1171494595c7a39b8a76e820bbc0bed8 *DESCRIPTION
08324d49454acb64188cf62623a1e0cb *NAMESPACE
8f41acffe68735aa7449b5e66a9812b1 *R/add.everywhere.R
34423edfd64ed1b237c63a0364288bdf *R/add.random.R
17eb477b7b99dbdf228b0694b6ed01f4 *R/add.species.to.genus.R
f0df86c98d2fd0c6d76f49ca3172d129 *R/allFurcTrees.R
a6af1ca434dee085fa30425844755b7a *R/anc.Bayes.R
3c8609f74444d2799e73e133e71cdc4b *R/anc.ML.R
4ea5611b8e0354bd06dabbc878dcd41a *R/anc.trend.R
f78777b0203972d9edf8deef4579d268 *R/ancThresh.R
a6e7c12432775c0db331677fb7161d07 *R/backbonePhylo.R
2b89c2213576296b322a09aa9c9e0dcb *R/bmPlot.R
0d03bcd21044ddeee058865f32156f3d *R/branching.diffusion.R
2ad5f3aa5021c7cc67269d6cb21e4ffd *R/brownie.lite.R
6c3bf1e39384f5e24d711ec7ac0d0a2c *R/brownieREML.R
fe5f6324e28faf554ce2eb9fb9787ea0 *R/contMap.R
de2967fe371b7ed8797c822f2272aecf *R/densityMap.R
b707fc247b889daacea864a75e0915ed *R/drop.tip.simmap.R
bd862cef57b58a4221f0c761d4284d88 *R/estDiversity.R
0919b8e73cf8c0ed1c84a1033cc933a5 *R/evol.rate.mcmc.R
3d4680366f8b1b63b8a196f7372ca299 *R/evol.vcv.R
b645683560ce499323142e5bb8917e3e *R/evolvcv.lite.R
164c5aba763c4823fae1a2747cbbdde8 *R/exhaustiveMP.R
9894f4104c7750ce0613c2794262d447 *R/export.as.xml.R
d884d94280dc89ae0d994fda542b2189 *R/fancyTree.R
b501eb99601bdc68adc0192b4face752 *R/fastAnc.R
de4661e9387e345e11ba6a96f6dfb690 *R/fastBM.R
0d3ae4cfb0e9fb73cf0cddc37d8d0fb7 *R/findMRCA.R
79d5c1bc8b38484815275308c3aa01d5 *R/fitBayes.R
984fab2bf406a04876c19b8d4d6e4ec7 *R/fitDiversityModel.R
845b53ce3f60f6ed7d3728a67da0ecfc *R/getExtant.R
b16b9534c1eb7d1757a070d7c58e5aaa *R/ltt.R
5a03095333cdc6926135e17a06b5718b *R/ltt95.R
429a79ff1742fc3a8f628d441df34710 *R/make.era.map.R
cfc2877bc3d81794be29d6b97bfaa683 *R/make.simmap.R
23b9e915f9fc8b9c46d81c573afbbedc *R/map.overlap.R
467b138389c02b0a6d8e42c8dd2da324 *R/map.to.singleton.R
bf6c23b046ed30ee9e9183582aceb070 *R/mcmcBM.R
659b234e9ff4b00daa511a06f72d53d2 *R/mcmcBM.full.R
9fc1c1054aa693a9ad32044d21e9f8c4 *R/mcmcLambda.R
b040e1eaf64ad302cdbbc1c0cb742cd7 *R/mrp.supertree.R
7e33687b42d9ee02d52ae36834f4c122 *R/multi.mantel.R
33b3968d9f4a82d3faaee75dae4ebdec *R/multiRF.R
af3ee4b2e3a749a9d0040ca6fceb40a5 *R/optim.phylo.ls.R
32cf021867e184c4d17912a931b8d2e5 *R/paintSubTree.R
952ff55370bb3fa70c3351bc342bd473 *R/pbtree.R
0432d301015fb3848dbab54f3740d56e *R/pgls.Ives.R
b4c4bd523ed7b6e4742cf3eacdcc681e *R/phenogram.R
4db055cf75d6a3d2e7cda5a91cafd137 *R/phyl.RMA.R
636d5d590f0c6a7cfafae4f13df2d57e *R/phyl.cca.R
067743180672ac2b90d1e160186fe0de *R/phyl.pairedttest.R
a3b5765e0818b44f0c88a0a99c96f7c4 *R/phyl.pca.R
6eb0e229b575c66b578eb9e3de320e4f *R/phyl.resid.R
61ce28205af41c938d4e0966ef38010a *R/phylANOVA.R
a9ee72f2b8de28580cb11bd664038aa0 *R/phylo.to.map.R
