4d413628eae3212c863a48e833fadd99 *DESCRIPTION
3f70cc4ca9183c2c54af2c3aa6207562 *NAMESPACE
4354bbec52d3a2ec899c0a7ed11fb35a *NEWS.md
a86663fb948c43125aef54cdcb4c710d *R/AutoGeneratedModelTypes.R
ddbd04140d20ee11288dd9ac87685c98 *R/BM.R
765f69d4c95d3a1d710669aeb681d336 *R/BMdrift.R
18687b1d31c29946d6306ef5baf5d6aa *R/DOU.R
7b083f4d6ff96207739f6d9035340e79 *R/DefaultModelTypes.R
989436342c18b2a359cc657070bfd192 *R/GaussianPCM.R
d51d4f5621770066b63fb66480db1b55 *R/JOU.R
b83a5abbd5b09f5d996185c28ea78288 *R/LatexTools.R
15e5bfac7fd092958997c2ffce36e46e *R/MixedGaussian.R
30c90687a370d846cb168e8e3b26b023 *R/OU.R
8f7d5ab312ad8e4044a8e8508ac23016 *R/PCM.R
1682aa646387591dec09de635cb99cd0 *R/PCMBaseTestObjects.R
338c516ae38a2691957d6b331d145896 *R/PCMParam.R
99a127bd5f6499bf1cdfab6ab7f10731 *R/PCMTable.R
b9461c5543db7affc31d3b0e89e3d4ed *R/PCMTree.R
7decf42af19cfa8bcfc9a2d6bcc1167c *R/Utilities.R
05e825667b90a7c77b0bbc3d6a186c2a *R/White.R
a8441b2592f05dda6a302987377d2e77 *R/matrixparametrizations.R
64c3ed72b8efddc618441e43f9d1f837 *R/zzz.R
cdebb48367f5a565735d8b05190df456 *README.md
ac03ab00030c058048ae80a2f9bba066 *build/vignette.rds
466f3d064aad6748c2b857d4c7b226cf *data/PCMBaseTestObjects.rda
d5fef50df80327ded737bd53a241bd33 *data/dataFig3.rda
b28495ef65a03cc281197b4a92b02b41 *inst/CITATION
2f804ce2babc19664f67c2dd1f754c0a *inst/doc/PCMBase.R
df689e311f1a90ae6786d58913051784 *inst/doc/PCMBase.Rmd
1d2cd0b1ed2aa37303fbf2c67845c60a *inst/doc/PCMBase.html
6e4e52d3ef7b2f5d1b461f2832e447e9 *inst/doc/PCMCreateModel.R
dcde5e145b3f786552c84f7820cab582 *inst/doc/PCMCreateModel.Rmd
52d551b3feb4afa6950ee2004df10ae7 *inst/doc/PCMCreateModel.html
93a4b2963a8e2f78c3a3c1333a22efd3 *inst/doc/PCMParam.R
4c6426caba57e48bf0108dca4fbe875d *inst/doc/PCMParam.Rmd
4bb4aef2f20b027379c5dd468d85d863 *inst/doc/PCMParam.html
7d5f3ba0fe5861ca722f7fa57630f1af *inst/doc/PCMTracePruning.R
2b5b21f495136ac7ae102ba866fe1c11 *inst/doc/PCMTracePruning.Rmd
6d4c699e747b4ce7ca13089bc68d59c8 *inst/doc/PCMTracePruning.html
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5ec51ceea26e9839de26868112cdaee4 *man/Args_MixedGaussian_MGPMScalarOUType.Rd
e4bfa283a94bdcbdbe48aef73f3c1e98 *man/Args_MixedGaussian_MGPMSurfaceOUType.Rd
a0b58f8a2f06113a87bccefc8c9d2645 *man/FormatCellAsLatex.Rd
a77ddb3b88495d6fd7be38432fd095a9 *man/FormatTableAsLatex.Rd
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28e408352668c4d421edc316b6ea4e87 *man/MGPMSurfaceOUType.Rd
195852f8b955184f010e6eb8480c3cde *man/MatchListMembers.Rd
b96a2eca32dee549440076156593d8e5 *man/MixedGaussian.Rd
247cfd850be93a55d5e09d914e819362 *man/MixedGaussianTemplate.Rd
0ff68726cb52ea644174223bcf77d810 *man/PCM.Rd
