8230760f8cb7d20da4d072cd23de0eee *DESCRIPTION
d0736be652fa9c371e051fa34681ba81 *NAMESPACE
63f44fbee7629169a789397a0f4cee0d *R/BAMMlikelihood.R
543484729e4c2a4c3b35f29c00fbf23b *R/NU.branching.times.R
1a41cc515bd31e1a9afa6ffe2eb4526d *R/addBAMMlegend.R
fd3bfbc22fbcea805c711b220afa83f4 *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
d74e41b94fc6f7ba2f55aef097618c59 *R/assignColorBreaks.R
5e6ea93375884ba0439999deb28cb570 *R/bammcolors.R
4b80cc858dda24602e1ed7a30b9ee825 *R/barLegend.R
4862c6aedd6abff3de1805271cd6b3fa *R/branchMeanRateExponential.R
fc101c15e2620c7421e3968bb5384987 *R/cohorts.R
6a78ea3776dffed9f2e682430cdeb265 *R/colorMap.R
ded9e93e6c76664cb7bd7bfc15939ae1 *R/computeBayesFactors.R
9b7bf54a057225d69ad051bc41adbc6b *R/credibleShiftSet.R
f5430311f8c94760f2996c1c13a4def6 *R/cumulativeShiftProbsTree.R
561665af3a094cbab8e8d0e1e23a84e0 *R/distinctShiftConfigurations.R
8133cf873d122432a6ae8eb207704e8f *R/dtRates.R
70370fd2c208f839c9db738095a95476 *R/exponentialRate.R
b3806382988d1816d5a4515ed4e5c377 *R/fxnDeps.R
02a68a0925d01fb105cb3f959b8e4cc8 *R/generateControlFile.R
96634f414e2a33f2798d0f001bf2be8b *R/getBestShiftConfiguration.R
81acba04fcdc13a16ec03d47f8c9f812 *R/getBranchShiftPriors.R
68accff10ab2cc4f679e4c00cf2935db *R/getCladeRates.R
08b8233ba91f81cb240e003f54397904 *R/getCohortMatrix.R
79262ab1eda873c773557179b19918a5 *R/getDesc.R
74fd00a933409320d8f05da2d0e855c9 *R/getEventData.R
20886b34bd5b787057463b9f7e18bacb *R/getJenksBreaks.R
6d95810cf7823e4352a1fe6ff4b44e29 *R/getMarginalBranchRateMatrix.R
e48694ca713a99dffa29dad623193ba3 *R/getMeanBranchLengthTree.R
cc5fd1d2f1654421435c312fc1ec9ec0 *R/getPathToRoot.R
88ad32daaa1dc2519c67173d61159e8f *R/getRateThroughTimeMatrix.R
0b3ae5dbd09d517cbd6b76855a065a63 *R/getRecursiveSequence.R
0c1f36cf3e8bcda32ab3ac28808eac7e *R/getSequenceForwardTraversal.R
7afb8a38d0403904b4c8313870f754b1 *R/getShiftNodesFromIndex.R
270a14ca850f02f9e2d302d199bc5de0 *R/getSpanningTaxonPair.R
693f32920e1812750c2f5131a6b434e7 *R/getStartStopTimes.R
14dcb9fd640285633443bfc44fa1d503 *R/getTipRates.R
daf9c480426d0357075c939f5db07b1f *R/getmrca.R
618d603ef55c26f80ae4b7975aef3294 *R/inv.logit.R
8f1ff6b7910c7e8f9c2c61bfb56ba57b *R/logit.R
7ec5b6b492b7fd582adc0206664acb35 *R/marginalOddsRatioBranches.R
368373ef24a7e4bc1a76c524f39496c3 *R/marginalShiftProbsTree.R
bcc0037a4f28b3fb2e0e6363a7be3049 *R/maximumShiftCredibility.R
e16d449321ee26bc8fc9436930a8995e *R/mkdtsegsPhylo.R
e1da57910a5fb4972cd4dddbc03eab39 *R/mkdtsegsPolar.R
eea2d2fabe9277ec97e8758a5bade8d3 *R/phylogeneticMean.R
4ae9dd5cbf5c373f1984652a43242425 *R/plot.bammdata.R
6046fc14b71c05b4bf9fd31ad0a28963 *R/plot.bammshifts.R
a134617e1ed370b8331aae5dab002984 *R/plot.credibleshiftset.R
be277e6ed8de84582c005070f0feeb85 *R/plotPrior.R
38125daceea61857e312e41785a620b9 *R/plotRateThroughTime.R
67e8e6b3f70e5cd8d4c46211ca85261e *R/print.bammdata.R
b9c867db26f7fc3e0819d8d9939917df *R/print.credibleshiftset.R
dedd9b383d3dfba7d3ad072999ecae0a *R/rateLegend.R
9d8c018e3d82ba4224d0f5c91d0f346a *R/ratesHistogram.R
05449bd029a2291958a6c00fa8c4340e *R/recursivelySetNodeStates.R
f8932cb96a22c7a4e77c1282a62a7c39 *R/richColors.R
aa1062a46bbf74409a4a64033fffc1b9 *R/samplingProbs.R
a6f654afef98c5a6cc9a10af887064dd *R/segMap.R
e2619c728cf7087fe6208650ecc5a06e *R/setBAMMpriors.R
b868796cd7ddd0db15bc0b7fe7d19da2 *R/setPhyloTreeCoords.R
3af600912ba356d4d20fd68b4d87eb44 *R/setPolarTreeCoords.R
