974edcd5af8563d4581cf211f31b5d2d *DESCRIPTION
ea442abf5802fca070183620291e73ac *NAMESPACE
d20e2536df159b135910539829ad1c9d *R/BAMMtools-internal.R
3d0e4968fa47dae11ffd073fae57343e *R/addBAMMshifts.R
e5a6e62f153e0ca6a1c654ef52667615 *R/arc.R
b05623a864ead1e49b3f9aea1afdcf17 *R/areEventConfigurationsIdentical.R
a38d5ecc904d59c99bd0603fd997098a *R/areShiftSetsEqual.R
12607dd9cb8633128f4ec98c9a8dd5f6 *R/as.bammdata.R
6d88a1a9363cb6307edb789347352032 *R/as.phylo.bammdata.R
70839c99ba80e95bb94cd937f32f58c4 *R/as.phylo.branchprior.R
4dd393a58a021505cf94441d74fd6309 *R/assignColorBreaks.R
fec3bc3e0a452d82d222bd81766d15b7 *R/bammcolors.R
6a6caf7bdddb5f3930cb477ae48ad426 *R/barLegend.R
9bb40ea92117e8151b0f33a90a514db4 *R/bayesFactorBranches.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
fc439f519ccca747b7c1ad3f929c2efd *R/cohorts.R
86ea243b7dc03976d4b3e7ae9f9ddf18 *R/colorMap.R
287a62a619d9cb48a56d5ec6198eae6b *R/computeBayesFactors.R
0f3d6cc2b6788c9c9f291faa7f58b93d *R/credibleShiftSet.R
f5430311f8c94760f2996c1c13a4def6 *R/cumulativeShiftProbsTree.R
f8b76227ac51d28bf91facb481579d8c *R/distinctShiftConfigurations.R
1a907aba5e4fb150139ce00f23fc696b *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
ef599e68ddea56052f92d703bc118559 *R/getBestShiftConfiguration.R
917ba9ff99f8ae3574f00c694f737152 *R/getBranchShiftPriors.R
61e175acf1201daedfbb4726e9f3d983 *R/getCladeRates.R
08b8233ba91f81cb240e003f54397904 *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
2ae2ad43acc6e05d1d861b29b0c51d15 *R/getEventData.R
6d95810cf7823e4352a1fe6ff4b44e29 *R/getMarginalBranchRateMatrix.R
e48694ca713a99dffa29dad623193ba3 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
3d855acfb8273d200dafc5f6633b08f4 *R/getRateThroughTimeMatrix.R
0b3ae5dbd09d517cbd6b76855a065a63 *R/getRecursiveSequence.R
0c1f36cf3e8bcda32ab3ac28808eac7e *R/getSequenceForwardTraversal.R
7afb8a38d0403904b4c8313870f754b1 *R/getShiftNodesFromIndex.R
270a14ca850f02f9e2d302d199bc5de0 *R/getSpanningTaxonPair.R
0f8573d760f2ed9f450ee0d3667f25ec *R/getStartStopTimes.R
14dcb9fd640285633443bfc44fa1d503 *R/getTipRates.R
daf9c480426d0357075c939f5db07b1f *R/getmrca.R
618d603ef55c26f80ae4b7975aef3294 *R/inv.logit.R
8f1ff6b7910c7e8f9c2c61bfb56ba57b *R/logit.R
368373ef24a7e4bc1a76c524f39496c3 *R/marginalShiftProbsTree.R
bcc0037a4f28b3fb2e0e6363a7be3049 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
eea2d2fabe9277ec97e8758a5bade8d3 *R/phylogeneticMean.R
396c15787834a206a6d156e7752ba70b *R/plot.bammdata.R
f5546472dbf2e5a980356ad9538f12e0 *R/plot.bammshifts.R
d4829f690ca84a88e8eb714699c291f2 *R/plot.credibleshiftset.R
5e3559deff361a40a337ba746f0c5483 *R/plotRateThroughTime.R
67e8e6b3f70e5cd8d4c46211ca85261e *R/print.bammdata.R
f7d4a16ab60d7d8976a83fbc09b6c987 *R/print.branchprior.R
b9c867db26f7fc3e0819d8d9939917df *R/print.credibleshiftset.R
dedd9b383d3dfba7d3ad072999ecae0a *R/rateLegend.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
f8932cb96a22c7a4e77c1282a62a7c39 *R/richColors.R
f0ff3f12bf37dd81eecb657eb9198d70 *R/samplingProbs.R
025221d2c5fee14d61c20b8613f95842 *R/segMap.R
2199d125b21290eb3212c6da28707b69 *R/setBAMMpriors.R
da7db97fe3696ade80e943fd764bedbb *R/setPhyloTreeCoords.R
5cb086a0c9fea46aafc49132bc15686c *R/setPolarTreeCoords.R
ee1cf966b6252bba68167d482631a65e *R/speciesByRatesMatrix.R
