f098434682aa4146e773ade347d25d9c *DESCRIPTION
952945f9d272cd3982902cb322f180c9 *NAMESPACE
6dc96bcb441e4baa5d370aebb2e2cacc *R/BAMMtools-data.R
abbd4ed7f525ac9b819df3206702d90c *R/BAMMtools-package.R
3808ddbf58b7b344f455d1a7a5f9c51b *R/NU.branching.times.R
375ee8688cf0e7467a083fa27dbdcfca *R/addBAMMlegend.R
ba7fc53754917c310c43c0fe99f8ffb6 *R/addBAMMshifts.R
e5a6e62f153e0ca6a1c654ef52667615 *R/arc.R
b05623a864ead1e49b3f9aea1afdcf17 *R/areEventConfigurationsIdentical.R
a38d5ecc904d59c99bd0603fd997098a *R/areShiftSetsEqual.R
c18e40abca4178fbe4f926d8c381b534 *R/as.bammdata.R
9e106cd43ad02aae75f5c7778209c05f *R/as.phylo.bammdata.R
fa9ac81cc222f3c9284da07d325ad8b2 *R/assignColorBreaks.R
8fe614bdb4610f0b0d06351803f70ec3 *R/bammLikelihood.R
cc3613953499a44b796905fa486ebea4 *R/bammcolors.R
14ab222b064dff05966b4a62c868466e *R/barLegend.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
51672440e837c05514be879eec84d877 *R/cohorts.R
9caf07d321cc246df832682b482f4c91 *R/colorMap.R
3fb971003581b62dfec91c4e4f09af9b *R/computeBayesFactors.R
5066a3088c362592443d2325ccf9339b *R/credibleShiftSet.R
03d44ff85bf6c76ab7e5d75eed0a4b8b *R/cumulativeShiftProbsTree.R
b0aec62b5edc90230871ae47af69b95d *R/distinctShiftConfigurations.R
2adc13250c1fdd99ec99c2b87d93c7ea *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
1aaa787cfff7d486c62731ce5c54377b *R/generateControlFile.R
665739c1bd1c0eae1ecc55f7f9f25bba *R/getBestShiftConfiguration.R
03de738941eb583f482f45fcecaef8e4 *R/getBranchShiftPriors.R
75fa60996e529aadc66aedc6015e3b23 *R/getCladeRates.R
03d14e140d16e9b76da018892933d2bf *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
dfda965c4a76d806a52562d24620e616 *R/getEventData.R
091092ff9d1126d89dd5f86bb137720c *R/getJenksBreaks.R
0c52c98ab80737382eae0f5b9f0edfd1 *R/getMarginalBranchRateMatrix.R
f49a610f371018884a2734036f8b5e80 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
020f75c20aa6c90d77a7a257b4f12334 *R/getRateThroughTimeMatrix.R
0b3ae5dbd09d517cbd6b76855a065a63 *R/getRecursiveSequence.R
0c1f36cf3e8bcda32ab3ac28808eac7e *R/getSequenceForwardTraversal.R
b942810527770d48c0c4d5b8fec41528 *R/getShiftNodesFromIndex.R
270a14ca850f02f9e2d302d199bc5de0 *R/getSpanningTaxonPair.R
693f32920e1812750c2f5131a6b434e7 *R/getStartStopTimes.R
f1a494e7498b52877b12dd64a5494659 *R/getTipRates.R
df91926c6d959076a24fed244c440c93 *R/getmrca.R
618d603ef55c26f80ae4b7975aef3294 *R/inv.logit.R
8f1ff6b7910c7e8f9c2c61bfb56ba57b *R/logit.R
c98f2512af89eb7f443506b68de9b489 *R/marginalOddsRatioBranches.R
