9f322e8fa0139b3d2e887bb8beca2efb *DESCRIPTION
e3ee557853b528a3957d56f1b4a079d0 *NAMESPACE
ee8f279c7051fd15e5f3b69a78b13d42 *R/add.everywhere.R
00125e455cd6c2a9a162f414c82b31d3 *R/add.random.R
30f5b1a58539aec4b00e952018bed1d8 *R/add.species.to.genus.R
f0df86c98d2fd0c6d76f49ca3172d129 *R/allFurcTrees.R
f1b04dd672234dbaa538ed81128c98d4 *R/anc.Bayes.R
c6db742b446f38c7c86504917f38272a *R/anc.ML.R
227c5163b6303989b36dbe9d50a7f53b *R/anc.trend.R
c55f0fece713fbc45b33079be15116c0 *R/ancThresh.R
bc3139a0d0a2b4bef405deaae471973c *R/backbonePhylo.R
407a8eda9599282efeb717410e2028f2 *R/bd.R
403f6c3609b1b82650665a0a04eeba87 *R/bmPlot.R
97f2cdd07a3595bb221fe3e8618e23c6 *R/branching.diffusion.R
6e14486536afe403240be0ac32bb55e3 *R/brownie.lite.R
ffdd534a6c94d07b4ce58c7ae23c3a12 *R/brownieREML.R
23041be17a8649500816f415c7be2308 *R/collapseTree.R
1001c3a0359677faf03cd3912d5aacd5 *R/compare.chronograms.R
be284dbd922c8e640b06f22aeea30eb6 *R/consensus.edges.R
68a21244d41c2e62759f84fdef32eb10 *R/contMap.R
6d0a63f22957b3ac4ff7e52bc54d1dd2 *R/cophylo.R
ece9154811c9dafff59917deb9acab13 *R/cospeciation.R
3792931067053330a2d723861a43c40f *R/densityMap.R
41e1a34a8e376e9811df795dd5c7552e *R/densityTree.R
285cba23251473079aca3438e0f2ae00 *R/dotTree.R
69b6d14462faeaf904236868259f6e7c *R/drop.tip.simmap.R
00b980b1a6af6880330cfb00cb9b2282 *R/estDiversity.R
1c597d646176b3277a8b0b231f791ca2 *R/evol.rate.mcmc.R
868cab31eaeca1f3cf672e02fa12367a *R/evol.vcv.R
7fce29a2380742242da78258aebc5835 *R/evolvcv.lite.R
164c5aba763c4823fae1a2747cbbdde8 *R/exhaustiveMP.R
0c94431c709b011b1a19a5238b7a3352 *R/export.as.xml.R
9350aabf7ef37f0106accab137eca290 *R/fancyTree.R
3de0353dd6102f6b93a69edbabd14a30 *R/fastAnc.R
1fb690b492fa00b02e86eaf49b5e48b6 *R/fastBM.R
fd4043fe4370b493b19344fc752bcdf5 *R/fitBayes.R
350a3fce5519e4b03cb5acfc01d2c55d *R/fitDiversityModel.R
236eb656a503c8c6cef2b6c476f9f647 *R/fitMk.R
2e794826087ce98675c88ac57b1afa53 *R/fitPagel.R
14efc2d387e2360f9f37721f7a6b77a6 *R/locate.fossil.R
36eed593b2ed2f89c1dfdb8d37bc047d *R/locate.yeti.R
e41cd28e97c6101b3e0c7c4b955abb1a *R/ls.consensus.R
bacc73c39e4d2b4149bd1795531aa6f9 *R/ltt.R
e6f7e2cc99e35ae5f094ce4e2c5fe841 *R/ltt95.R
07c37a4c09941dfa8088c4eb91ef5c4a *R/make.era.map.R
19ae2b9108863abe6fe1bd661a69e19e *R/make.simmap.R
b535cd4a22f407601477a0c787a8f869 *R/map.overlap.R
746ca01035baf52f94704cb916bd8e20 *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
b0a7ce4dbb6e426d2aa1315c30ea9ce8 *R/multiRF.R
861e9b7abaf0ae0ec1c712b1176b2bc6 *R/optim.phylo.ls.R
4251fbfa33b24cedd655a575878bee3a *R/paintSubTree.R
e9e01ad2df33334424ddb0453603c336 *R/pbtree.R
6f36e57da63ae80801b696355963c55d *R/pgls.Ives.R