552efe1eaa120ffdb523e558184ad975 *R/subsetEventData.R
dea17a1eb79feaac99d8896d52a368bf *R/subtreeBAMM.R
050996e39e4d2a4e1ab93fbc8bf62d13 *R/summary.bammdata.R
4f0c80db48ed4ff39f87586f353505f9 *R/summary.branchprior.R
2422e76b1fb383f11eedf27adfeaef88 *R/summary.credibleshiftset.R
820754915fe198ba940b9b065bbf1ace *R/testTimeVariableBranches.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
a9048048296e66e381e0638ba94ef8b0 *R/transparentColor.R
2c513ff5bb92119f0ca937e044197b5b *data/events.primates.rda
f50b894898a8450b46a172f2643de385 *data/events.whales.rda
68a8cefba1e34da002fe953539f0d103 *data/mass.primates.rda
579e4113a795baf825a05b717ce6ebf1 *data/mcmc.primates.rda
38efab774cb9840efd44d3156998fad6 *data/mcmc.whales.rda
277eb4583c3966e5097c6791e4262956 *data/primates.rda
00454c6c0cb86f3aef07fe9be8d7065b *data/prior.primates.rda
cacba46a6cd013026c87eecba28e7ccf *data/prior.whales.rda
91d5b49597bd7cc09636f935a88f86d0 *data/whales.rda
754af1a71031d5980071e65dac3ad3ff *man/BAMMtools-data.Rd
a347224b741beefa924c55e848b2bd8f *man/BAMMtools-internal.Rd
1bd95044571c7d40e04ac8d834f9b6e8 *man/BAMMtools-package.Rd
dd9bc54aa0159c8382c42873da0a9164 *man/ShiftProbsTree.Rd
0a1df1a9afa286bf114d7945867857ec *man/addBAMMshifts.Rd
5a5a5a33310be82ab59ccd0fb285e5c1 *man/assignColorBreaks.Rd
24b53be09ac7b6a23e5235db46357c6d *man/bayesFactorBranches.Rd
b10ada9906e33deb85179c6b85d8e172 *man/cohorts.Rd
5a2918f94f5e0792caed413ef76fc876 *man/computeBayesFactors.Rd
bc09f99a0416feba14150372a7eaf45e *man/credibleShiftSet.Rd
cea1da178c7852015767249b3573a6a2 *man/distinctShiftConfigurations.Rd
a07cfefe249e22cc23b3923746bbaeb2 *man/dtRates.Rd
5f699c559ddcda34877977fe92052cae *man/getBestShiftConfiguration.Rd
45dc4920205728e573575c0058b33488 *man/getBranchShiftPriors.Rd
19565e8c006f26673a810af35bc26fc0 *man/getCladeRates.Rd
b1b75df6b089ecd714d67115c200d990 *man/getCohortMatrix.Rd
42f36a95322aeb28f08aa16c676d9126 *man/getEventData.Rd
ceefbadcf9e76433dff446ec6ae7b4db *man/getMarginalBranchRateMatrix.Rd
d0e5616955b6c5123db1ddb8e712006c *man/getMeanBranchLengthTree.Rd
945b5609949866ef950438f96faab8d3 *man/getRateThroughTimeMatrix.Rd
c634ff1fef731fa27c4a1d42791a8ea0 *man/getShiftNodesFromIndex.Rd
806adc93038689e7dd57987535d7da94 *man/getTipRates.Rd
4e2f81bbca7bb92c5e0584479640795f *man/getmrca.Rd
56b0ad1503bae77ad00f4405f02cfe15 *man/maximumShiftCredibility.Rd
422ef8839978929f9d3bc25115a82d52 *man/plot.bammdata.Rd
3bd32e4aa381d8148b0730fa020a9e49 *man/plot.bammshifts.Rd
c8e2d0b92945c80d00f11d406c72c2b2 *man/plot.credibleshiftset.Rd
24bff760c919671eda05571f9e0ea3f4 *man/plotRateThroughTime.Rd
67581456f237bd2a4a34705b5a4bc954 *man/samplingProbs.Rd
f52db29f0697a1bd7415d074cc9a3584 *man/setBAMMpriors.Rd
32a569c273f616082bfe24be9aee2b14 *man/speciesByRatesMatrix.Rd
5149de0aca65a0e852fba708ef9fab40 *man/subsetEventData.Rd
7c1d8aa49e45a43a3e644913d9bcee08 *man/subtreeBAMM.Rd
31c6a7c378a940851a28d04bba3829a3 *man/summary.bammdata.Rd
04b221bc38a4e8e776e19a461f7d9a77 *man/summary.branchprior.Rd
511fe1bdeb24ac0146c2ede6ed125f01 *man/summary.credibleshiftset.Rd
fe1f71ef0ab279e851fed3753d882e4e *man/testTimeVariableBranches.Rd
163c1c799f50b44886d9d1a8f97cdfd7 *src/cohort_matrix.c
5eefe99082d44336cb7b7fcf14ee7d4f *src/dtrates.c
b8944cfbb74f1d1de89fed9f0fc477e7 *src/treetraverse.c