e0d1abd73f81213a063aec667771d1a5 *R/marginalShiftProbsTree.R
f869c229beaf2380ea9e39c557d9e761 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
3a0f88c7b5128f3b06050f8a61b1ee4e *R/phylogeneticMean.R
4d403f7daba4a01a1a1c1991b2a9ed81 *R/plot.bammdata.R
632b64f11a911224ca82c50b7d270117 *R/plot.bammshifts.R
fd1245926409256cc4d161258c0544ab *R/plot.credibleshiftset.R
07d5a5c4632df1129f16c8476d639cd9 *R/plotPrior.R
33053f7945e48ac7d4e5e7d0b3a51272 *R/plotRateThroughTime.R
2cb4dfb0a2881f56fd219e7a860e2dbc *R/print.bammdata.R
0bf839e46103f7bad66fa6416f1f8617 *R/rateLegend.R
323b9c86f19a7a6df7c20f993d2ee78a *R/ratesHistogram.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
22786dd78381a872d3cd956fb1ab4a04 *R/samplingProbs.R
a6f654afef98c5a6cc9a10af887064dd *R/segMap.R
d4f7d835692a631e3bd85ed2c5627331 *R/setBAMMpriors.R
b868796cd7ddd0db15bc0b7fe7d19da2 *R/setPhyloTreeCoords.R
3af600912ba356d4d20fd68b4d87eb44 *R/setPolarTreeCoords.R
0ac2e47dea3ac7a2edb90f38f3371a13 *R/speciesByRatesMatrix.R
cad53795de7f109f60c53bec60da253b *R/stepBF.R
4b5a59dbbd0650a29b321ec844e4249c *R/subsetEventData.R
399a96defd06441ffd9e9b8696d26805 *R/subtreeBAMM.R
f59fc836c849730a18e02b93d896cef5 *R/summary.bammdata.R
21e9c6eb6fcfc320e4f783e01b267ee1 *R/summary.credibleshiftset.R
8983790363563fdcac06a37652e7a1d7 *R/testTimeVariableBranches.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
b9de50ff0bf97f88502ce7681ba9cab7 *R/traitDependentBAMM.R
15a7e0dc70a3ba73af7139512d8b8acd *R/transparentColor.R
c07f19b0f1c7574359c733ca8f95b138 *R/writeEventData.R
a84b8da30c6888af9dd5cbdba1e0a19d *data/events.fishes.rda
5231573194ca3ab2859effe9f39f2035 *data/events.primates.rda
58e320ab7285570a254049cf8cb40ec7 *data/events.whales.rda
b5a3d68cbffb63774827c8d7d570973c *data/fishes.rda
0a748481bc26239f7dc35f81f51eaf62 *data/mass.primates.rda
40cb98ddc3ba2e159a416fe370ee5c28 *data/mcmc.primates.rda
b6bcd695dff6e5814e4aee7893b9d25b *data/mcmc.whales.rda
1c56bd4d1351f14bc8511523e1a3f984 *data/primates.rda
a75aebe6580d30cb05097acf449a367b *data/traits.fishes.rda
72235ac247577c1d1a87983dcefc585f *data/whales.rda
fc5fc624c96e944bf9e0aa67ca635941 *inst/CITATION
b00927416a9358173b21c0ae9fb69734 *man/BAMMlikelihood.Rd
cb56a3e63d1ff7a3fdec67d3870bdd32 *man/BAMMtools-data.Rd
bb03e24d51359837775c3f3015c2ddf5 *man/BAMMtools.Rd
bfec1843fd1c10f3fae77c15c17847a1 *man/ShiftProbsTree.Rd
f7eccb6cddfd1d19da99d3f095036b59 *man/addBAMMlegend.Rd
af101fefbbab5588d56084270c4c43cf *man/addBAMMshifts.Rd
5c12bde350d8300231e6e89413be672f *man/assignColorBreaks.Rd
