39722d935ddc1bf5613a55df0ad33df8 *DESCRIPTION
c03b07815f6ac8b310185ecf8cfbde35 *NAMESPACE
8f41acffe68735aa7449b5e66a9812b1 *R/add.everywhere.R
34423edfd64ed1b237c63a0364288bdf *R/add.random.R
f0df86c98d2fd0c6d76f49ca3172d129 *R/allFurcTrees.R
9e3fa7bb801b628a7026052364234602 *R/anc.Bayes.R
3c8609f74444d2799e73e133e71cdc4b *R/anc.ML.R
a54afd1cc9c251f5e00a5e8efc5ca924 *R/anc.trend.R
3ce097ddf9ce3d9e2eb38dd981baa22e *R/ancThresh.R
cbc7784cba23e6b20efe0f2d21e1de3c *R/bmPlot.R
0676ff6e0a9c20313ef37088dcc65a63 *R/branching.diffusion.R
b95f8c330bf17c808ffbd2304da73ea0 *R/brownie.lite.R
6c3bf1e39384f5e24d711ec7ac0d0a2c *R/brownieREML.R
47af3970ab6fbdb59561b469e13bb3dc *R/contMap.R
1b57f07bc4027e5c806a7fd5706ad0eb *R/densityMap.R
b707fc247b889daacea864a75e0915ed *R/drop.tip.simmap.R
bd862cef57b58a4221f0c761d4284d88 *R/estDiversity.R
7469de53938ca9c617c767bc7ad5b807 *R/evol.rate.mcmc.R
c8b2499580977bb323ad9e009fdeb9d9 *R/evol.vcv.R
b645683560ce499323142e5bb8917e3e *R/evolvcv.lite.R
164c5aba763c4823fae1a2747cbbdde8 *R/exhaustiveMP.R
9894f4104c7750ce0613c2794262d447 *R/export.as.xml.R
0427bdce4949386604f62e1fcc976231 *R/fancyTree.R
b501eb99601bdc68adc0192b4face752 *R/fastAnc.R
bfe9d45e7a126e26d4ea0c10e7851350 *R/fastBM.R
0d3ae4cfb0e9fb73cf0cddc37d8d0fb7 *R/findMRCA.R
79d5c1bc8b38484815275308c3aa01d5 *R/fitBayes.R
984fab2bf406a04876c19b8d4d6e4ec7 *R/fitDiversityModel.R
845b53ce3f60f6ed7d3728a67da0ecfc *R/getExtant.R
1dd29274a867dc1643a706f932bb1c82 *R/ltt.R
f7087031d627e16e1c82a5d57ef621d9 *R/ltt95.R
1a57f7ae8dcf530cbda30b282d513aa0 *R/make.era.map.R
cfc2877bc3d81794be29d6b97bfaa683 *R/make.simmap.R
23b9e915f9fc8b9c46d81c573afbbedc *R/map.overlap.R
bf6c23b046ed30ee9e9183582aceb070 *R/mcmcBM.R
659b234e9ff4b00daa511a06f72d53d2 *R/mcmcBM.full.R
9fc1c1054aa693a9ad32044d21e9f8c4 *R/mcmcLambda.R
b040e1eaf64ad302cdbbc1c0cb742cd7 *R/mrp.supertree.R
7e33687b42d9ee02d52ae36834f4c122 *R/multi.mantel.R
af3ee4b2e3a749a9d0040ca6fceb40a5 *R/optim.phylo.ls.R
39dcfe7cb658f1d4cf9ad3f8fb0fbd0d *R/paintSubTree.R
4775c63959c4bc43104285b6b4503ef4 *R/pbtree.R
ab294d8c9b023fe314930627be675030 *R/pgls.Ives.R
3c6be712d3b1142dc73ad6ab7d41beb4 *R/phenogram.R
4db055cf75d6a3d2e7cda5a91cafd137 *R/phyl.RMA.R
d98d7bec0847aa686ef9b37b044489bb *R/phyl.cca.R
067743180672ac2b90d1e160186fe0de *R/phyl.pairedttest.R
c9f68d7c48ed3961941c58d5059404e3 *R/phyl.pca.R
6eb0e229b575c66b578eb9e3de320e4f *R/phyl.resid.R
c1aaeb796e42be5177ecb36c5a6df15c *R/phylANOVA.R
3cdc3672565ca5e32043fc57c4ce55be *R/phylomorphospace.R
02f3c8bae14e614dc7dda0555ecd32e8 *R/phylomorphospace3d.R
7e17223f27118288d71aeff1f4843c44 *R/phylosig.R
29743a26462613241deeeceef4aa79e6 *R/plotBranchbyTrait.R
d85d4a3f9917e32e63682449467108c8 *R/plotSimmap.R
a6ad0505ea4dc71d375cdda3b17e7017 *R/plotTree.R
eb798ee8249519bd2afc6c132f24a065 *R/ratebystate.R
02f63bb9101ed6bf2e655d1d16a86033 *R/read.newick.R
3efb9fb72cf2e6d517750dd34647606c *R/read.simmap.R
70c86da3b51847705f3114ff102e4df2 *R/rerootingMethod.R
afe6e31be39046604a479f8180ddb100 *R/sampleFrom.R