c853275ca3e6404e9cba102491e431a9 *man/PCMAbCdEf.Rd
41b32bf7f03bc2137b18cf2a31c0c33b *man/PCMAddToListAttribute.Rd
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995b32c0b55dae27ccca4c7c7f2ef2dd *man/PCMBaseIsADevRelease.Rd
db22160a3cc4a03b3b0e4afb030ead24 *man/PCMBaseTestObjects.Rd
00c0ec2dfffed44f38ed935441ddfa6a *man/PCMColorPalette.Rd
c80ee8d547e334a79eebef61afed9d95 *man/PCMCombineListAttribute.Rd
9d0d7854cbb14d2b4f4b3918cc6defa0 *man/PCMCond.GaussianPCM.Rd
882154ed9e5284155312088fc5046221 *man/PCMCond.Rd
2234ebf46046dd613fbcc16db903c5e5 *man/PCMCondVOU.Rd
4d568fc311f279b14c96939bb8081472 *man/PCMCreateLikelihood.Rd
402c572d2827d629bc4d45447c092b68 *man/PCMDefaultModelTypes.Rd
37b57f107bebfd6154a5baa0c7f88f5c *man/PCMDefaultObject.Rd
a089c175e744a7eabe995dd4c8d5fbe3 *man/PCMDescribe.Rd
a13f3f7a1413ad494fd06d747c41270e *man/PCMDescribeParameters.Rd
a042e910c40d451dc6349ff84d4274c4 *man/PCMExtractDimensions.Rd
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69f59a9b5c215775a14f56d72be7198f *man/PCMFindMethod.Rd
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b8da2f9a3827a404828bcdb832642583 *man/PCMGenerateModelTypes.Rd
55bd2bd6a46103c4ede184743163c38e *man/PCMGenerateParameterizations.Rd
5a4a402c22085ce180c83f5dfa58e810 *man/PCMGetAttribute.Rd
7509bc61abaa01a5cf2a0db083c6e9e9 *man/PCMGetVecParamsRegimesAndModels.Rd
1a65ca5ad5defbab1e32f545cdc20e23 *man/PCMInfo.Rd
90085e068c83281b8f58e39384fd3a69 *man/PCMLik.Rd
fe84589be12345066b4756566ff18df2 *man/PCMLikDmvNorm.Rd
11883783ca0bd9a252eb86ae1ce94566 *man/PCMLikTrace.Rd
4a83c52ba9c7ab6c6988bed7b2ba6974 *man/PCMListMembers.Rd
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7c8235827f0133fab3799c756085cb23 *man/PCMLmr.Rd
24792f8461c150a9fdae75e1ea2477ae *man/PCMMapModelTypesToRegimes.Rd
113157bff43ee83fbd16ef8ecf916cc5 *man/PCMMean.Rd
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5b9100e3516eb30910bf274055871e71 *man/PCMModelTypes.Rd
b9c9218251549237888a3b3f369026bc *man/PCMModels.Rd
80398fd84578d08b1f705f93dfd993a5 *man/PCMNumRegimes.Rd
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7dd9afc668a8e481e36fcfdccc8a8684 *man/PCMOptions.Rd
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6853e9a4a297f00a49a028f1a6dca1a6 *man/PCMPLambdaP_1.Rd
117b514bd0ae9a913105d933ab48b824 *man/PCMPairSums.Rd
bb18822ac477c0d75304292561189448 *man/PCMParam.Rd
786a45e6ac5458024d0bdfca43330a34 *man/PCMParamBindRegimeParams.Rd
4b178e57cfe2f6a6d322934b31bab673 *man/PCMParamCount.Rd
11460dc86416380a2acd36503a06d09b *man/PCMParamGetShortVector.Rd
f587b37cf1a4a8c02e3e7dc346c5a657 *man/PCMParamLoadOrStore.Rd
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8623f0ac08368ee37eb716d9f4a75b89 *man/PCMParamLowerLimit.Rd