b87fcf346d6958747a1ac162fb805b9e *man/cohorts.Rd
3538483f4a1010d60102640b614e5924 *man/computeBayesFactors.Rd
a64122a97010565ca7a6c9c35a1f7469 *man/credibleShiftSet.Rd
d1f1aefb858597cdbd3d7fa2787bdbb5 *man/distinctShiftConfigurations.Rd
3edff0bfc3abab9522c1e12a4489999a *man/dtRates.Rd
6328b03bc8c2de09c8fe3121797a2435 *man/generateControlFile.Rd
d9aed38fbe2f6881d83c0455463cf69c *man/getBestShiftConfiguration.Rd
5feecba56c773e477082df18b0e31739 *man/getBranchShiftPriors.Rd
5c9cb5848844feaac41b7072b0a121f8 *man/getCladeRates.Rd
d4b0fdfe71d2a89484e59177541ab52c *man/getCohortMatrix.Rd
400c38d364f52c5758f7828100022f38 *man/getEventData.Rd
f0168ea10ee1af44a125be94435cc184 *man/getJenksBreaks.Rd
8df0e4594541bed399a4d5cf046501f6 *man/getMarginalBranchRateMatrix.Rd
1532ca1367157a3827db0b2854097ce8 *man/getMeanBranchLengthTree.Rd
5e5bccfdb2cc5effedea527b9ab2a158 *man/getRateThroughTimeMatrix.Rd
948994e93ccb053761c9191a827b2ccd *man/getShiftNodesFromIndex.Rd
c5f3e8fe79dae8de618b91db1863d89b *man/getTipRates.Rd
4291afeeec74eda002b6c56458ad54d1 *man/getmrca.Rd
061333f28101c9dd9c635779d1420cf4 *man/marginalOddsRatioBranches.Rd
c00cf79802bdde81123c3885c270b067 *man/maximumShiftCredibility.Rd
91892c4c50d06c139d8a70dc8640a4f9 *man/plot.Rd
a477b8b10df95c3cb32f04bc1aff67fd *man/plot.bammshifts.Rd
8bb535327a04b21c97196ac0ad4786a9 *man/plot.credibleshiftset.Rd
20ce7726740d5953bf78ef72787b201e *man/plotPrior.Rd
8305bfa475da95d3a36ce08857bc8a75 *man/plotRateThroughTime.Rd
f9b0bb7d4253427e8bef3b625f6320dc *man/ratesHistogram.Rd
5d129cedf118b74548b83c45048ace63 *man/richColors.Rd
270e1d18ebe5705c16799dd2c484c159 *man/samplingProbs.Rd
9d83c098b92fa3112787bac9ecfa15eb *man/setBAMMpriors.Rd
048cd9b8d9a4855912e1bc8ac047836b *man/speciesByRatesMatrix.Rd
41acc98eb049e7f46ac3ab9d69fee1d5 *man/stepBF.Rd
2d90082ba047f0842a1be1242d8b9e77 *man/subsetEventData.Rd
7645daa9fe57ad2e7b667b16c413c002 *man/subtreeBAMM.Rd
f34c5ef9f046bdcb0c338833156550cd *man/summary.bammdata.Rd
0a6247545e4b909de753275e0826090c *man/summary.credibleshiftset.Rd
3fba0a1211d8ee4554f5ed01d6f8e376 *man/testTimeVariableBranches.Rd
d47baae2112efdc5a5de1965c5405dc3 *man/traitDependentBAMM.Rd
6f65d5892c5673776f389f276752f94b *man/transparentColor.Rd
267c7602b6d086eee0aee98b7524f975 *man/writeEventData.Rd
6899f042dc94058ebbf77f735b6f4eb0 *src/BAMMtools_init.c
163c1c799f50b44886d9d1a8f97cdfd7 *src/cohort_matrix.c
5eefe99082d44336cb7b7fcf14ee7d4f *src/dtrates.c
16bc6cd0ee25afe4b842a16c1ce6d70e *src/jenksBrks.c
3f21d3a7abe2f1192f0f765dabab446d *src/treetraverse.c
