802c29aa6a3087d9cd74266e7b1bf63a *DESCRIPTION
689b5ef66536b7c7ce83f2ab2c8edc02 *NAMESPACE
ee8f279c7051fd15e5f3b69a78b13d42 *R/add.everywhere.R
00125e455cd6c2a9a162f414c82b31d3 *R/add.random.R
30f5b1a58539aec4b00e952018bed1d8 *R/add.species.to.genus.R
f0df86c98d2fd0c6d76f49ca3172d129 *R/allFurcTrees.R
870b0d63778e3933d4debceb6591878f *R/anc.Bayes.R
e0b9ab2b01c0331dbae14d4cab8f484d *R/anc.ML.R
8d5d598ff8e8c9e7574b5c6b812129d5 *R/anc.trend.R
bbd91949f7bac7c83b82f813e768098b *R/ancThresh.R
94bff500f2aa61917d6703462332c618 *R/backbonePhylo.R
403f6c3609b1b82650665a0a04eeba87 *R/bmPlot.R
97f2cdd07a3595bb221fe3e8618e23c6 *R/branching.diffusion.R
6e14486536afe403240be0ac32bb55e3 *R/brownie.lite.R
ffdd534a6c94d07b4ce58c7ae23c3a12 *R/brownieREML.R
961a5a8585392b4713edf3397a7115c4 *R/collapseTree.R
de21e15cc10c6021c1b1eeb672e032ba *R/contMap.R
d40fe80664d0ddc1dad1a11fd029ecf8 *R/cophylo.R
6d3987901075dbb846d4cc0ab430531a *R/densityMap.R
c93967a21535fa5ac5fe0ed27ea64c07 *R/densityTree.R
441f0bff08077f598d2c1b3579fee9e2 *R/dotTree.R
69b6d14462faeaf904236868259f6e7c *R/drop.tip.simmap.R
00b980b1a6af6880330cfb00cb9b2282 *R/estDiversity.R
c3ec38b00bdd80775a5a99a3b3e8c007 *R/evol.rate.mcmc.R
f5826a6f07e30c03fd91f0d2fbe50e49 *R/evol.vcv.R
9b3cd7339f8647034930c08711d41a1c *R/evolvcv.lite.R
164c5aba763c4823fae1a2747cbbdde8 *R/exhaustiveMP.R
0c94431c709b011b1a19a5238b7a3352 *R/export.as.xml.R
1019809a18204e4301d9b5e9794af553 *R/fancyTree.R
3de0353dd6102f6b93a69edbabd14a30 *R/fastAnc.R
1b1e3136904e650f9f822c9f1314a8ad *R/fastBM.R
c9216efc0ab85b13885cd0708d698fbc *R/fitBayes.R
350a3fce5519e4b03cb5acfc01d2c55d *R/fitDiversityModel.R
91905076666961ba0ba62f2d755f490e *R/fitMk.R
3d928ba3e7ee2dbd3a10fbc48f6f3b67 *R/fitPagel.R
a8a474d3956da9f202f470dfd6e4a45a *R/locate.fossil.R
36eed593b2ed2f89c1dfdb8d37bc047d *R/locate.yeti.R
bacc73c39e4d2b4149bd1795531aa6f9 *R/ltt.R
e6f7e2cc99e35ae5f094ce4e2c5fe841 *R/ltt95.R
07c37a4c09941dfa8088c4eb91ef5c4a *R/make.era.map.R
70601de28807bc57eed3037f57fb7f75 *R/make.simmap.R
2f545b7e68a2646aedd3ca945459c8c2 *R/map.overlap.R
5a30f7f5db85ac8d3fec4e058c15097a *R/map.to.singleton.R
bf6c23b046ed30ee9e9183582aceb070 *R/mcmcBM.R
659b234e9ff4b00daa511a06f72d53d2 *R/mcmcBM.full.R
9fc1c1054aa693a9ad32044d21e9f8c4 *R/mcmcLambda.R
fc4256396ce1f5ddb507ba23411de327 *R/mrp.supertree.R
7e33687b42d9ee02d52ae36834f4c122 *R/multi.mantel.R
34c72210381fa6ba622d377d6c13aeac *R/multiRF.R
861e9b7abaf0ae0ec1c712b1176b2bc6 *R/optim.phylo.ls.R
