5a17d30e0a29f98b7cdec40eea71278b *DESCRIPTION
0bc5511c2538b0158e0313ab2eb3e570 *NAMESPACE
763c2768ceff26252be606180f1ce086 *NEWS.md
27c9a6c8f132ce67953f03763cdd790e *R/AutoGeneratedModelTypes.R
e6eae56de3369e85730157124a2e798c *R/BM.R
5b03617cddb0172474b73784443b2aa3 *R/DOU.R
96ff58cddb9b705cf5543267d759155b *R/DefaultModelTypes.R
46d33491ebb39e0d4a1282e8f4f2202c *R/GaussianPCM.R
8fa43dcf1f6487072b9e06408e288cc3 *R/JOU.R
5040fac3be76ac44abafef9a269aaa61 *R/MixedGaussian.R
458cf2b481984150f5082710396c0dd5 *R/OU.R
a64bd0b7cf3810d402518ba8ec36c60e *R/PCM.R
33b2ecba11d0332c02a5d64ab7b6be22 *R/PCMBaseTestObjects.R
d9cfbe35c5c2285e9074c856df384ed5 *R/PCMParam.R
48f3b04bd861c9077897b527e082346c *R/PCMTree.R
d2bc295674ad0c1fafe6335959e28428 *R/Utilities.R
60f45f6e1c80c3b412b4e9fa338ac000 *R/White.R
6fea370a4925caca89b50cc2fdd12a1e *R/matrixparametrizations.R
5fa1b1734d3dec2b046720da1ad0fed1 *R/zzz.R
c840f4cc96af89b4297ef255dadbbeb9 *README.md
31ddd877f7d216c37d73396a002f8998 *build/vignette.rds
9d912dc102bb32ae3ee83927a6679266 *data/PCMBaseTestObjects.rda
1cce25a39bb1e8435cd44a8a7b7131fb *inst/CITATION
80a0445289b58f28d401896fc1a609a9 *inst/doc/PCMBase.R
a4a46431659ece2ed853f85a71fd6905 *inst/doc/PCMBase.Rmd
af3090745f4e2053f78b6d68f044a8fb *inst/doc/PCMBase.html
82a2e93ad4efbb4df26fb9881e72edbb *inst/doc/PCMParam.R
1d1824db0f88efeedcdf19ee18ea4c36 *inst/doc/PCMParam.Rmd
1ab08d93967eed0d59628378de79adea *inst/doc/PCMParam.html
ac2a90e3707afae180b135fbf66d6c86 *man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd
5ec51ceea26e9839de26868112cdaee4 *man/Args_MixedGaussian_MGPMScalarOUType.Rd
e4bfa283a94bdcbdbe48aef73f3c1e98 *man/Args_MixedGaussian_MGPMSurfaceOUType.Rd
c4e2ee286af9072b818e6e39396f993b *man/MGPMScalarOUType.Rd
28e408352668c4d421edc316b6ea4e87 *man/MGPMSurfaceOUType.Rd
371efde45ee0d87c649f1f7c8490b408 *man/MixedGaussian.Rd
f58d91bbf4b416b34dd7a4dde5dcb51d *man/PCM.Rd
e5fca184e5fc9d7c869ee7432b480933 *man/PCMAbCdEf.Rd
b0bd49ac9a139fa11387556a07b9c5b4 *man/PCMApplyTransformation.Rd
d814c0f2f95e40839dad170377e938cf *man/PCMBaseIsADevRelease.Rd
806c6e7107fb88a5d4cdb8d4955a4e99 *man/PCMBaseTestObjects.Rd
39b08ef48406308c6bba54f56175218a *man/PCMColorPalette.Rd
035cab67d4e92b30d8c244f8cf2756d8 *man/PCMCond.GaussianPCM.Rd
0384d133da46505afc6418bc9f0de6ee *man/PCMCond.Rd
f3987f61f3f8007d4f2cd6a2429a1dc8 *man/PCMCondVOU.Rd
bf530108e1df45dd427a398a412be334 *man/PCMCreateLikelihood.Rd
22be33e77d8aff19a898a88f180f42c2 *man/PCMDefaultModelTypes.Rd
890f88b6a41197f74be32a3d2fb98137 *man/PCMDefaultObject.Rd
a089c175e744a7eabe995dd4c8d5fbe3 *man/PCMDescribe.Rd
a13f3f7a1413ad494fd06d747c41270e *man/PCMDescribeParameters.Rd
bcc1e2c5c2e00e365508eee9eaacd9a0 *man/PCMFixParameter.Rd
6a6a527eb756b81ef6319cc24f2fdd87 *man/PCMGenerateModelTypes.Rd
