man/PCMTreeGetLabels.Rd
bbf6576345903c74cd3d5fbcb84bdb3d *man/PCMTreeGetParent.Rd
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753bba09b25e206c4e597cc08d6db2f4 *man/PCMTreeGetStartingNodesRegimes.Rd
70d945a2567d1c47450fb014fac546e5 *man/PCMTreeGetTipsInRegime.Rd
727f991cf7dce93973b9fddef79212e9 *man/PCMTreeInsertSingletons.Rd
4ecddef21068e0d932363465400f5077 *man/PCMTreeJumps.Rd
c370c4524946e15f6d34073511b1b8ed *man/PCMTreeListCladePartitions.Rd
2923d095c6217551c4b482473c7e52cd *man/PCMTreeListDescendants.Rd
be6a7cf33b739d1c266131900a8f78ef *man/PCMTreeListRootPaths.Rd
3721772ceecd101042c1338cf29621ce *man/PCMTreeLocateEpochOnBranches.Rd
adc0269f5d923cce4e303f060e06e75d *man/PCMTreeLocateMidpointsOnBranches.Rd
7abcf92bc0571050074b6c25bd5597c0 *man/PCMTreeMatchLabels.Rd
e6be3333d6ff690aa97c4613995182ec *man/PCMTreeMatchRegimesWithModel.Rd
3f18db130e9459866835018dc2fe52ee *man/PCMTreeMatrixNodesInSameRegime.Rd
464d32c14677a4e3d82af6fa575177ff *man/PCMTreeMatrixTipsInSameRegime.Rd
e5d57f3dc25c408a3185c25556505c15 *man/PCMTreeNearestNodesToEpoch.Rd
a12e848441ef1561eb246e7726570de7 *man/PCMTreeNodeTimes.Rd
99994bf427147ecd65b38c4d9b4d3220 *man/PCMTreeNumNodes.Rd
75b520171bca101c1e0fb4ab57466e51 *man/PCMTreeNumTips.Rd
b51766489a26cc3117bac39e27c5125e *man/PCMTreeNumUniqueRegimes.Rd
66574d23c43a37528a0697b4dd862740 *man/PCMTreePlot.Rd
031d196e1a855b81c508ef3902841198 *man/PCMTreePostorder.Rd
74d9e3540aa6d3aa1f4d3fc95434c9bf *man/PCMTreePreorder.Rd
324a01ee7ec1357104c1c971fff09ada *man/PCMTreeSetDefaultRegime.Rd
16786740b56ad1b3d5bc13a8c49df78a *man/PCMTreeSetLabels.Rd
821e77195222d5700d27b05b3aa2e369 *man/PCMTreeSetRegimes.Rd
9e4ae1f51d38a73ffb6180b2d1f29141 *man/PCMTreeSplitAtNode.Rd
3400251698a41dada03cee3ac91c3bf4 *man/PCMTreeTableAncestors.Rd
f550ffd5bd5f086d2bfcf48070e3071b *man/PCMTreeToString.Rd
fbe9b6fb502853ab594b39092a2f567d *man/PCMTreeUniqueRegimes.Rd
77e5632f87a64ab291dc43808d7fc76a *man/PCMUnfixParameter.Rd
f6386b7e11a17f0a2764793b2d89cd88 *man/PCMVar.Rd
46c14961a115d00cfcde5ac62dc55dae *man/PCMVarAtTime.Rd
88101e184540f12d44ea44225dbe2b7a *man/White.Rd
c4684187833ca05999ee1bfe7e1d68eb *man/is.MixedGaussian.Rd
08c1de6e3beb0ee5fdadefcc032ace1f *man/is.PCM.Rd
0256896808108a7bdd315477b5e9aa5a *tests/testthat.R
15b40e30dcacfe17ce4634845343b7f6 *tests/testthat/Rplots.pdf
f5a6e7057c4fc9ed0610dc4eda9ab877 *tests/testthat/test-MixedGaussian.R
e4150f908a6f8cbbd6798e713fd64506 *tests/testthat/test-PCM.R
ebfd85a3c057a4b7acbd7bd767cd747e *tests/testthat/test-PCMLik-BM.R
3750b455e43a43cabd8dbcc3cb966055 *tests/testthat/test-PCMLik-DOU.R
c4fc81734172cce0458738185cc93898 *tests/testthat/test-PCMLik-OU.R
8a587ff8f4457269b2c9907653c083f8 *tests/testthat/test-PCMSim.R
b8aff174514718c12380ce32128e24bd *tests/testthat/test-PCMTree.R
b4796ec667eeb4717235174a10ca051c *tests/testthat/test-Transformations.R
312d012647dba940e7bdf821a40f6d11 *tests/testthat/testobjects.RData
9c8b0c08a3c307c3905898b4d8fc6337 *vignettes/PCMBase.Rmd
1d1824db0f88efeedcdf19ee18ea4c36 *vignettes/PCMParam.Rmd
a43abc461db11feed68d0e073881b0dd *vignettes/REFERENCES-R.bib
e9d50ca8a728511d2bd299090a6b4aca *vignettes/REFERENCES.bib