4251fbfa33b24cedd655a575878bee3a *R/paintSubTree.R
e9e01ad2df33334424ddb0453603c336 *R/pbtree.R
f2a982b5f97086cbf4a92fa1b8d7dcc1 *R/pgls.Ives.R
7417031fef112a7f72d0bb1fb9f0291e *R/phenogram.R
bf7bd9694f000c60660eae9aa83f1e08 *R/phyl.RMA.R
c718c75c55026ee77424678de40e312a *R/phyl.cca.R
bd4da491297a9551360b5b0f361bbee1 *R/phyl.pairedttest.R
4004dd6f1284c6d2ae040ae1e70461b0 *R/phyl.pca.R
17d0e8f613fafc8cf7e0a719120dd9cd *R/phyl.resid.R
dc0b91b6560444a2d39cf4e4d97cf64e *R/phylANOVA.R
bb3e73a0b7019d95a1dd41229cc351d8 *R/phylo.heatmap.R
df00c4d517266ced4e98bd033efc26a2 *R/phylo.to.map.R
153f94b487776dcbe9423b5507b324a0 *R/phylomorphospace.R
8a7141585b7209118b95a388b1a49e94 *R/phylomorphospace3d.R
88e81eb2a2b9844e2694fb586524bfd8 *R/phylosig.R
3c4626885f3fb4686a4145466065b466 *R/plotBranchbyTrait.R
acc5b9155c42c1fff9fab30490c5be1a *R/plotSimmap.R
0bd1095b569c32024cb2ec5a619b1277 *R/plotTree.wBars.R
5f7e8af1992e4d31ad68ce8b4a6040f2 *R/ratebystate.R
b4e99e600f978e241b35fc575934c394 *R/rateshift.R
3728a1ffd45d16f796792eade4696c2b *R/read.newick.R
8d676810a59c68f20f5fc37bfe9b841a *R/read.simmap.R
9db20084dfa14c5410cd56e10da5b69d *R/rerootingMethod.R
afd2a4767a1ea01dec349a236ed79d94 *R/roundPhylogram.R
d8a6bb753f6779a1dd49e769b18775a0 *R/sim.corrs.R
2c508d4f4d57938a29537b9f747ba315 *R/sim.history.R
a1a6c8453c68f9eefb75a4b3752b664a *R/sim.rates.R
5ae6a2a091d203ecc04ad6081e11293d *R/skewers.R
606ad5a902660277dce5f3ef7fed7461 *R/splitplotTree.R
c8bfa07dd3238d97fcaafe5a369e5e89 *R/starTree.R
0567456c325cbac2c305158ffa05df91 *R/strahlerNumber.R
d720d00ce443a13811c6a8e4050c0d87 *R/threshBayes.R
9f0d812885926166083c90b120cf2713 *R/treeSlice.R
effd2e91c9426e75274f5cd3b18a2378 *R/utilities.R
f44bcfed80ecb7907483c41065052109 *R/write.simmap.R
67b049f3e083513ff41ab9ca2bd940b5 *R/writeAncestors.R
65bf87a538f44806311e8914317b242c *R/writeNexus.R
3ab25de6b1e5d2b15860347db6d973d5 *data/anoletree.rda
0eb3bef3466bd6d264c669571621c2d1 *inst/CITATION
6e0520cdf344af4cff9a562547c11093 *man/add.arrow.Rd
811a88a3a787b509246b4167a6c832a5 *man/add.color.bar.Rd
c4648d392c28e54efbf6b106d5d52aa8 *man/add.everywhere.Rd
f40f62b75c2719a2a96b914daa6a140b *man/add.random.Rd
54b5cce6e4c6f9cdcce89a82bdc7da36 *man/add.simmap.legend.Rd
9254424cc5f1a5d092ef04134ef7a1db *man/add.species.to.genus.Rd
ddbaa1f624e77bd0b5c8be0fb07b407a *man/allFurcTrees.Rd
fabcee226507890a78ee980aa266fe6e *man/anc.Bayes.Rd
8526771ae97e991dd1f77c969cf07a28 *man/anc.ML.Rd