037dd6e8323b2d6585a025d2c28fb23f *man/PCMGenerateParameterizations.Rd
9404c583ef62d46d89a08a843c904798 *man/PCMGetVecParamsRegimesAndModels.Rd
52bdc7d390bae7aa068ff03b1d09ab21 *man/PCMInfo.Rd
d5758eb1c54cb495eb6d2c30349c7cb7 *man/PCMLik.Rd
aa28f2b09d9f65f01728444dd4d18727 *man/PCMLikDmvNorm.Rd
fde879da74211b7e4f572c2000027f00 *man/PCMListParameterizations.Rd
b330175e119f3f85cb229ea743f0f070 *man/PCMLmr.Rd
24792f8461c150a9fdae75e1ea2477ae *man/PCMMapModelTypesToRegimes.Rd
03556120940c92df350876a48768146d *man/PCMMean.Rd
16251a51661461438c8b1313dd6db0e4 *man/PCMMeanAtTime.Rd
5b9100e3516eb30910bf274055871e71 *man/PCMModelTypes.Rd
b9c9218251549237888a3b3f369026bc *man/PCMModels.Rd
80398fd84578d08b1f705f93dfd993a5 *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
5e60d599a9232621755d459370e995ce *man/PCMParamCount.Rd
11460dc86416380a2acd36503a06d09b *man/PCMParamGetShortVector.Rd
4564fa741dc725989cd1ec291bc129bf *man/PCMParamLoadOrStore.Rd
8623f0ac08368ee37eb716d9f4a75b89 *man/PCMParamLowerLimit.Rd
23a2c5b70ce91d02aa776f557a7ffe2d *man/PCMParamRandomVecParams.Rd
61f5d433b6c6493000086c32e2431366 *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
d8e8a277192cab02c186c6b797f701be *man/PCMPlotTraitData2D.Rd
0b3a871b3f718f226f9550ed86c33095 *man/PCMPresentCoordinates.Rd
0a7e57805a399e1b90ae75596656d567 *man/PCMRegimes.Rd
9e9b0beca1322d36126d41cce474dd22 *man/PCMSim.Rd
20f8dc305adbd913d74f1eeffeebcb9e *man/PCMSpecify.Rd
f5582c1a4d5f100660d5c7227d543e5a *man/PCMTableParameterizations.Rd
ea1dbc1cf6fe88150566884725d69f4b *man/PCMTrajectory.Rd
af4d0d68036a021d02d753217e095897 *man/PCMTree.Rd
679163eae5bcc25b4371784e077be5da *man/PCMTreeBackbonePartition.Rd
a983d04d7cd97940d53340fcc0cb7c70 *man/PCMTreeDropClade.Rd
52d18622c1022bc9042ce2adb5d80ad8 *man/PCMTreeDtNodes.Rd
4630200a73c657b0fe9511db9befd5fb *man/PCMTreeEdgeTimes.Rd
f8104d6e0b31acb5b6c956b326003df6 *man/PCMTreeEvalNestedEDxOnTree.Rd
385e5da2c90cbb7f0fe7eb9aaa2f7606 *man/PCMTreeExtractClade.Rd
d2ef15d3c3db7edb12cff391437a4d3d *man/PCMTreeGetBranchLength.Rd
d35816b075d6cbef1bab25b3e9bfa7d5 *man/PCMTreeGetDaughters.Rd
d84361a998d13597e8c7d7b1cbdbd237 *man/PCMTreeGetLabels.Rd
bbf6576345903c74cd3d5fbcb84bdb3d *man/PCMTreeGetParent.Rd
e4be7d1cbc279d4256d30d6b62b73304 *man/PCMTreeGetPartNames.Rd
74b6689cd53ceaeba852a92d82402db4 *man/PCMTreeGetPartRegimes.Rd
1beb1f7da6ed643e247d4c8671c7d4ab *man/PCMTreeGetPartition.Rd
d3e993817efb4a9921b759d1c01d240a *man/PCMTreeGetPartsForNodes.Rd
b9e38ea6f035836796379239e4e773c3 *man/PCMTreeGetRegimesForEdges.Rd
d783a98a967380742b17765c108984b1 *man/PCMTreeGetRegimesForNodes.Rd
86dcbc0fe8974b9b4f62095d643102ec *man/PCMTreeGetTipsInPart.Rd
37ab9ad153243c84e02357f38eac80d3 *man/PCMTreeInsertSingletons.Rd
4ecddef21068e0d932363465400f5077 *man/PCMTreeJumps.Rd
