9efc0ce6ca871f08aad7dc204883d5e7 *DESCRIPTION
504edfee1cbbe2a20c834d034cac574c *NAMESPACE
6dc96bcb441e4baa5d370aebb2e2cacc *R/BAMMtools-data.R
f66a90ed504efc8d0ec4a941ad6f5af3 *R/BAMMtools-package.R
543484729e4c2a4c3b35f29c00fbf23b *R/NU.branching.times.R
94324a2f79866681b474d87ae01e2332 *R/addBAMMlegend.R
e883dfe8e708d68b955c94801260de05 *R/addBAMMshifts.R
e5a6e62f153e0ca6a1c654ef52667615 *R/arc.R
b05623a864ead1e49b3f9aea1afdcf17 *R/areEventConfigurationsIdentical.R
a38d5ecc904d59c99bd0603fd997098a *R/areShiftSetsEqual.R
a4c12ab83b62653a6c0bd43dea8a81fe *R/as.bammdata.R
e159937d52efc68a940142d864664cfc *R/as.phylo.bammdata.R
fa9ac81cc222f3c9284da07d325ad8b2 *R/assignColorBreaks.R
b734fdde5f38f4aa4fe08357c7602ba3 *R/bammLikelihood.R
cc3613953499a44b796905fa486ebea4 *R/bammcolors.R
14ab222b064dff05966b4a62c868466e *R/barLegend.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
4525ec1dcd49eea62bf7b49401d85c65 *R/cohorts.R
b1f5c4c3e37893ce4b4be72d5cff5df8 *R/colorMap.R
8623279cd53af217616d706ec7b59e4b *R/computeBayesFactors.R
2794c79e0097cfb9ff756dc132084eab *R/credibleShiftSet.R
2c3a95e90008851ba02fffb12e9f8bd3 *R/cumulativeShiftProbsTree.R
7515f58bd8ec3c67329b2d8f09fe2af6 *R/distinctShiftConfigurations.R
6e1f965037325030ba3caf1378fd690d *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
3d89616f7eac0546ea7de0e3f34f2c09 *R/generateControlFile.R
114db2103b3216fcb3f5ca039bc25836 *R/getBestShiftConfiguration.R
4145e0a6987a29b972eecbf982a52a4e *R/getBranchShiftPriors.R
549bf88280e9f73046d460d0bea4f223 *R/getCladeRates.R
d5c7df8250479dd726f3de56f5e192ca *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
23a145355c176060b0984a1553e8100d *R/getEventData.R
091092ff9d1126d89dd5f86bb137720c *R/getJenksBreaks.R
d934fae2ad5dba8a9c94e9306d015c16 *R/getMarginalBranchRateMatrix.R
39b0559daf978c45ea071122bd1d85bf *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
19491eeec61c1164f8ba9d467191f443 *R/getRateThroughTimeMatrix.R
0b3ae5dbd09d517cbd6b76855a065a63 *R/getRecursiveSequence.R
0c1f36cf3e8bcda32ab3ac28808eac7e *R/getSequenceForwardTraversal.R
b942810527770d48c0c4d5b8fec41528 *R/getShiftNodesFromIndex.R
270a14ca850f02f9e2d302d199bc5de0 *R/getSpanningTaxonPair.R
693f32920e1812750c2f5131a6b434e7 *R/getStartStopTimes.R
2cb8b72e22a97a14a9c9a037de7bbc31 *R/getTipRates.R
df91926c6d959076a24fed244c440c93 *R/getmrca.R
618d603ef55c26f80ae4b7975aef3294 *R/inv.logit.R
8f1ff6b7910c7e8f9c2c61bfb56ba57b *R/logit.R
562b2ebf82329c607eb32e799deee15e *R/marginalOddsRatioBranches.R
cdf04a6c5b96928b796bf98756a6d8dd *R/marginalShiftProbsTree.R
e3422c9c2baae8e7e19ccb7660b7aa72 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
eea2d2fabe9277ec97e8758a5bade8d3 *R/phylogeneticMean.R
b7db9944b400115168884ff99f8bd3dd *R/plot.bammdata.R
2e190f63badb9aa9802afaa77e1cb2cf *R/plot.bammshifts.R
f3589bbabea1572ef3a612423d3a8bbf *R/plot.credibleshiftset.R
31e1d0dd5af150a3511e0d2fce0baa2d *R/plotPrior.R
635b6d12a9b0ee5e28f63991c5077d24 *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
5b45e05c3d9ffe741db8095fe138aa7f *R/speciesByRatesMatrix.R
99fa0d7ab5f92fa431ea10d70632d485 *R/stepBF.R
bd8eada1986a64f6722665041110bbb0 *R/subsetEventData.R
6415600bac9a470c34418c2575efc276 *R/subtreeBAMM.R
0ee83a2de40c8a2b4883bb70367add18 *R/summary.bammdata.R