0a3f71e1a3714c0fc5ed5fce53b9aa54 *R/phenogram.R
93cdbb83a29c009a6381af932cb78b87 *R/phyl.RMA.R
3cbec3ddb43718bf824e1b4b5b1bb92b *R/phyl.cca.R
bd4da491297a9551360b5b0f361bbee1 *R/phyl.pairedttest.R
f489cc46a3084533493e7d2dff93472e *R/phyl.pca.R
17d0e8f613fafc8cf7e0a719120dd9cd *R/phyl.resid.R
9265547de9fc901a0e0af7d58706b142 *R/phylANOVA.R
5f9b57848acd0490c9c4842be5d1e1be *R/phylo.heatmap.R
f3265e161476c0c2640a416e22ca388e *R/phylo.to.map.R
153f94b487776dcbe9423b5507b324a0 *R/phylomorphospace.R
808ecaff96a106ea4656b73469c0324e *R/phylomorphospace3d.R
88e81eb2a2b9844e2694fb586524bfd8 *R/phylosig.R
e33f55e3b5f7397f8c40678aee95569a *R/plotBranchbyTrait.R
6aed422c3ef54dd7180e45bd400245f0 *R/plotSimmap.R
a58e6ab65dca2e69dde3266c9d05e51e *R/plotTree.errorbars.R
381d0fdc229e41ed1ba89d9b6c0d7da5 *R/plotTree.wBars.R
e7561a8816b5c347add2e44718311157 *R/ratebystate.R
7261be7cfca4d3837fede235a02c66d7 *R/ratebytree.R
5f808f6878e031af61d4042b0dcbcb5e *R/rateshift.R
10aa4276f62187281eaa23d509df6f58 *R/read.newick.R
8d676810a59c68f20f5fc37bfe9b841a *R/read.simmap.R
12ccdaef8c21e222bfbe7f946de5514b *R/rerootingMethod.R
ba26eefe861f14105c46ee13652c5b66 *R/resolveNodes.R
9bb4ea1e15eaeba8b3ea0f4ffc3c9255 *R/roundPhylogram.R
d8a6bb753f6779a1dd49e769b18775a0 *R/sim.corrs.R
d697c6e91f3041682671cb5f8db8818d *R/sim.history.R
f83f44a29df59f5ff489e0120c4c328b *R/sim.rates.R
5ae6a2a091d203ecc04ad6081e11293d *R/skewers.R
606ad5a902660277dce5f3ef7fed7461 *R/splitplotTree.R
c8bfa07dd3238d97fcaafe5a369e5e89 *R/starTree.R
0567456c325cbac2c305158ffa05df91 *R/strahlerNumber.R
447734ac15b7770e5024af04220dcd1a *R/threshBayes.R
7e547545cd50de19581af1e1c179e967 *R/treeSlice.R
c83cb56994fa6eaa102a870b5d005b08 *R/utilities.R
1b4554bf48441cd340449ea0360bcbb8 *R/write.simmap.R
67b049f3e083513ff41ab9ca2bd940b5 *R/writeAncestors.R
65bf87a538f44806311e8914317b242c *R/writeNexus.R
3ab25de6b1e5d2b15860347db6d973d5 *data/anoletree.rda
0eb3bef3466bd6d264c669571621c2d1 *inst/CITATION
a42234316b9c07cea61f6dc37aa855e1 *man/add.arrow.Rd
77fe3499abcd34af02fc571931597b79 *man/add.color.bar.Rd
4c61574818477466c1e568cc917535b5 *man/add.everywhere.Rd
0dad38ab36dfc6171120c7a224f7532a *man/add.random.Rd
54b5cce6e4c6f9cdcce89a82bdc7da36 *man/add.simmap.legend.Rd
107516e7cc218b2ac851551a122b720d *man/add.species.to.genus.Rd
fa8cb1ee2a166a10032c51b707478324 *man/aic.w.Rd
ddbaa1f624e77bd0b5c8be0fb07b407a *man/allFurcTrees.Rd
85936328bf79f82b91cf3bc471435be1 *man/anc.Bayes.Rd
f939ffa214d08b6d1b92a2f90ea5112a *man/anc.ML.Rd
42b510e0e3d422a7f6444f6714ccb36b *man/anc.trend.Rd
9ac79b1dc9310be258548c6e8920fa2a *man/ancThresh.Rd