a734b9387333dc2d9a5ece1f8ee06f98 *R/sim.corrs.R
93eadaa496ee4f08c105476ffdac92aa *R/sim.history.R
f21071a47bc22c9c76ef3136ff4fe821 *R/sim.rates.R
81c463a99ba91e04785a4848d2e5d56b *R/splitplotTree.R
c8bfa07dd3238d97fcaafe5a369e5e89 *R/starTree.R
294b44455f046ca307d1e315be199161 *R/strahlerNumber.R
ae99c9aeb8f0553d3addf1475ea35562 *R/threshBayes.R
a38bac98b4681cee859750b8193a9a9b *R/treeSlice.R
187bb73de129730e964387576858a5c4 *R/utilities.R
c6fdcd385bd2cb7778a9afb90465ef02 *R/vcvPhylo.R
7282f87b3143db28b7e982e86d90b6e5 *R/write.simmap.R
8a960b2dfaa3924ae71d485d68ea66b3 *R/writeAncestors.R
c6d9cb0dbedb17c4cc0d4e16032da623 *R/writeNexus.R
b882d12a50b9f13670b5c4c3c8277353 *R/xkcdTree.R
7d2e91dbd4b3232a312d1e1a45e3794b *data/anoletree.rda
0eb3bef3466bd6d264c669571621c2d1 *inst/CITATION
6a009acd5e740471d54e69af6cc459f8 *man/add.color.bar.Rd
8cd659affc487ed1c87684f4af22d6f4 *man/add.everywhere.Rd
418e31bb002eed3a17a689a42bba1f0a *man/add.random.Rd
025b97f5ea2b9e92786c634b1e9095ad *man/add.simmap.legend.Rd
56ef96a939c1da2260e9a357159ca1b8 *man/allFurcTrees.Rd
3c97aada2b9d26a9b0e5ce758f73a0d8 *man/anc.Bayes.Rd
2cc3324753f95a908e7ea7556101074a *man/anc.ML.Rd
688bd6ddda1d0868d5fc1c99aeabf913 *man/anc.trend.Rd
878a754a7ae355b5e03d42d63528af32 *man/ancThresh.Rd
270aa878ffa2155d4b88c8597560e5ee *man/anoletree.Rd
ea777b14c4c81179dba20bdacac83220 *man/applyBranchLengths.Rd
271c19a7c36f14d6a3d95cf15c17b4c4 *man/ave.rates.Rd
c7a9dc675989bad1879f97ce6b72d839 *man/bind.tip.Rd
6e2baa93f4b1cbf0e99533512943f138 *man/bmPlot.Rd
09bece048a76feb211b379e6139ffe97 *man/branching.diffusion.Rd
43e206a2700dcd0f8b400dc0629adf46 *man/brownie.lite.Rd
b21b76c3d3787cd73da1c6f6283d6cfb *man/brownieREML.Rd
97e5990f8b2789fcc27b6058a310c886 *man/collapse.to.star.Rd
ed54ec43bb442ef956dda90659dee706 *man/contMap.Rd
4c4d9f203ae18b5805942ecf94515c17 *man/countSimmap.Rd
730131ceaf8bd54735236848c5518a59 *man/densityMap.Rd
77a06a97789d75eff8eb2956dfa2a4ae *man/describe.simmap.Rd
b487c9bd7fd35fded9b504be04720b13 *man/drop.clade.Rd
50f170ae3ac8fc131156cf3a2e198e59 *man/drop.tip.simmap.Rd
cb411ce7439196294695c1310b45f3f0 *man/estDiversity.Rd
f38a7d4f1a64fe1a97cbb8b8a4886ff9 *man/evol.rate.mcmc.Rd
ef3d9f9f42301f909283b5a2a16a2379 *man/evol.vcv.Rd
fb20b784a2e6a8b5132c9dc1fec47f0d *man/evolvcv.lite.Rd
e0d8835c85d1b8c03fad9696682e38f2 *man/exhaustiveMP.Rd
58055ed656d6e86d1dd2e216c83e971e *man/expm.Rd
31c5b8c068ff84be62c141c3cf963d6a *man/export.as.xml.Rd
c2a18240632e20a17d8d39825c6536fc *man/fancyTree.Rd
0a1755fceb23ccbc24f91aaec79d8104 *man/fastAnc.Rd
c314b680a328c56796c2a06731e7f445 *man/fastBM.Rd
fb6f80835997cf23124484ffd5b45219 *man/fastMRCA.Rd
e3ccd18c21589980d10bf8e2cbf9ce9c *man/findMRCA.Rd
ed24dfe4b7441a978351684a245204ee *man/fitBayes.Rd
762119d9f7e0daa449e37731b54ff6a8 *man/fitDiversityModel.Rd
399ce8f145714e16bf2140c8c1c2e826 *man/gammatest.Rd
5526e2450e0f0784c9142509ed5e0b56 *man/getCladesofSize.Rd
9e3851d3318a20a7556e1e97b6c1cce4 *man/getDescendants.Rd
1e0c81dc5b4169a68828c7e6e07a714b *man/getExtant.Rd