ffd06ce1e79ddefbac18768ceed13cff *man/anc.trend.Rd
e3e5266415d303b5e3be4454fc1ad814 *man/ancThresh.Rd
ce35fca6daf7f9827e051c70d63c2adf *man/anoletree.Rd
5401106ec92900c68ed09e53a5b07d3c *man/applyBranchLengths.Rd
3e59cf4772028c0afc738956ca2d9d72 *man/ave.rates.Rd
48f05a7772ca02709bbd77e8b588afdb *man/bind.tip.Rd
cc14a92f9406c1cd8e2ad5204bdd226f *man/bmPlot.Rd
946c923c56d2a62725a8dcd7fe7f0b49 *man/branching.diffusion.Rd
1a0b8180cf042d0bf526a0e3f58b5868 *man/brownie.lite.Rd
2de40ca82db32d5a517c956a71db3aa8 *man/brownieREML.Rd
c8b9d111427d0d5123f8006b1c4244f5 *man/cladelabels.Rd
0f1e1addf1457ffa1a6a2241b516f2aa *man/collapse.to.star.Rd
d860a425bca88fdba3651f80d5100fee *man/collapseTree.Rd
8dec4a062c4087f74b693649d1c03c25 *man/contMap.Rd
c3bc82fe791f3392b2ea86a6165308a3 *man/cophylo.Rd
1c53948802e8f694b01440e03a198dbb *man/countSimmap.Rd
7154c84255d7a9beb3242be7cf53c34f *man/densityMap.Rd
1674824c0d293093e47a3abab7274c79 *man/densityTree.Rd
9bd07912e9a9dd7590d94c9f9c0195a2 *man/describe.simmap.Rd
14fcb67d7dcc50dbb30eb3be919bc021 *man/di2multi.simmap.Rd
fe55d1d28fae8c2d13cf025f51235c35 *man/dotTree.Rd
c92235efc1cf6791a2871a0b59bf94b1 *man/drop.clade.Rd
139cf35fd81a07386ea5489a3c8a549e *man/drop.leaves.Rd
4dbacec8bf2b24739708948c5c6f2251 *man/drop.tip.contMap.Rd
0f4c4d6f030921fe8f033e54a5ba2226 *man/drop.tip.simmap.Rd
ddcd0b3224754d09a211b6e3e8514819 *man/edgeProbs.Rd
6c00e1009e2f8fb0684f9169cc4347ab *man/estDiversity.Rd
92568d07ab9b97f0604f54aa219f5342 *man/evol.rate.mcmc.Rd
3fd9a42853666acc3eca0becbeb860dd *man/evol.vcv.Rd
c5acaa9f3fb37921bf56ac296dbbfa90 *man/evolvcv.lite.Rd
e93d92ff11f1f830540896a8129603e8 *man/exhaustiveMP.Rd
22001f60bdc699b30ab0250e61eb879d *man/expm.Rd
24fbe29405d7d63b20381cbe63c3685f *man/export.as.xml.Rd
69ef7934a38c50a132bb4970d14f13d6 *man/fancyTree.Rd
582bf7995d196ead7d088f2663532e19 *man/fastAnc.Rd
7505dd6d4438240378937ee7142ce199 *man/fastBM.Rd
db8b24db98df1581869d03abfea3b29d *man/fastMRCA.Rd
2defe383bef2ae470adceb82ce9643a8 *man/findMRCA.Rd
dfe572c4d2cddc4f27f3837f7e1f763d *man/fitBayes.Rd
fd6dfbcd9836f3d550d058f2946c4fc9 *man/fitDiversityModel.Rd
b8baa78fd1530bba40ff2decf329e2a5 *man/fitMk.Rd
41f7e79f0dd12a787d4e4dcee3b57e8e *man/fitPagel.Rd
63efc2cf840c0de75ede0e4645625192 *man/gammatest.Rd
88ad5870c14512c74ed6c88688cb9367 *man/genSeq.Rd
6ca10ad3d8ae7823a3ebebeaaa903a26 *man/getCladesofSize.Rd
aca2f6bc9375ff45e24dee0a2558e956 *man/getDescendants.Rd
0f66e89c8d5de9f7906cfc629dbde129 *man/getExtant.Rd