9ee43b3984459b93625cb3171605821e *man/anoletree.Rd
5401106ec92900c68ed09e53a5b07d3c *man/applyBranchLengths.Rd
9438d11405f55849b8b13173e0aa677f *man/as.multiPhylo.Rd
3e59cf4772028c0afc738956ca2d9d72 *man/ave.rates.Rd
68be8a968b68910972815c5e610818cd *man/averageTree.Rd
4c391c3b9f17f1a0e0c8c2bd04da9048 *man/bd.Rd
af6f23faf7f0ecb3c466875b900379aa *man/bind.tip.Rd
03055c413de00dafb1073b21281d165a *man/bind.tree.simmap.Rd
cc14a92f9406c1cd8e2ad5204bdd226f *man/bmPlot.Rd
af944211704ace15627339af01988499 *man/branching.diffusion.Rd
824377a34400a62869f6a0ed1d86c52d *man/brownie.lite.Rd
f2d030a482fbf47b134a82612b7817e7 *man/brownieREML.Rd
abeb701a5213e15d9e24816563654492 *man/cladelabels.Rd
0f1e1addf1457ffa1a6a2241b516f2aa *man/collapse.to.star.Rd
d860a425bca88fdba3651f80d5100fee *man/collapseTree.Rd
987d8540202b55e971529542f2b12f5a *man/compare.chronograms.Rd
8134029f04090ff83a7a8d4b3b92da56 *man/consensus.edges.Rd
c26dcd996d2c5d86a8cfb43206921fe4 *man/contMap.Rd
b92e5d59971e2644948b3144e42ca05e *man/cophylo.Rd
317b82dc60100850b36380cbc1bc0414 *man/cospeciation.Rd
1c53948802e8f694b01440e03a198dbb *man/countSimmap.Rd
44b463769214182e756294911bf65ff9 *man/density.multiSimmap.Rd
473862be45bc652c0389ec2c0754f473 *man/densityMap.Rd
e37396af91b60fbd5d4761e632d6d230 *man/densityTree.Rd
ae007bd9a1d1e3eb349e739bd3fd5bbc *man/describe.simmap.Rd
22a091511c91853a24929280592e3151 *man/di2multi.simmap.Rd
fa1a86c9c436d6a78de5a5762d0f81fe *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
925393ffab907bc5693992d93bddcbbb *man/evol.rate.mcmc.Rd
540e9f4aa0ce27faeed1f4a7945749c1 *man/evol.vcv.Rd
766f946ebf98e312547c576d5412d0d2 *man/evolvcv.lite.Rd
e93d92ff11f1f830540896a8129603e8 *man/exhaustiveMP.Rd
45729cc9dfdd0f4f158b82aba2e35797 *man/expand.clade.Rd
22001f60bdc699b30ab0250e61eb879d *man/expm.Rd
24fbe29405d7d63b20381cbe63c3685f *man/export.as.xml.Rd
60822881cc6b40b5d764d1fe26bfefba *man/fancyTree.Rd
a175a7386cec6984d78031de56350d55 *man/fastAnc.Rd
4b4c57d045a77d6038356712712083d6 *man/fastBM.Rd
8054a9de57c13610d28e3e832b9aea91 *man/fastMRCA.Rd
2aecfd3a3e42ff5a6187e142af8bfe90 *man/findMRCA.Rd
9d730cf1622b491b3712bdd3d857f8cb *man/fit.bd.Rd
49ed43ad08cbd76688cea935958535d2 *man/fitBayes.Rd
fd6dfbcd9836f3d550d058f2946c4fc9 *man/fitDiversityModel.Rd
b4eb17f4a35656aaf0b7d5c0b85cce84 *man/fitMk.Rd
bea2ad13789c51fcb577038d9319a4aa *man/fitPagel.Rd
e292601c1c799d10f98b7b34608592e2 *man/force.ultrametric.Rd
0fb00f64019835a6cf7d510df62c1cc1 *man/gammatest.Rd
88ad5870c14512c74ed6c88688cb9367 *man/genSeq.Rd
ce2d83c87228d4d36e5d3793841f9968 *man/geo.legend.Rd
5a4045e1e1a45a93828388e5619da248 *man/get.treepos.Rd