529d2545bd8652c3d81807d26d3d2b4e *R/phylomorphospace.R
e70d8c9491116b2ac107035af05bff71 *R/phylomorphospace3d.R
7e17223f27118288d71aeff1f4843c44 *R/phylosig.R
9ee4cb733268431f46459caba6a1fd7a *R/plotBranchbyTrait.R
0e06d9202faa9cfc88ce68a605a10bf1 *R/plotSimmap.R
eb798ee8249519bd2afc6c132f24a065 *R/ratebystate.R
1c590708fed31ebaba52763d510f25bb *R/rateshift.R
02f63bb9101ed6bf2e655d1d16a86033 *R/read.newick.R
3efb9fb72cf2e6d517750dd34647606c *R/read.simmap.R
70c86da3b51847705f3114ff102e4df2 *R/rerootingMethod.R
54a7286b38ed9310390c726c151a25af *R/roundPhylogram.R
a734b9387333dc2d9a5ece1f8ee06f98 *R/sim.corrs.R
ba0d663181e5969c26c5135138eedf06 *R/sim.history.R
f21071a47bc22c9c76ef3136ff4fe821 *R/sim.rates.R
5ae6a2a091d203ecc04ad6081e11293d *R/skewers.R
81c463a99ba91e04785a4848d2e5d56b *R/splitplotTree.R
c8bfa07dd3238d97fcaafe5a369e5e89 *R/starTree.R
8340c2be787b0b7ac420ff68140d1267 *R/strahlerNumber.R
ae99c9aeb8f0553d3addf1475ea35562 *R/threshBayes.R
a38bac98b4681cee859750b8193a9a9b *R/treeSlice.R
a8b02380b0ee49f4355bc0a9ad4e0e8e *R/utilities.R
7282f87b3143db28b7e982e86d90b6e5 *R/write.simmap.R
8a960b2dfaa3924ae71d485d68ea66b3 *R/writeAncestors.R
c6d9cb0dbedb17c4cc0d4e16032da623 *R/writeNexus.R
93c8e79ef949a21de4bfe83d817c32fb *data/anoletree.rda
0eb3bef3466bd6d264c669571621c2d1 *inst/CITATION
ec77726fbbcab60bca3fba16b672e710 *man/add.color.bar.Rd
8cd659affc487ed1c87684f4af22d6f4 *man/add.everywhere.Rd
418e31bb002eed3a17a689a42bba1f0a *man/add.random.Rd
55a9aabae0482186024bb2dbd7042894 *man/add.simmap.legend.Rd
73fe0c6dcf46053a664b61b3a52ac92f *man/add.species.to.genus.Rd
56ef96a939c1da2260e9a357159ca1b8 *man/allFurcTrees.Rd
78156ebd031cdf762b0eecd398c6d731 *man/anc.Bayes.Rd
514921c714c498a71b109442a8e1281e *man/anc.ML.Rd
89f06bb2de5a7c6ef9a33244d413894a *man/anc.trend.Rd
a64d05be4605456e12c836c877d6d0b6 *man/ancThresh.Rd
c3f15aa8c755d1e29a26270e0c719921 *man/anoletree.Rd
ea777b14c4c81179dba20bdacac83220 *man/applyBranchLengths.Rd
271c19a7c36f14d6a3d95cf15c17b4c4 *man/ave.rates.Rd
c7a9dc675989bad1879f97ce6b72d839 *man/bind.tip.Rd
be9b74c16aa2e5b807d2bc2762ffdae3 *man/bmPlot.Rd
09bece048a76feb211b379e6139ffe97 *man/branching.diffusion.Rd
c13330bd2cea720f9caece9a3b05164c *man/brownie.lite.Rd
b21b76c3d3787cd73da1c6f6283d6cfb *man/brownieREML.Rd
cf2391807768f91b9f19becdaaebd2d4 *man/cladelabels.Rd
97e5990f8b2789fcc27b6058a310c886 *man/collapse.to.star.Rd
358c0386dcb07f18292948bb84cae6a2 *man/contMap.Rd
4c4d9f203ae18b5805942ecf94515c17 *man/countSimmap.Rd
e408b77752ed56ba397ebbb6e73d9a6c *man/densityMap.Rd
77a06a97789d75eff8eb2956dfa2a4ae *man/describe.simmap.Rd
4fc21d57e922618248f629a6a4fd1eef *man/di2multi.simmap.Rd
b487c9bd7fd35fded9b504be04720b13 *man/drop.clade.Rd
598b3da5ec869e9727e409c631d907ed *man/drop.leaves.Rd