e294e767d9894c8246ab52e536cdd605 *man/PCMParamRandomVecParams.Rd
5607ed6685e342c17c2275c6140bc89c *man/PCMParamSetByName.Rd
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33880c1550ebc228be86d3e7e8b33df1 *man/PCMParamUpperLimit.Rd
ce7e8c7fd1c23f360f49cef2cd4188ce *man/PCMParentClasses.Rd
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9c1c5fd7ac14127927f4b392bb3999f3 *man/PCMPlotGaussianSample2D.Rd
5799fcfdd5c9e644de22ee62a0e4433c *man/PCMPlotMath.Rd
82af11bca02d301de7e0e65bfdc2ec95 *man/PCMPlotTraitData2D.Rd
97e1d4c650764bde2ecefe1a65cbf9f6 *man/PCMPresentCoordinates.Rd
0a7e57805a399e1b90ae75596656d567 *man/PCMRegimes.Rd
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7a3cb434209a6adb6fb0d7ed8cd2cce4 *man/PCMSpecify.Rd
0ace0a54664561dba10bd4f6f222a6d4 *man/PCMTable.Rd
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8ad716f0249e9cc7a94f0e498a2f8f7e *man/PCMTrajectory.Rd
f7d1ccb6240895972f19f5e06f01184d *man/PCMTree.Rd
9c0978f7ed5d0002fa7f7343bf6024e5 *man/PCMTreeBackbonePartition.Rd
8a11eb104a98e9573227868179695e74 *man/PCMTreeDropClade.Rd
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4630200a73c657b0fe9511db9befd5fb *man/PCMTreeEdgeTimes.Rd
07ae497619b51840fcc83822466b3ecf *man/PCMTreeEvalNestedEDxOnTree.Rd
0f7b8c683507dd3774a325e94a91239d *man/PCMTreeExtractClade.Rd
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316b6b8204fd141f43b34c5a4a20ffdf *man/PCMTreeGetLabels.Rd
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74b6689cd53ceaeba852a92d82402db4 *man/PCMTreeGetPartRegimes.Rd
1beb1f7da6ed643e247d4c8671c7d4ab *man/PCMTreeGetPartition.Rd
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b9e38ea6f035836796379239e4e773c3 *man/PCMTreeGetRegimesForEdges.Rd
d783a98a967380742b17765c108984b1 *man/PCMTreeGetRegimesForNodes.Rd
402b4c75abf97ef33031cd75303b6e10 *man/PCMTreeGetTipsInPart.Rd
1d88f6983bd89015310edb89485bb362 *man/PCMTreeGetTipsInRegime.Rd
82c4a11998efb204738fc5e09fcdb807 *man/PCMTreeInsertSingletons.Rd
40fb6ab3566e4c863c472c2c77ba1cf8 *man/PCMTreeJumps.Rd
cf830523747634e41a92524bc077517c *man/PCMTreeListAllPartitions.Rd
64fd8cae32d1d53fe92e51fdc02623de *man/PCMTreeListCladePartitions.Rd
7f185437e139e6cc7a768409e383e0a1 *man/PCMTreeListDescendants.Rd
be6a7cf33b739d1c266131900a8f78ef *man/PCMTreeListRootPaths.Rd
1bb523c639b9114064b0d9c418f5413e *man/PCMTreeLocateEpochOnBranches.Rd
4055ec50ee43127b356ee269e1f221b4 *man/PCMTreeLocateMidpointsOnBranches.Rd
86b0855b61d58554629f443b29b1dd56 *man/PCMTreeMatchLabels.Rd
5530bda71c591974de2ff7b0bb5ac48e *man/PCMTreeMatrixNodesInSamePart.Rd
1b89e5dec6411806cabb98606955af9a *man/PCMTreeNearestNodesToEpoch.Rd