6ca10ad3d8ae7823a3ebebeaaa903a26 *man/getCladesofSize.Rd
c0c1d5e26dc66625ca962d1b1a9e3fb1 *man/getDescendants.Rd
0f66e89c8d5de9f7906cfc629dbde129 *man/getExtant.Rd
bb47201dbb86e33244d79ed06b53bace *man/getSisters.Rd
50941930ec6026a6fb9b0020a7e9e3e3 *man/getStates.Rd
8b8dc22bbb4f27f8643c92132893220f *man/labelnodes.Rd
882bbf621c5c8e6c0922c21cf5308d67 *man/ladderize.simmap.Rd
c2a04357ebedc51867f98d3e24ef0d66 *man/lambda.transform.Rd
633387cd5519193a2e183285e7e4fb79 *man/likMlambda.Rd
6f8d9fe13ce8560d4e1dcfcabceb0cd9 *man/linklabels.Rd
3149b5b7a824f424f799ab3e522d6850 *man/locate.fossil.Rd
d274dca0554874d3a3476906e281093a *man/locate.yeti.Rd
a09a3cd5616557bd09ba88e990addd40 *man/ls.tree.Rd
164517a355a60693d56b4ba8e52ccb18 *man/ltt.Rd
c8a084cfa70fc7ac4d490f417464f366 *man/ltt95.Rd
6d740cef8fb4052ed7f5bbcfa2a04ff5 *man/make.era.map.Rd
96d5c8d0131da1b48028859c2a466ac2 *man/make.simmap.Rd
be50a7f1d10a39f31540435c910608f4 *man/map.overlap.Rd
24dd9c40965fe5929fc5f43392ff7111 *man/map.to.singleton.Rd
7bc0bf4a400013d8506a144b98663d09 *man/mapped.states.Rd
f9c95d7c4652d4817305122c51ceb3ce *man/markChanges.Rd
9327c748a5fc71e19d97b336959cea8e *man/matchNodes.Rd
e566946585ec51d6df130403eac7b996 *man/mergeMappedStates.Rd
b0292289c5c0bdea68bd39cba4e51fcb *man/midpoint.root.Rd
f440b9606b045b5ccf5466afe4c30ca2 *man/minRotate.Rd
d3a51d0c0191486546c6c67e9456b0a5 *man/minSplit.Rd
434ad8f86e0b41f3078f91a33ab2370d *man/modified.Grafen.Rd
8fd67c7bee19ff3ec51d70d15811f15a *man/mrp.supertree.Rd
73a2a40506cc9e62da97a20c7e74a1b8 *man/multi.mantel.Rd
5caa16465c09c6c2840f712fab95d08e *man/multiC.Rd
3c941d1cbd831b77c07e82845a0bff29 *man/multiRF.Rd
771381f4158bb262fd0a9c7df8c33508 *man/nodeHeights.Rd
b8061afef967e33d70e5646761eea00e *man/nodelabels.cophylo.Rd
ee79b7944822d46d87eaf91cae11d477 *man/optim.phylo.ls.Rd
63d57fedac44429aea25ebf22f53c772 *man/orderMappedEdge.Rd
342aa020929fb830ffbfb869be45a526 *man/paintSubTree.Rd
4aec9a1fefe5f96ac6652a0e5fcc63eb *man/paste.tree.Rd
f5c03b1a3eeba0ee10d31e06c0dbae64 *man/pbtree.Rd
15b7eb28339e9434bd8fcf3e493d943d *man/pgls.Ives.Rd
735e181c4a63b8a7888a137a6f08c163 *man/phenogram.Rd
f333aaf7288b2a3a7bba9fdb23c41f74 *man/phyl.RMA.Rd
3d17ac3e055a980bca3c14b258fa47ec *man/phyl.cca.Rd
804ec3000422b5f2e1f30d80f114b8b2 *man/phyl.pairedttest.Rd
ce49878deb460e417a875e63b45e25b7 *man/phyl.pca.Rd
38cdeda5e6c9e2cc9a3131ef1ee321ba *man/phyl.resid.Rd
2f54dd0b2b5ce5d36193c97b1a611921 *man/phyl.vcv.Rd
31064c35f9f1f368c0bd38c3e2a009dd *man/phylANOVA.Rd
b816f2e3fac3e259d0f1f57baf626678 *man/phylo.heatmap.Rd
a5d27821336d48d6dc44595026f0994e *man/phylo.to.map.Rd
929da1bd71e71af5ce25243d9516c14e *man/phylo.toBackbone.Rd
