e32a1c77f7fe608d3b1771d6dcaae495 *DESCRIPTION
504edfee1cbbe2a20c834d034cac574c *NAMESPACE
6dc96bcb441e4baa5d370aebb2e2cacc *R/BAMMtools-data.R
f66a90ed504efc8d0ec4a941ad6f5af3 *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
2794c79e0097cfb9ff756dc132084eab *R/credibleShiftSet.R
03d44ff85bf6c76ab7e5d75eed0a4b8b *R/cumulativeShiftProbsTree.R
7515f58bd8ec3c67329b2d8f09fe2af6 *R/distinctShiftConfigurations.R
97928c8734ff9bf19c2f526853565492 *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
8d384a4826b350f6fed713ad55a231be *R/generateControlFile.R
665739c1bd1c0eae1ecc55f7f9f25bba *R/getBestShiftConfiguration.R
4145e0a6987a29b972eecbf982a52a4e *R/getBranchShiftPriors.R
da5811f16f60b552df2ffd1a16f6ff1d *R/getCladeRates.R
810f566d81d709d6251cb0514479ccf2 *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
3ee291789fb5cbd2e660681c5a5e916d *R/getEventData.R
091092ff9d1126d89dd5f86bb137720c *R/getJenksBreaks.R
e44be3c72197dd777da355bd9454a697 *R/getMarginalBranchRateMatrix.R
592502e9ee46f9ad0fe64d916dd9ae02 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
850369b484bb28dabc6fad8823170a2c *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
dbb5bdaaac16dc539386e1248ed75155 *R/marginalShiftProbsTree.R
19986db3d32f7ed0728d9080fe3865a9 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
3a0f88c7b5128f3b06050f8a61b1ee4e *R/phylogeneticMean.R
ad6538b509aa0397e6d34bf26012e189 *R/plot.bammdata.R
2ae2e18b0f67c6a0260751561a2fe6dd *R/plot.bammshifts.R
e3fd4f977a84ac22bf78d6c4a88142d1 *R/plot.credibleshiftset.R
07d5a5c4632df1129f16c8476d639cd9 *R/plotPrior.R
dfb0a01cbb350cecb97b0d49af5e85fc *R/plotRateThroughTime.R
2cb4dfb0a2881f56fd219e7a860e2dbc *R/print.bammdata.R
0bf839e46103f7bad66fa6416f1f8617 *R/rateLegend.R
d61d56fc80e2c9ca6f00a98ea6e4bdb6 *R/ratesHistogram.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
8ca3b11b821da397e49bc27e13cba982 *R/samplingProbs.R
a6f654afef98c5a6cc9a10af887064dd *R/segMap.R
642375d4b204e489b17b4462dc80551d *R/setBAMMpriors.R
b868796cd7ddd0db15bc0b7fe7d19da2 *R/setPhyloTreeCoords.R
3af600912ba356d4d20fd68b4d87eb44 *R/setPolarTreeCoords.R
1150d3ceed630e422bb3d618391e956b *R/speciesByRatesMatrix.R
40c0964678e1802c0f2fdf5eea79c7d6 *R/stepBF.R
4b5a59dbbd0650a29b321ec844e4249c *R/subsetEventData.R
399a96defd06441ffd9e9b8696d26805 *R/subtreeBAMM.R
0ee83a2de40c8a2b4883bb70367add18 *R/summary.bammdata.R
4e612dd04640879e0713623677e201b1 *R/summary.credibleshiftset.R
e83b5fc500dc60fb37002c3e9c89e850 *R/testTimeVariableBranches.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
fda0d43d3f1182166ab9a4f37be488c9 *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
c02d32e306f4ee0f5f45f2cc3c78ad52 *man/BAMMtools.Rd
bb32a47e25e0477f246e9c747e8c490c *man/ShiftProbsTree.Rd
f397bf4ce19a17280d3234bf25332f62 *man/addBAMMlegend.Rd
d7b2b5df570cef1b2c7784fe380f1de5 *man/addBAMMshifts.Rd
5c12bde350d8300231e6e89413be672f *man/assignColorBreaks.Rd
4940c6e5c9d7a6792213382fc44addb1 *man/cohorts.Rd
a2f77e0b463bb58e474f9d8942253da3 *man/computeBayesFactors.Rd
b7c5dde59e0c8088d842518596f237af *man/credibleShiftSet.Rd
c66842cdc2bceb4c2e96edd9c4baf0e4 *man/distinctShiftConfigurations.Rd
a2eca069268cc0b715e172fa8ad45eb7 *man/dtRates.Rd
2472bea2e3c28e09d0b659737ea92c75 *man/generateControlFile.Rd
d9aed38fbe2f6881d83c0455463cf69c *man/getBestShiftConfiguration.Rd
23aafe94eada38e4ab33690ec63e2cde *man/getBranchShiftPriors.Rd
9c9801aba7b1388879c818fa08d19f06 *man/getCladeRates.Rd
31db251521b12eb904bff374ba6276dd *man/getCohortMatrix.Rd
6ff76f225513199ea27178a2db624dcc *man/getEventData.Rd
f0168ea10ee1af44a125be94435cc184 *man/getJenksBreaks.Rd
62dcb60e189c7dd3c097ea0f9b5f9947 *man/getMarginalBranchRateMatrix.Rd
b8d69581c3e1b1f181a61cb7a96f37fe *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
870d02867eba4e2c54964313e3002c62 *man/plot.bammdata.Rd
4e89cdcac8dfde7edacc0a23ef50f826 *man/plot.bammshifts.Rd
aae2ef372bc918302052efcd513c4ae0 *man/plot.credibleshiftset.Rd
20ce7726740d5953bf78ef72787b201e *man/plotPrior.Rd
3d6c9804e96c2f4c9387071d0e86a776 *man/plotRateThroughTime.Rd
3d658b3c706cbae78232eec905e5d659 *man/ratesHistogram.Rd
5d129cedf118b74548b83c45048ace63 *man/richColors.Rd
43f4c9feaa64b0646ee62dd8aea13ef4 *man/samplingProbs.Rd
19d218a7ef353025ed182defc521d965 *man/setBAMMpriors.Rd
b10c0323849eaaf54e67c55496168063 *man/speciesByRatesMatrix.Rd
d4a07950122ba0425934458013612300 *man/stepBF.Rd
2d90082ba047f0842a1be1242d8b9e77 *man/subsetEventData.Rd
7645daa9fe57ad2e7b667b16c413c002 *man/subtreeBAMM.Rd
9aeaaa9496e0f4767f527618d9aa60fc *man/summary.bammdata.Rd
ef48d58393dcb671e206be45c407469a *man/summary.credibleshiftset.Rd
5b81374a84ba7541f1b05b9a72cbb54b *man/testTimeVariableBranches.Rd
bd528d1ce10c740d937fb8699b77bea1 *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