acf4a33137cfe673886c075cc5a2ee0c *man/getSisters.Rd
50941930ec6026a6fb9b0020a7e9e3e3 *man/getStates.Rd
882bbf621c5c8e6c0922c21cf5308d67 *man/ladderize.simmap.Rd
c2a04357ebedc51867f98d3e24ef0d66 *man/lambda.transform.Rd
633387cd5519193a2e183285e7e4fb79 *man/likMlambda.Rd
3149b5b7a824f424f799ab3e522d6850 *man/locate.fossil.Rd
d274dca0554874d3a3476906e281093a *man/locate.yeti.Rd
a09a3cd5616557bd09ba88e990addd40 *man/ls.tree.Rd
164517a355a60693d56b4ba8e52ccb18 *man/ltt.Rd
fed051823f388fb54a6cb38c2da4e5a3 *man/ltt95.Rd
cf7e13fd79fec035abe59959454442f2 *man/make.era.map.Rd
edc94b0dfc1667270675a80b96bd05a1 *man/make.simmap.Rd
b394835f519da73f8fd866dccaef03d0 *man/map.overlap.Rd
25e364e9799a5eeda4991ae4d6307158 *man/map.to.singleton.Rd
f9c95d7c4652d4817305122c51ceb3ce *man/markChanges.Rd
7b63ed10331213eb811ecba82d6069c6 *man/matchNodes.Rd
e566946585ec51d6df130403eac7b996 *man/mergeMappedStates.Rd
65087a43d13d28c223e6c45694898660 *man/midpoint.root.Rd
f21244054f576ed5f7c509e7257bd09d *man/minRotate.Rd
d3a51d0c0191486546c6c67e9456b0a5 *man/minSplit.Rd
8fd67c7bee19ff3ec51d70d15811f15a *man/mrp.supertree.Rd
73a2a40506cc9e62da97a20c7e74a1b8 *man/multi.mantel.Rd
4d4c8e8e68c52b2579e894405b2b3700 *man/multiC.Rd
a41f61fdc924782d384641050dbec043 *man/multiRF.Rd
771381f4158bb262fd0a9c7df8c33508 *man/nodeHeights.Rd
b8061afef967e33d70e5646761eea00e *man/nodelabels.cophylo.Rd
efde4d328a419a7d4c7144db6dcb1968 *man/optim.phylo.ls.Rd
63d57fedac44429aea25ebf22f53c772 *man/orderMappedEdge.Rd
cdef7f35a83cc40e7e6b66fab4878fb4 *man/paintSubTree.Rd
4aec9a1fefe5f96ac6652a0e5fcc63eb *man/paste.tree.Rd
03b649e30413e0fa68c291128b8c4b00 *man/pbtree.Rd
1d69c86e95a461c0730689a304bef896 *man/pgls.Ives.Rd
35dc07574c676121d6bd389f225510f9 *man/phenogram.Rd
3480827c1991f6373cff7eaf8817fa35 *man/phyl.RMA.Rd
609bfaa749f8a6ef81a4559dd0033394 *man/phyl.cca.Rd
f8a7579313d3a9b152cbcc280d24a8d0 *man/phyl.pairedttest.Rd
27859b7f2c58b2c8e25029bce9bc7084 *man/phyl.pca.Rd
1ca0bfa0ac52441f921b34a080a25fb8 *man/phyl.resid.Rd
2f54dd0b2b5ce5d36193c97b1a611921 *man/phyl.vcv.Rd
415be9008226b2042bb574697283417c *man/phylANOVA.Rd
b7aba8cf03e7ccdb0495d728ce216cbb *man/phylo.heatmap.Rd
48d842cbd77de69e39a631648fd66447 *man/phylo.to.map.Rd
c9f37b2f0f5fc62bede73242d27b47c1 *man/phylo.toBackbone.Rd
3a1b3861ce38f29feca5081c7acc4908 *man/phyloDesign.Rd
c8e067485dc173b613127a874e4b6d79 *man/phylomorphospace.Rd
fc93761c29bb6f522c6363e5ec9e87a0 *man/phylomorphospace3d.Rd