3a1b3861ce38f29feca5081c7acc4908 *man/phyloDesign.Rd
a1f7f9d8cdd43c5872156128d1596294 *man/phylomorphospace.Rd
b82dd727b2a6717a6fefab297a491ab3 *man/phylomorphospace3d.Rd
18a569e5bf535e689d85ded39eb166a6 *man/phylosig.Rd
b1215539c6b3d560e8b0782d290197cc *man/phytools-package.Rd
aecc4ccca42174f15c6280dbb5aa13fe *man/plot.backbonePhylo.Rd
674746269036e9bf5645e31bab29207e *man/plotBranchbyTrait.Rd
cf7911a80ce4148ea610f1b9105a104f *man/plotSimmap.Rd
b36ef27480457d0dc3f32c490e997a7d *man/plotThresh.Rd
7abaec7aa366e41647df0bf3073a36ef *man/plotTree.Rd
028fb0ca902c0cf9ffcdc47ad85da56e *man/plotTree.errorbars.Rd
41e493dcd031566263d3208834f882b8 *man/plotTree.wBars.Rd
9c8297109561037f067dd7d469f12acb *man/posterior.evolrate.Rd
9f409f4328ac4802d1700eec2233361b *man/posthoc.Rd
4bfa72a7ac47c3e185164f8c35dd5e13 *man/print.backbonePhylo.Rd
290d33851c41fa14071fbf4a03fdab8c *man/ratebystate.Rd
ae9589a66cf69dfa1cae3434abcb7082 *man/ratebytree.Rd
1ec56f1e5610a932300c356e7b1242d1 *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
3af87269dc3bca7472fdba1c179cbdba *man/reroot.Rd
a78caf77645c2aee01642551aa4cffab *man/rerootingMethod.Rd
7fb2034ee0d06ddd28baf54a19a5df31 *man/rescaleSimmap.Rd
e136bc897dd8258ec0038da1fda579aa *man/resolveNode.Rd
e1d563fcfc4085113c43b6191046463f *man/rotateNodes.Rd
62ccf8e731d76584828667850f3e4d5c *man/roundBranches.Rd
113dfd2e24ee88ec929f865a41b014ee *man/roundPhylogram.Rd
582c0539a965268cb3783ec1cfc69341 *man/rstate.Rd
56d1e0ab7594a041e03a96cf512b7c56 *man/sampleFrom.Rd
4ff599d27cce8dd9f6a61b1b83167c36 *man/setMap.Rd
cdb9901fa0e51ebb9ede03b79d569d43 *man/sim.corrs.Rd
41192c407722bf7018c3b90750b84e1a *man/sim.history.Rd
d4619609a325632ef2c834f485c505b0 *man/sim.ratebystate.Rd
246a5aaa7168a0ff7cc9168d4395d4b5 *man/sim.rates.Rd
e0716598bfe6497b75aac3a5de7d1d1a *man/skewers.Rd
8afbcc3a0809d9abc1337996402b395f *man/splitEdgeColor.Rd
f0b7c55fe94d87a63fcc473557ba356c *man/splitTree.Rd
c4c25d51cb5afc0a3ca9e8c50aa4f8a5 *man/splitplotTree.Rd
e3ebd622b81458023c71dc8b846bc8bc *man/starTree.Rd
e3cb564ff8ac467e211b63893e5bd8ab *man/strahlerNumber.Rd
0b0799df20ba1704886813ac53e62843 *man/threshBayes.Rd
4c943bdc70f92faf2626a05b4dd5737a *man/threshDIC.Rd
1f469e57b425d3d1368c1b5a20f6677e *man/threshState.Rd
75b7d2745c01bd834c7b1b8523b9859e *man/to.matrix.Rd
fd4b7e0ad5c598fbc1d33cd733a49164 *man/treeSlice.Rd
4f2a39ca94120586ad59463cc247bf83 *man/untangle.Rd
8698e88dd7441c86162d8ab4eddf3439 *man/vcvPhylo.Rd
58a800384eddd90f48ea26c6f515c1fb *man/write.simmap.Rd
9ae66799d04b136a287a1038d6f70fd7 *man/writeAncestors.Rd
81b95726f7c7c8b1308d35fc5a9e9d2e *man/writeNexus.Rd