f8aa3f4c29e457b7c3c51feb0846914c *man/PCMTreeListAllPartitions.Rd
6b1cffec4d7c268ff01be128d9bc44a8 *man/PCMTreeListCladePartitions.Rd
2923d095c6217551c4b482473c7e52cd *man/PCMTreeListDescendants.Rd
be6a7cf33b739d1c266131900a8f78ef *man/PCMTreeListRootPaths.Rd
3721772ceecd101042c1338cf29621ce *man/PCMTreeLocateEpochOnBranches.Rd
4055ec50ee43127b356ee269e1f221b4 *man/PCMTreeLocateMidpointsOnBranches.Rd
351d50dbc95eaed498366fc4aa74561a *man/PCMTreeMatchLabels.Rd
198b39d60cc22602e3b9dc952cabd132 *man/PCMTreeMatrixNodesInSamePart.Rd
1b89e5dec6411806cabb98606955af9a *man/PCMTreeNearestNodesToEpoch.Rd
5b0ed9fd1c3db68fe659561fe025bd96 *man/PCMTreeNodeTimes.Rd
99994bf427147ecd65b38c4d9b4d3220 *man/PCMTreeNumNodes.Rd
5acb6387d19f4742bdf1a9c7fe4bb238 *man/PCMTreeNumParts.Rd
75b520171bca101c1e0fb4ab57466e51 *man/PCMTreeNumTips.Rd
363e96edd6904c984091c8240c3086b0 *man/PCMTreePlot.Rd
4d5a6a6385be91a7212333b8dfe85fbd *man/PCMTreePostorder.Rd
26dbfffcebfc57b575d68dcb817d0431 *man/PCMTreePreorder.Rd
9a80748e220f4cc79787a0d1ffa907b8 *man/PCMTreeSetLabels.Rd
550ead4f79a0674fc95c1a4554663116 *man/PCMTreeSetPartRegimes.Rd
221a3ecaa30ff129b80035ebce4fa1f8 *man/PCMTreeSetPartition.Rd
db2b1d87a0d626d49463cd28d6e37cc2 *man/PCMTreeSetRegimesForEdges.Rd
eb9c269b1c49e281800a2dac162a1241 *man/PCMTreeSplitAtNode.Rd
1c2c4f55de022c2b0d42292987a20e9c *man/PCMTreeTableAncestors.Rd
0d4fc93c4355a1244c9e7f49ef4861ba *man/PCMTreeToString.Rd
77e5632f87a64ab291dc43808d7fc76a *man/PCMUnfixParameter.Rd
04200e024b6888eea961825daa42dbaa *man/PCMVar.Rd
c98826382b813bc861f290ed0f494f2e *man/PCMVarAtTime.Rd
f74b965d1e436753253e232e03a8a596 *man/TruePositiveRate.Rd
88101e184540f12d44ea44225dbe2b7a *man/White.Rd
c4684187833ca05999ee1bfe7e1d68eb *man/is.MixedGaussian.Rd
08c1de6e3beb0ee5fdadefcc032ace1f *man/is.PCM.Rd
e30d7d4868bf9cbffed90058214f3c7d *man/is.PCMTree.Rd
0256896808108a7bdd315477b5e9aa5a *tests/testthat.R
cf1dcdc3b501c151140b3b723359080a *tests/testthat/Rplots.pdf
cee9f0ca26fe0004cab416ec1a59bb3c *tests/testthat/test-MixedGaussian.R
6cacbf65c9c179f2c2893d283157e78f *tests/testthat/test-PCM.R
78ed008042e362d26890fbae80cc7033 *tests/testthat/test-PCMLik-BM.R
813b0e0c30e7c33fbb764d06bc802ee9 *tests/testthat/test-PCMLik-DOU.R
0497f972fe26722252b3b88ec24a0274 *tests/testthat/test-PCMLik-OU.R
8d675f40683d3107d2b31685da57d5ae *tests/testthat/test-PCMParam.R
05e8605efb840ef5a20b4a4a104c884e *tests/testthat/test-PCMSim.R
c1ebc54f0f160438c7bada8910d3a1c0 *tests/testthat/test-PCMTree.R
ba1c1d519d8d567db1c74c357e798e70 *tests/testthat/test-Transformations.R
a4a46431659ece2ed853f85a71fd6905 *vignettes/PCMBase.Rmd
1d1824db0f88efeedcdf19ee18ea4c36 *vignettes/PCMParam.Rmd
bffd9121aa89f7cfb86a4765fd796753 *vignettes/REFERENCES-R.bib
0a35b1b2dfe775906d78d1f44fde9570 *vignettes/REFERENCES.bib
