6ea2ddf8093c540615498b42e9155528 *DESCRIPTION
c76eedf6869b984bcbde410ae0a8bd63 *NAMESPACE
6dc96bcb441e4baa5d370aebb2e2cacc *R/BAMMtools-data.R
abbd4ed7f525ac9b819df3206702d90c *R/BAMMtools-package.R
3808ddbf58b7b344f455d1a7a5f9c51b *R/NU.branching.times.R
931f0e31f8847f8a2408ec50bf23573c *R/addBAMMlegend.R
9040b9a8241c3468b27fe65a0e67e4ea *R/addBAMMshifts.R
e5a6e62f153e0ca6a1c654ef52667615 *R/arc.R
b05623a864ead1e49b3f9aea1afdcf17 *R/areEventConfigurationsIdentical.R
a38d5ecc904d59c99bd0603fd997098a *R/areShiftSetsEqual.R
a4c12ab83b62653a6c0bd43dea8a81fe *R/as.bammdata.R
9e106cd43ad02aae75f5c7778209c05f *R/as.phylo.bammdata.R
fa9ac81cc222f3c9284da07d325ad8b2 *R/assignColorBreaks.R
346e3f308d9446a27995d458fec91f20 *R/bammLikelihood.R
cc3613953499a44b796905fa486ebea4 *R/bammcolors.R
14ab222b064dff05966b4a62c868466e *R/barLegend.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
4525ec1dcd49eea62bf7b49401d85c65 *R/cohorts.R
9caf07d321cc246df832682b482f4c91 *R/colorMap.R
4ca3dfcfd2055bf4d02922bf3c9e02a2 *R/computeBayesFactors.R
5066a3088c362592443d2325ccf9339b *R/credibleShiftSet.R
03d44ff85bf6c76ab7e5d75eed0a4b8b *R/cumulativeShiftProbsTree.R
7515f58bd8ec3c67329b2d8f09fe2af6 *R/distinctShiftConfigurations.R
d1110567ad4702ab85f87209535c3e4d *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
1aaa787cfff7d486c62731ce5c54377b *R/generateControlFile.R
665739c1bd1c0eae1ecc55f7f9f25bba *R/getBestShiftConfiguration.R
03de738941eb583f482f45fcecaef8e4 *R/getBranchShiftPriors.R
ec106c5f2cf4502f5987480b84d15014 *R/getCladeRates.R
03d14e140d16e9b76da018892933d2bf *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
736a5fc0520010f4d1ce2172b3dc21a7 *R/getEventData.R
091092ff9d1126d89dd5f86bb137720c *R/getJenksBreaks.R
e44be3c72197dd777da355bd9454a697 *R/getMarginalBranchRateMatrix.R
e5ea27c60c777f7f68d125b4703c0516 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
c746a7ba5ef75388d72afb65ed001ea5 *R/getRateThroughTimeMatrix.R
0b3ae5dbd09d517cbd6b76855a065a63 *R/getRecursiveSequence.R
0c1f36cf3e8bcda32ab3ac28808eac7e *R/getSequenceForwardTraversal.R
b942810527770d48c0c4d5b8fec41528 *R/getShiftNodesFromIndex.R
270a14ca850f02f9e2d302d199bc5de0 *R/getSpanningTaxonPair.R
693f32920e1812750c2f5131a6b434e7 *R/getStartStopTimes.R
4d43395fe73b589ddf11b5d1a0427586 *R/getTipRates.R
df91926c6d959076a24fed244c440c93 *R/getmrca.R
618d603ef55c26f80ae4b7975aef3294 *R/inv.logit.R
8f1ff6b7910c7e8f9c2c61bfb56ba57b *R/logit.R
c98f2512af89eb7f443506b68de9b489 *R/marginalOddsRatioBranches.R
e0d1abd73f81213a063aec667771d1a5 *R/marginalShiftProbsTree.R
19986db3d32f7ed0728d9080fe3865a9 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
3a0f88c7b5128f3b06050f8a61b1ee4e *R/phylogeneticMean.R
85bff53db8af0ae11827613d69153ef2 *R/plot.bammdata.R
43ab700eeed8c67b21d867fc293dfcd0 *R/plot.bammshifts.R
b90d859b5a343a07521b072ad380d441 *R/plot.credibleshiftset.R
07d5a5c4632df1129f16c8476d639cd9 *R/plotPrior.R
3bb472ebb42e7920f1f1c5496f2350f2 *R/plotRateThroughTime.R
