6020dc0639906de2047bee52e22dd50f *DESCRIPTION
98672089cd0de1b7877590d70d29db99 *NAMESPACE
d20e2536df159b135910539829ad1c9d *R/BAMMtools-internal.R
7931f12b02e4efeb9c01b469eca69b37 *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
a1fa1cb4e8c0f0fb623391e756f8a6fb *R/assignColorBreaks.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
cacfb22ad23704fd8921ef2656db1fc2 *R/colorMap.R
306486bb342e95bffdba6a28011d5bb4 *R/computeBayesFactors.R
25aed9122fe077712a0a49dac9d9f8ef *R/credibleShiftSet.R
f5430311f8c94760f2996c1c13a4def6 *R/cumulativeShiftProbsTree.R
48fd0fb66b2b8ae9aa5df2d3c6875ee8 *R/distinctShiftConfigurations.R
8421456e04f9973c5b54677f67a38350 *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
52e410a70909ffc230c2ff5117df26c5 *R/getBestShiftConfiguration.R
8135cd0285382564e11a8ae14301eb7d *R/getBranchShiftPriors.R
61e175acf1201daedfbb4726e9f3d983 *R/getCladeRates.R
63fc4e68a904cb48133cccd015ac5189 *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
e19b5b8d1746cb1f5a14a97885f0676d *R/getEventData.R
6d95810cf7823e4352a1fe6ff4b44e29 *R/getMarginalBranchRateMatrix.R
e48694ca713a99dffa29dad623193ba3 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
3de4c19a21a08928d8542951b36e8955 *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
a319d7859a42aec23f89c3f36d0367ff *R/plot.bammdata.R
47eb57d388ec8366ba08093e67d3606f *R/plot.bammshifts.R
551ab01ea22e4627a6ec307053cb3b55 *R/plot.credibleshiftset.R
5c4f1ed9c3b5411dc88370e3a0fc0316 *R/plotRateThroughTime.R
7f52150cf825a24b23f803bc66951b9d *R/print.bammdata.R
f7d4a16ab60d7d8976a83fbc09b6c987 *R/print.branchprior.R
b9c867db26f7fc3e0819d8d9939917df *R/print.credibleshiftset.R
d28d2fc6c3492c3c58c37bf4711b91e1 *R/rateLegend.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
f8932cb96a22c7a4e77c1282a62a7c39 *R/richColors.R
f0ff3f12bf37dd81eecb657eb9198d70 *R/samplingProbs.R
025221d2c5fee14d61c20b8613f95842 *R/segMap.R
f5777462943aa9a0c9a8db38aaba5b35 *R/setBAMMpriors.R
da7db97fe3696ade80e943fd764bedbb *R/setPhyloTreeCoords.R
5cb086a0c9fea46aafc49132bc15686c *R/setPolarTreeCoords.R
ee1cf966b6252bba68167d482631a65e *R/speciesByRatesMatrix.R
f8f7a8bb7ddaffa617910502534c1597 *R/subsetEventData.R
8840770548e925d0bea7999a2b6d196d *R/subtreeBAMM.R
8ae0bd18dba758bb9a9bd1df9e415d12 *R/summary.bammdata.R
0b2f0fdbeb629173dd5f1a07ab70b44c *R/summary.branchprior.R
e328538b032706a06f59c8ef8f0d8215 *R/summary.credibleshiftset.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
a9048048296e66e381e0638ba94ef8b0 *R/transparentColor.R
9f08b0b7918afcfbe448362995e2e40c *data/events.primates.rda
14dc623acea4506c3144e1dc5e8eb856 *data/events.whales.rda
68a8cefba1e34da002fe953539f0d103 *data/mass.primates.rda
8c3ec32fe9937d4efaea0d77214bd46d *data/mcmc.primates.rda
7e4054f8ff49f15c06f7c920e68cdb43 *data/mcmc.whales.rda
277eb4583c3966e5097c6791e4262956 *data/primates.rda
87ccc9c3c5bc4ddfade61e68f8703965 *data/prior.primates.rda
f5720de21940a37a757336f96d8330a8 *data/prior.whales.rda
91d5b49597bd7cc09636f935a88f86d0 *data/whales.rda
754af1a71031d5980071e65dac3ad3ff *man/BAMMtools-data.Rd
90ecac618eb03b4bf7921e26498a830f *man/BAMMtools-internal.Rd
490f6268a4307d80844415877a677dc0 *man/BAMMtools-package.Rd
dd9bc54aa0159c8382c42873da0a9164 *man/ShiftProbsTree.Rd
3bf88e13fcec217385f4fcab3fb30697 *man/addBAMMshifts.Rd
18185be1bb6bf1dd2f30ce9db23f8250 *man/assignColorBreaks.Rd
b2e5ab84f603434f87faf28716710915 *man/computeBayesFactors.Rd
bbe176e7f9a845732c813b3e0197d870 *man/credibleShiftSet.Rd
4602042e8f5bde6af672402828b2f283 *man/distinctShiftConfigurations.Rd
a07cfefe249e22cc23b3923746bbaeb2 *man/dtRates.Rd
c4dfb1e1ef3a106645566469dff39bff *man/getBestShiftConfiguration.Rd
f08b7731d0ae562372db20adbf0dac5e *man/getBranchShiftPriors.Rd
19565e8c006f26673a810af35bc26fc0 *man/getCladeRates.Rd
b1b75df6b089ecd714d67115c200d990 *man/getCohortMatrix.Rd
42f36a95322aeb28f08aa16c676d9126 *man/getEventData.Rd
ceefbadcf9e76433dff446ec6ae7b4db *man/getMarginalBranchRateMatrix.Rd
d0e5616955b6c5123db1ddb8e712006c *man/getMeanBranchLengthTree.Rd
2def3330d5a89ec7db55d33e22a50b7a *man/getRateThroughTimeMatrix.Rd
c634ff1fef731fa27c4a1d42791a8ea0 *man/getShiftNodesFromIndex.Rd
806adc93038689e7dd57987535d7da94 *man/getTipRates.Rd
4e2f81bbca7bb92c5e0584479640795f *man/getmrca.Rd
56b0ad1503bae77ad00f4405f02cfe15 *man/maximumShiftCredibility.Rd
e3583420a003b68d497b0adfed0131cc *man/plot.bammdata.Rd
3d3567078b5a3e30e3c6ef2d6689b7f8 *man/plot.bammshifts.Rd
df27d80e2058bcc96675a3dc0c5f1228 *man/plot.credibleshiftset.Rd
6422e13bee447bf29134698f52c09b89 *man/plotRateThroughTime.Rd
836e39b2f038b1acff510d636f681b3d *man/samplingProbs.Rd
ffeea7b7058d79d50dabcceef2b97332 *man/setBAMMpriors.Rd
32a569c273f616082bfe24be9aee2b14 *man/speciesByRatesMatrix.Rd
366213fe49b056ed2310f3d89a5d1583 *man/subsetEventData.Rd
7c1d8aa49e45a43a3e644913d9bcee08 *man/subtreeBAMM.Rd
f6ccc040be280f726c30bf25ae99d7c8 *man/summary.bammdata.Rd
04b221bc38a4e8e776e19a461f7d9a77 *man/summary.branchprior.Rd
b279a64ffeac7686a4ac89f2eee55f49 *man/summary.credibleshiftset.Rd
5eefe99082d44336cb7b7fcf14ee7d4f *src/dtrates.c
b8944cfbb74f1d1de89fed9f0fc477e7 *src/treetraverse.c