4e612dd04640879e0713623677e201b1 *R/summary.credibleshiftset.R
e83b5fc500dc60fb37002c3e9c89e850 *R/testTimeVariableBranches.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
a0b9ad76df6bddec1f7fc2fca2af4277 *R/traitDependentBAMM.R
15a7e0dc70a3ba73af7139512d8b8acd *R/transparentColor.R
90904c659a71babbc7fda14d1cf22881 *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
9c2e872a02d62088453d620f3dc77b1a *man/BAMMlikelihood.Rd
9d01cfe8d252021ac9a2d53826717570 *man/BAMMtools-data.Rd
84e755894afa621d4561797cfe808985 *man/BAMMtools.Rd
bc644d0ffc7e838dbe472f01e3ad6723 *man/ShiftProbsTree.Rd
02abcdb4d090e374f609793c08da0ecb *man/addBAMMlegend.Rd
08529debab776f72eff0e03095785916 *man/addBAMMshifts.Rd
636d53b6125c7dbc13b116f3e798efa1 *man/assignColorBreaks.Rd
23601db480eea342d8cecee757b051c5 *man/cohorts.Rd
1a5764731e2d3d348df22de5a4459f15 *man/computeBayesFactors.Rd
8b7a66cb6d5b6a8caec53a1fb7b7ee84 *man/credibleShiftSet.Rd
63fe2b24fd0d810ba268bdb623931946 *man/distinctShiftConfigurations.Rd
a753c7a1599632cf383145f8554eaade *man/dtRates.Rd
ba300b02a9d10d5232d2da0d1afce84f *man/generateControlFile.Rd
4c1256822669a4777c643aec7b1d4297 *man/getBestShiftConfiguration.Rd
d904414f6a986a9eafc46b5b85cb701f *man/getBranchShiftPriors.Rd
b1c60d0c208a720470562077ce7c66bd *man/getCladeRates.Rd
5eda7fe84aa5c42bad3bff64301ec321 *man/getCohortMatrix.Rd
661157b699115e5f7125c2359e989d48 *man/getEventData.Rd
5166253a57edaeb9f272bec6305455eb *man/getJenksBreaks.Rd
3b2b3ee563cff6fe560d54957cc83663 *man/getMarginalBranchRateMatrix.Rd
1972ef104c164840d0bd98ad1edf9b71 *man/getMeanBranchLengthTree.Rd
bafd8d4d0b2f6c0b340b3181fae25017 *man/getRateThroughTimeMatrix.Rd
b78cab0b31fcee1fe65a2e0852316552 *man/getShiftNodesFromIndex.Rd
d24bec7b1a7e336b168a8b13d1a11a7f *man/getTipRates.Rd
198c1a6fdd8c3ac08c58605f99526848 *man/getmrca.Rd
48625c9734eb7dad9dd1a122b3c6b1b1 *man/marginalOddsRatioBranches.Rd
09075aa1bd41cd1ecd8d4fc7c2203245 *man/maximumShiftCredibility.Rd
1d332d3e04168492456330b91e16d150 *man/plot.bammdata.Rd
b9d7967566e2f3425a7a421e0e14abf8 *man/plot.bammshifts.Rd
24fe36e7d89736f4284059f0838292de *man/plot.credibleshiftset.Rd
83c264d12c585193e34336aaffe10e63 *man/plotPrior.Rd
b7929ea80c8cdbf452dc2fb0e32701ab *man/plotRateThroughTime.Rd
9d762c664b0b65ad5c83d3aca0d0d450 *man/ratesHistogram.Rd
b69f45225eaef63817153fc59fb0b0d6 *man/richColors.Rd
1f4d24db62cd4ad86e2f1f7513e1c680 *man/samplingProbs.Rd
75ea9abc9b9742c2b2521a3af918a923 *man/setBAMMpriors.Rd
ea779646f54caefdf9735a0f64c3fa5c *man/speciesByRatesMatrix.Rd
d4f458bf0ebcbd1ea32344fe9c3b0aff *man/stepBF.Rd
772d275b1d4cb4880963cfaab28cbec4 *man/subsetEventData.Rd
e2c384bbc32ee5fc48ecd38912c7333f *man/subtreeBAMM.Rd
438f2c8b6ec718ce6ce5c6525d13c7b0 *man/summary.bammdata.Rd
bf22ec6c2436e9915ce54cdcfff5b7c7 *man/summary.credibleshiftset.Rd
16488cdf23b1adfa3c2f9a9d07517ba9 *man/testTimeVariableBranches.Rd
0b3c71eda59b485d2ccdee7eff4d6e80 *man/traitDependentBAMM.Rd
fff297fe58738b9ef1cbecb2c4ade485 *man/transparentColor.Rd
7ec8280386b24f81889eddc15a2255a8 *man/writeEventData.Rd
163c1c799f50b44886d9d1a8f97cdfd7 *src/cohort_matrix.c
5eefe99082d44336cb7b7fcf14ee7d4f *src/dtrates.c
16bc6cd0ee25afe4b842a16c1ce6d70e *src/jenksBrks.c
3f21d3a7abe2f1192f0f765dabab446d *src/treetraverse.c