28ea31077f4deaceb4435e0bff387ba6 *man/getSisters.Rd
7990607df7e27b5abfcb3b3f3933ef11 *man/getStates.Rd
eac387b3068a5498a27c26c4ac54932e *man/lambda.transform.Rd
fe9a9a76cd0531668fad334181fedea9 *man/likMlambda.Rd
3e82e41fa5770ec7fc4214a008f148fd *man/ls.tree.Rd
582a719054490eba5902f570c0d2e437 *man/ltt.Rd
f31ebdbe4ddfcfd97d7dc2b37858a139 *man/ltt95.Rd
550414d4c073dae8bdae5198d6f41003 *man/make.era.map.Rd
aae86ee706ba77f950f5d2b948eb5ed1 *man/make.simmap.Rd
c9a96a78b07076a8d752910470d196a2 *man/map.overlap.Rd
8cd9aadd82908d074d3d62acb457b1bd *man/matchNodes.Rd
a3bbb218c0230eb8be0eaa9d5aabb139 *man/mergeMappedStates.Rd
5eae92d74e381d59b572629138d9f803 *man/minSplit.Rd
458c6557e76da5239e165a8ed15210ad *man/mrp.supertree.Rd
9dab37745b43bebceda793a36c257c44 *man/multi.mantel.Rd
258317bbd7c01316d28b843b24daacba *man/multiC.Rd
95474133e7fd552e1de43c94bf4664ae *man/nodeHeights.Rd
75e285f060c4d1ffb60d561d49f7a2b4 *man/optim.phylo.ls.Rd
85272eebb2bd1404fe8784395b719a1e *man/orderMappedEdge.Rd
c56488ff498531eaf2457ad1a3daaed0 *man/paintSubTree.Rd
8a879df9dafcf215d94307752af00e25 *man/paste.tree.Rd
8b3acd8a21b06ffc46bb3a3be5b8abc1 *man/pbtree.Rd
d0db50c734dbb3dfff17bac838444212 *man/pgls.Ives.Rd
828f9dc6a3036c3ca9f04cd7f6dca31b *man/phenogram.Rd
023f11d98a022359c1c917fab3e64b1a *man/phyl.RMA.Rd
f2a7fa4fc839708ea7cd2828b3eee5d6 *man/phyl.cca.Rd
3d832b1c1e5a3738b38d30a968b41c1c *man/phyl.pairedttest.Rd
9777bd50d5eda3fb5b5596dd31d5c813 *man/phyl.pca.Rd
9ca22aa9fbb4ec750a48148925213ceb *man/phyl.resid.Rd
a4593bf88863e5ab7f7b38e9642f0df3 *man/phyl.vcv.Rd
765a679deff76405a430e9d06e7a8211 *man/phylANOVA.Rd
952632ae04f5a456c1b7045a9afc6c6c *man/phyloDesign.Rd
9efc6f61278c9138ee78450fb0d44000 *man/phylomorphospace.Rd
9b8a446559d655808452ae31e20fe99b *man/phylomorphospace3d.Rd
256d8600e921388f4c4d997038e34c64 *man/phylosig.Rd
0a6373513621bc26c8573db69d7bba54 *man/phytools-package.Rd
540efa593d83a972a20b788d1a1520a9 *man/plotBranchbyTrait.Rd
75e50f1a2dc5503171235ee163c95ec7 *man/plotSimmap.Rd
9ffd7f3c541e22452a2b0b6cbf07c54a *man/plotThresh.Rd
a310d77a5906c2d4baa360c05cb14a6f *man/plotTree.Rd
9c8297109561037f067dd7d469f12acb *man/posterior.evolrate.Rd
f1e7fb49afcbb107963bfb564e9b2a42 *man/ratebystate.Rd
949bf73091e93a276e94b5113fc4c839 *man/read.newick.Rd
f4414980d69db5b1724dfd8d46cd1adf *man/read.simmap.Rd
06a9d0985e7ed90a6d0c3f6abc2f4553 *man/reorderSimmap.Rd
3b61f786fa38661019bca4108e32d2c8 *man/repPhylo.Rd
04c5fa39043ed2988168d2db2441b1f7 *man/reroot.Rd
743fdc04ce309029b1d54885c590e80c *man/rerootingMethod.Rd
a9bd507ac70c35c02224fec4cab27de5 *man/rescaleSimmap.Rd
d76ce440666ffb39e807bd6b30a417d0 *man/roundBranches.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
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
9e6236f58eee882e09f81f0e76687753 *man/vcvPhylo.Rd
7b8c5bddf98303598dc6ce52a598610b *man/write.simmap.Rd
bfc639c71b7cb2519b5fadb94d3f6eb0 *man/writeAncestors.Rd
4b852e9e82198281126f9440ca804fed *man/writeNexus.Rd
f0a6a44e22743af61d4eae6cbe2cda94 *man/xkcdTree.Rd