5b0ed9fd1c3db68fe659561fe025bd96 *man/PCMTreeNodeTimes.Rd
99994bf427147ecd65b38c4d9b4d3220 *man/PCMTreeNumNodes.Rd
5acb6387d19f4742bdf1a9c7fe4bb238 *man/PCMTreeNumParts.Rd
75b520171bca101c1e0fb4ab57466e51 *man/PCMTreeNumTips.Rd
c6e1f77ed61fca12f4a4a4189397302c *man/PCMTreePlot.Rd
4d5a6a6385be91a7212333b8dfe85fbd *man/PCMTreePostorder.Rd
26dbfffcebfc57b575d68dcb817d0431 *man/PCMTreePreorder.Rd
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35ed741db7548b18ef6613a52e1e0dd8 *man/PCMTreeSetPartRegimes.Rd
dd4afb63bcea2a12999ae18ce6d57b24 *man/PCMTreeSetPartition.Rd
931344f6cd8011c413126aa6029bf140 *man/PCMTreeSetRegimesForEdges.Rd
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1c2c4f55de022c2b0d42292987a20e9c *man/PCMTreeTableAncestors.Rd
0d4fc93c4355a1244c9e7f49ef4861ba *man/PCMTreeToString.Rd
93cc7cbd273000ac0919c7bed216d813 *man/PCMTreeVCV.Rd
77e5632f87a64ab291dc43808d7fc76a *man/PCMUnfixParameter.Rd
c619957aefa968faf224093e9f81a0d6 *man/PCMVar.Rd
bfb910b5a6b439fe44caf345c93f04a4 *man/PCMVarAtTime.Rd
91afcb52d50e9e0a470eedbc58cbf3ef *man/RequireSuggestedPackages.Rd
f74b965d1e436753253e232e03a8a596 *man/TruePositiveRate.Rd
c04ccaad36fa42bbed402b256b691713 *man/UpperTriFactor.Rd
88101e184540f12d44ea44225dbe2b7a *man/White.Rd
3afa15c4a172a6d08f1042949dbfe8b3 *man/as.MixedGaussian.Rd
3cf4e72155c2fbec4ed7d65bb8c62257 *man/dataFig3.Rd
8550ff17cc3c6e12a1fff6c38a4b08e0 *man/is.GaussianPCM.Rd
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e30d7d4868bf9cbffed90058214f3c7d *man/is.PCMTree.Rd
5a27c4a26932c915832e4725c0caa884 *tests/README.txt
0256896808108a7bdd315477b5e9aa5a *tests/testthat.R
f8cab6cfeb03ea4c825387b045bcd75d *tests/testthat/test-MixedGaussian.R
edcb75eeb0f4c8c6ef236b22cd96e278 *tests/testthat/test-PCM.R
80d2e35b5d29bcd1e1af15932dd3c479 *tests/testthat/test-PCMLik-BM.R
112b6b99685449ddd0e8a1ad136bf084 *tests/testthat/test-PCMLik-BMdrift.R
ecb31450587a175b9b61f8fcf5bc1f8c *tests/testthat/test-PCMLik-DOU.R
c41efd87eeb8c66ada9eeb11c0d9de9d *tests/testthat/test-PCMLik-OU.R
161d8edfc297d3662ee7108ebeeaca99 *tests/testthat/test-PCMParam.R
06ca48e4d0f68d9990f09989b05b6b39 *tests/testthat/test-PCMSim.R
167ccfc5ff09ba51388d9145ad2c6586 *tests/testthat/test-PCMTree.R
cac4f2ee1d47b3b02d887bd2cedaffed *tests/testthat/test-Transformations.R
32e9c1a6bd68ff370306c4bbb9d6224a *vignettes/Fig1.pdf
df689e311f1a90ae6786d58913051784 *vignettes/PCMBase.Rmd
dcde5e145b3f786552c84f7820cab582 *vignettes/PCMCreateModel.Rmd
4c6426caba57e48bf0108dca4fbe875d *vignettes/PCMParam.Rmd
2b5b21f495136ac7ae102ba866fe1c11 *vignettes/PCMTracePruning.Rmd
9b59182e619ac62e620714c2a709615c *vignettes/REFERENCES-R.bib
c7c156e202a3369d0cb1743f84c9c95d *vignettes/REFERENCES.bib