1f76e92578b2f4d0ba684433afbeb6b1 *man/phylosig.Rd
b1215539c6b3d560e8b0782d290197cc *man/phytools-package.Rd
0aebb93e559aa737a47c895c0251451f *man/plot.backbonePhylo.Rd
0945d9031aaa5a134b1b826283c71e3c *man/plotBranchbyTrait.Rd
e5e38704a718dd60ccc887d0093fe996 *man/plotSimmap.Rd
f1d1986ccc887008e39d69cb10304b78 *man/plotThresh.Rd
7abaec7aa366e41647df0bf3073a36ef *man/plotTree.Rd
ba0685cfbebc25a91c44839903e05120 *man/plotTree.wBars.Rd
9c8297109561037f067dd7d469f12acb *man/posterior.evolrate.Rd
4bfa72a7ac47c3e185164f8c35dd5e13 *man/print.backbonePhylo.Rd
024dc088aa4b730b721a55c491e246c6 *man/ratebystate.Rd
a5f6db4f9ce0fe32a13eae6549800f52 *man/rateshift.Rd
83b256d15cc236468fc5a08c4c99e411 *man/read.newick.Rd
6cc642b69b90cc39e37a97e90792dc0f *man/read.simmap.Rd
0a719edd23de05fb878911f9cf05367e *man/reorder.backbonePhylo.Rd
1b9465c231435640da167fc86f10de30 *man/reorderSimmap.Rd
66b1bb2aaeca6af053fd7102d51bc93f *man/rep.phylo.Rd
1d869bd4761b12d96ce4384764a77577 *man/reroot.Rd
5314b3ae0990303eefe7e2de3a5043ce *man/rerootingMethod.Rd
7fb2034ee0d06ddd28baf54a19a5df31 *man/rescaleSimmap.Rd
a8ae2798a55350d0b9d5ef0fd741aa55 *man/rotateNodes.Rd
10b7f05d1c4dee978bf2c8112707a8b1 *man/roundBranches.Rd
6a2e95ff12365a48648ddaf647997748 *man/roundPhylogram.Rd
582c0539a965268cb3783ec1cfc69341 *man/rstate.Rd
56d1e0ab7594a041e03a96cf512b7c56 *man/sampleFrom.Rd
4ff599d27cce8dd9f6a61b1b83167c36 *man/setMap.Rd
0c97cd88c821ba9acbd840617138a7d1 *man/sim.corrs.Rd
93c139aabab47e2d13707a9f93ba3f8a *man/sim.history.Rd
d4619609a325632ef2c834f485c505b0 *man/sim.ratebystate.Rd
26d5d55a6aef33669de40554012e70d0 *man/sim.rates.Rd
e0716598bfe6497b75aac3a5de7d1d1a *man/skewers.Rd
8afbcc3a0809d9abc1337996402b395f *man/splitEdgeColor.Rd
f0b7c55fe94d87a63fcc473557ba356c *man/splitTree.Rd
ab26f179a0e1f7d25a9b69bae0288144 *man/splitplotTree.Rd
e3ebd622b81458023c71dc8b846bc8bc *man/starTree.Rd
e3cb564ff8ac467e211b63893e5bd8ab *man/strahlerNumber.Rd
8475cdeb499ca447c1d69383ab3bb153 *man/threshBayes.Rd
4c943bdc70f92faf2626a05b4dd5737a *man/threshDIC.Rd
1f469e57b425d3d1368c1b5a20f6677e *man/threshState.Rd
75b7d2745c01bd834c7b1b8523b9859e *man/to.matrix.Rd
0a2d6d80c5ebde33c07bd27bd1245ac7 *man/treeSlice.Rd
ab88b8c906a44c915f7933c77d1e2aac *man/untangle.Rd
8698e88dd7441c86162d8ab4eddf3439 *man/vcvPhylo.Rd
b5d6b316433d7c81241b36f472db0091 *man/write.simmap.Rd
22f63bf8e0898892ac0fcee7ebe0f936 *man/writeAncestors.Rd
81b95726f7c7c8b1308d35fc5a9e9d2e *man/writeNexus.Rd