50f170ae3ac8fc131156cf3a2e198e59 *man/drop.tip.simmap.Rd
cb411ce7439196294695c1310b45f3f0 *man/estDiversity.Rd
f38a7d4f1a64fe1a97cbb8b8a4886ff9 *man/evol.rate.mcmc.Rd
2d0b00e35015115bf38de3ed6ddd187b *man/evol.vcv.Rd
fb20b784a2e6a8b5132c9dc1fec47f0d *man/evolvcv.lite.Rd
e0d8835c85d1b8c03fad9696682e38f2 *man/exhaustiveMP.Rd
58055ed656d6e86d1dd2e216c83e971e *man/expm.Rd
31c5b8c068ff84be62c141c3cf963d6a *man/export.as.xml.Rd
89b0dee30744fd6363d05e218fbd8851 *man/fancyTree.Rd
962c8406a853f4c5843b0fec1cf4149d *man/fastAnc.Rd
1789096481f8a8b0857a698b4e400b29 *man/fastBM.Rd
d2968b412b8600c8e4008ecad9dda8e9 *man/fastMRCA.Rd
e3ccd18c21589980d10bf8e2cbf9ce9c *man/findMRCA.Rd
ed24dfe4b7441a978351684a245204ee *man/fitBayes.Rd
762119d9f7e0daa449e37731b54ff6a8 *man/fitDiversityModel.Rd
399ce8f145714e16bf2140c8c1c2e826 *man/gammatest.Rd
3ddc9be1fc573ee8be3d8721df44c854 *man/genSeq.Rd
5526e2450e0f0784c9142509ed5e0b56 *man/getCladesofSize.Rd
9e3851d3318a20a7556e1e97b6c1cce4 *man/getDescendants.Rd
1e0c81dc5b4169a68828c7e6e07a714b *man/getExtant.Rd
28ea31077f4deaceb4435e0bff387ba6 *man/getSisters.Rd
7990607df7e27b5abfcb3b3f3933ef11 *man/getStates.Rd
9dd87d88f17da7d2d4b4ecec9d353043 *man/lambda.transform.Rd
fe9a9a76cd0531668fad334181fedea9 *man/likMlambda.Rd
3e82e41fa5770ec7fc4214a008f148fd *man/ls.tree.Rd
87e0268d5d46dbb80d32c1e4f35f86ab *man/ltt.Rd
bf2ac0ea6ede63069881da5305131cfb *man/ltt95.Rd
56614733ddcbbb9a9de8e38645fb7d59 *man/make.era.map.Rd
aae86ee706ba77f950f5d2b948eb5ed1 *man/make.simmap.Rd
c9a96a78b07076a8d752910470d196a2 *man/map.overlap.Rd
fa1ad00dd05e5acd305fdcc5dab4faf7 *man/map.to.singleton.Rd
8cd9aadd82908d074d3d62acb457b1bd *man/matchNodes.Rd
a3bbb218c0230eb8be0eaa9d5aabb139 *man/mergeMappedStates.Rd
93e7b59862521d72f35a54f2be7b3619 *man/midpoint.root.Rd
b0ff2fdf11c1fb0044739612bc38c917 *man/minRotate.Rd
5eae92d74e381d59b572629138d9f803 *man/minSplit.Rd
458c6557e76da5239e165a8ed15210ad *man/mrp.supertree.Rd
9dab37745b43bebceda793a36c257c44 *man/multi.mantel.Rd
258317bbd7c01316d28b843b24daacba *man/multiC.Rd
35b03386697acfd98b825131d32ca16e *man/multiRF.Rd
6cd73556390217fff031d37c8a394fe7 *man/nodeHeights.Rd
75e285f060c4d1ffb60d561d49f7a2b4 *man/optim.phylo.ls.Rd
85272eebb2bd1404fe8784395b719a1e *man/orderMappedEdge.Rd
ec68d41500027bce18ab7c644f92b695 *man/paintSubTree.Rd
8a879df9dafcf215d94307752af00e25 *man/paste.tree.Rd
d28292e9b29295bbfc883deb399a05c7 *man/pbtree.Rd
2d9761aa536e62bf1a40a51236ab51e3 *man/pgls.Ives.Rd
828f9dc6a3036c3ca9f04cd7f6dca31b *man/phenogram.Rd
023f11d98a022359c1c917fab3e64b1a *man/phyl.RMA.Rd
f2a7fa4fc839708ea7cd2828b3eee5d6 *man/phyl.cca.Rd
3d832b1c1e5a3738b38d30a968b41c1c *man/phyl.pairedttest.Rd
cf8a35308a358545576f35bc1bd1c05c *man/phyl.pca.Rd