2cb4dfb0a2881f56fd219e7a860e2dbc *R/print.bammdata.R
0bf839e46103f7bad66fa6416f1f8617 *R/rateLegend.R
314f54c13c56c4769676ef82650759e9 *R/ratesHistogram.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
788ba2d34d143097ccaed5663dcd0697 *R/samplingProbs.R
a6f654afef98c5a6cc9a10af887064dd *R/segMap.R
642375d4b204e489b17b4462dc80551d *R/setBAMMpriors.R
b868796cd7ddd0db15bc0b7fe7d19da2 *R/setPhyloTreeCoords.R
3af600912ba356d4d20fd68b4d87eb44 *R/setPolarTreeCoords.R
942589c00b59216e6c9efe5034263702 *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
79a63f7d85aa6c1462708de20d2566a0 *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
834b84861bdef0da6a5bace4b55f7d90 *inst/CITATION
b00927416a9358173b21c0ae9fb69734 *man/BAMMlikelihood.Rd
cb56a3e63d1ff7a3fdec67d3870bdd32 *man/BAMMtools-data.Rd
bb03e24d51359837775c3f3015c2ddf5 *man/BAMMtools.Rd
bfec1843fd1c10f3fae77c15c17847a1 *man/ShiftProbsTree.Rd
f397bf4ce19a17280d3234bf25332f62 *man/addBAMMlegend.Rd
d7b2b5df570cef1b2c7784fe380f1de5 *man/addBAMMshifts.Rd
5c12bde350d8300231e6e89413be672f *man/assignColorBreaks.Rd
4940c6e5c9d7a6792213382fc44addb1 *man/cohorts.Rd
a2f77e0b463bb58e474f9d8942253da3 *man/computeBayesFactors.Rd
a64122a97010565ca7a6c9c35a1f7469 *man/credibleShiftSet.Rd
c66842cdc2bceb4c2e96edd9c4baf0e4 *man/distinctShiftConfigurations.Rd
c56af150e94a845e16b5b01c1e6039c1 *man/dtRates.Rd
6328b03bc8c2de09c8fe3121797a2435 *man/generateControlFile.Rd
d9aed38fbe2f6881d83c0455463cf69c *man/getBestShiftConfiguration.Rd
5feecba56c773e477082df18b0e31739 *man/getBranchShiftPriors.Rd
a47af54ce678a2cfe7f5db9edcb58212 *man/getCladeRates.Rd
d4b0fdfe71d2a89484e59177541ab52c *man/getCohortMatrix.Rd
6ff76f225513199ea27178a2db624dcc *man/getEventData.Rd
f0168ea10ee1af44a125be94435cc184 *man/getJenksBreaks.Rd
62dcb60e189c7dd3c097ea0f9b5f9947 *man/getMarginalBranchRateMatrix.Rd
9c264e63f4a52ef92bdcd24212fb0006 *man/getMeanBranchLengthTree.Rd
5e5bccfdb2cc5effedea527b9ab2a158 *man/getRateThroughTimeMatrix.Rd
948994e93ccb053761c9191a827b2ccd *man/getShiftNodesFromIndex.Rd
5cd1a1158aca7049b18040d66a6eab67 *man/getTipRates.Rd
4291afeeec74eda002b6c56458ad54d1 *man/getmrca.Rd
061333f28101c9dd9c635779d1420cf4 *man/marginalOddsRatioBranches.Rd
d425f57f01d808d5222ac254b33d86f5 *man/maximumShiftCredibility.Rd
cab8167517dfca6dc8f5865adb2ea502 *man/plot.Rd
a477b8b10df95c3cb32f04bc1aff67fd *man/plot.bammshifts.Rd
8bb535327a04b21c97196ac0ad4786a9 *man/plot.credibleshiftset.Rd
20ce7726740d5953bf78ef72787b201e *man/plotPrior.Rd
6697a0a184899313efc630a0f802c56f *man/plotRateThroughTime.Rd
f9b0bb7d4253427e8bef3b625f6320dc *man/ratesHistogram.Rd
5d129cedf118b74548b83c45048ace63 *man/richColors.Rd
270e1d18ebe5705c16799dd2c484c159 *man/samplingProbs.Rd
19d218a7ef353025ed182defc521d965 *man/setBAMMpriors.Rd
49e18208dd3d036838492598ce1c57da *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
be3d0566eeeda4f79b98ac78c771450c *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