b527d9f6d07e9ffd43bd6abbd9adbd90 *R/speciesByRatesMatrix.R
552efe1eaa120ffdb523e558184ad975 *R/subsetEventData.R
dea17a1eb79feaac99d8896d52a368bf *R/subtreeBAMM.R
050996e39e4d2a4e1ab93fbc8bf62d13 *R/summary.bammdata.R
2422e76b1fb383f11eedf27adfeaef88 *R/summary.credibleshiftset.R
820754915fe198ba940b9b065bbf1ace *R/testTimeVariableBranches.R
6eaebe9570735b8cf1acc2dfea8ede41 *R/timeIntegratedBranchRate.R
4ffe29afe99c89700fb390dd4c52dca4 *R/traitDependentBAMM.R
fdd588f5e9cf6e504c2175bcec429fe2 *R/transparentColor.R
13b06972239f32b81597af7bc7058328 *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
76a67b70048f2b84c892660f4fc2faf9 *man/BAMMlikelihood.Rd
8d5426f5d4ba3b9c4ed533f880c87a85 *man/BAMMtools-data.Rd
c74db3f4fab2c9f5d10863140667358f *man/BAMMtools-internal.Rd
89fae29c914ffdb9b460cef22cadcf8b *man/BAMMtools-package.Rd
1fe8a722f113270e78b4dacd3d87dfeb *man/ShiftProbsTree.Rd
b4d0c09cc78079852c3154bb5e3610a2 *man/addBAMMlegend.Rd
c455b98809f1c58c6aba2fe95e2aa89b *man/addBAMMshifts.Rd
db7cf4073b4ed0bf80c02616e5046c4a *man/assignColorBreaks.Rd
7c123e4464cceb7f0dbd72419e5abb22 *man/cohorts.Rd
28b74773e530b12eb381d1a6fc7bfd9c *man/computeBayesFactors.Rd
f9f3de51c9c646ffbd91ef5c141a4816 *man/credibleShiftSet.Rd
4eec3056ba3a2a09f39499b39250da85 *man/distinctShiftConfigurations.Rd
5e8ee54198ba738ddec68a7bae31324f *man/dtRates.Rd
30c8b6a295f4ef67901b1790d9ec86e6 *man/generateControlFile.Rd
17ebeb33c0a0d9cbec8c069adb8ead36 *man/getBestShiftConfiguration.Rd
8723e59a4d05da1edbddaf1dc8352853 *man/getBranchShiftPriors.Rd
f56634bd5b33fe85c808bb37fa4dc490 *man/getCladeRates.Rd
8a4e23cdce382de062777c38055e6cc9 *man/getCohortMatrix.Rd
6347a8a8a564ea6d1ee2a8f2b1a7c8e9 *man/getEventData.Rd
17b8645b52acadcc947d29faf9c7db88 *man/getJenksBreaks.Rd
ceefbadcf9e76433dff446ec6ae7b4db *man/getMarginalBranchRateMatrix.Rd
40df4e5dafb98993ff5f0d2d7dfa754c *man/getMeanBranchLengthTree.Rd
945b5609949866ef950438f96faab8d3 *man/getRateThroughTimeMatrix.Rd
79153c3e9ab884b3125140198ceec7a5 *man/getShiftNodesFromIndex.Rd
399819f9eddf9760f28f5f47716499c2 *man/getTipRates.Rd
4e2f81bbca7bb92c5e0584479640795f *man/getmrca.Rd
52fce9c690283c1b6a7719fa009f63b5 *man/marginalOddsRatioBranches.Rd
feaad2d2939646c62eb04689f1aa8942 *man/maximumShiftCredibility.Rd
d73ffb8743cfdbe673485008840bde45 *man/plot.bammdata.Rd
39324f70ad79c7bedccbc8cfbee9d05d *man/plot.bammshifts.Rd
4e26f0f379be74192bafcb5872dcefa3 *man/plot.credibleshiftset.Rd
e8a912217a5342f587f0352363cb6cd6 *man/plotPrior.Rd
d666c362e230c4282324273870a01d4f *man/plotRateThroughTime.Rd
a39537dd8cb260496fb50d6ae0bdfa5a *man/ratesHistogram.Rd
67581456f237bd2a4a34705b5a4bc954 *man/samplingProbs.Rd
b6dfa90d25498f5e590b80b0b80d277f *man/setBAMMpriors.Rd
90d06153d74c3f5d0499c5327aec873c *man/speciesByRatesMatrix.Rd
65e62570db37c9c6b2f8332c9fd74f77 *man/subsetEventData.Rd
4664012d963d5f6b13ff58bad76acab9 *man/subtreeBAMM.Rd
31c6a7c378a940851a28d04bba3829a3 *man/summary.bammdata.Rd
fb3185e7cfd3dbf19a5434755e9e5310 *man/summary.credibleshiftset.Rd
9b7e21f7b779a2f56669f6a6ce9af344 *man/testTimeVariableBranches.Rd
5ab5b7011733cc4fe68b45b3ed53ab7d *man/traitDependentBAMM.Rd
47c6555721190bb2bc5cae32a95b9981 *man/transparentColor.Rd
c0eb206e6869c0aaad9a56fb1acb7282 *man/writeEventData.Rd
163c1c799f50b44886d9d1a8f97cdfd7 *src/cohort_matrix.c
5eefe99082d44336cb7b7fcf14ee7d4f *src/dtrates.c
16bc6cd0ee25afe4b842a16c1ce6d70e *src/jenksBrks.c
3f21d3a7abe2f1192f0f765dabab446d *src/treetraverse.c