9ca22aa9fbb4ec750a48148925213ceb *man/phyl.resid.Rd
a4593bf88863e5ab7f7b38e9642f0df3 *man/phyl.vcv.Rd
765a679deff76405a430e9d06e7a8211 *man/phylANOVA.Rd
6066a8da4ab2dc612c825ee86ef17cee *man/phylo.to.map.Rd
2c8a96a4ce0ac1a697a2d50ead2d8cdd *man/phylo.toBackbone.Rd
952632ae04f5a456c1b7045a9afc6c6c *man/phyloDesign.Rd
84cc2419440c72089894ec0c4e6d82bb *man/phylomorphospace.Rd
93c529d5bc09c7a6f4b54de6f23582cf *man/phylomorphospace3d.Rd
256d8600e921388f4c4d997038e34c64 *man/phylosig.Rd
0a6373513621bc26c8573db69d7bba54 *man/phytools-package.Rd
f32977652f030b5f90149229af112e1e *man/plot.backbonePhylo.Rd
b850a4c63c872b6332a29e894ce63469 *man/plotBranchbyTrait.Rd
1d94b332ac099f92ca7187cd0c0b7d97 *man/plotSimmap.Rd
99829a0a4064a4da2925fff47fa2d4c6 *man/plotThresh.Rd
a310d77a5906c2d4baa360c05cb14a6f *man/plotTree.Rd
9c8297109561037f067dd7d469f12acb *man/posterior.evolrate.Rd
3640042ddf4586cdfd5c46b19ef5469a *man/print.backbonePhylo.Rd
f1e7fb49afcbb107963bfb564e9b2a42 *man/ratebystate.Rd
50cf0534083ea37e0563b49ae3f253ab *man/rateshift.Rd
949bf73091e93a276e94b5113fc4c839 *man/read.newick.Rd
f4414980d69db5b1724dfd8d46cd1adf *man/read.simmap.Rd
3933c71d3f9dd79db4dfaf40c2496356 *man/reorder.backbonePhylo.Rd
06a9d0985e7ed90a6d0c3f6abc2f4553 *man/reorderSimmap.Rd
3b61f786fa38661019bca4108e32d2c8 *man/repPhylo.Rd
04c5fa39043ed2988168d2db2441b1f7 *man/reroot.Rd
743fdc04ce309029b1d54885c590e80c *man/rerootingMethod.Rd
a9bd507ac70c35c02224fec4cab27de5 *man/rescaleSimmap.Rd
f022e7f0bf06903fc78194ee70af9198 *man/rotateNodes.Rd
70a72b27cfccf685aaca42e65799aa04 *man/roundBranches.Rd
ba1fb42069fbb5d893db3732bc28ebdd *man/roundPhylogram.Rd
0b1ccbcfbb14fa214e973f95ad5ddf93 *man/rstate.Rd
bf5a2cb9ba17f6a012194fe6a0ea7302 *man/sampleFrom.Rd
eea0368c67af7475f9b0ae5139e99795 *man/sim.corrs.Rd
aead504eebc71bd7c18a6a548f6cb2b4 *man/sim.history.Rd
65c096cb276fe981f5c746175de1df87 *man/sim.ratebystate.Rd
db26d4c655cb05940833712d961e36f1 *man/sim.rates.Rd
70b3282fe0561c12d3b899a4e1341a98 *man/skewers.Rd
4205324390fdd9f9da606cecd035111b *man/splitTree.Rd
9f8c7e71ef966ab29b7f4237ec21bff7 *man/splitplotTree.Rd
65eb71968523d6ccb83858c16a32e914 *man/starTree.Rd
6dd8274f5e00f48c66b30f2123bc877a *man/strahlerNumber.Rd
3128b3564cde4fc2d58a0e554177e177 *man/threshBayes.Rd
588791d27e2edd77fa74c1dca888d811 *man/threshDIC.Rd
9b3c080a406f7a94e433e8b50035329b *man/threshState.Rd
654a1bed8d43f1233353d1f0e9798ec8 *man/to.matrix.Rd
3ff793e732f500f77682c18a64afff8d *man/treeSlice.Rd
4b5826cdd32ae76cdec94433d60b9dcd *man/untangle.Rd
53addf42176b56b2cc4faf8df95d536c *man/vcvPhylo.Rd
7b8c5bddf98303598dc6ce52a598610b *man/write.simmap.Rd
bfc639c71b7cb2519b5fadb94d3f6eb0 *man/writeAncestors.Rd
4b852e9e82198281126f9440ca804fed *man/writeNexus.Rd
