5a15edcc8a507cdecb35f2001da9a459 *DESCRIPTION
515b8f7413189ebd9d18b2970ff43de4 *NAMESPACE
da9f65298c2b61db1e4721df4487903f *R/RevGadgets.R
8fc46d7c590a341cb55a33c9961ee450 *R/calculateShiftBayesFactor.R
d45599cd754bce7bbea499619efaf8f9 *R/colFun.R
a8d19b731ff84f5fda017bcd69b3a50f *R/combineTrace.R
d52452a79050e435923ed9e4876cff7f *R/densiTreeWithBranchData.R
dbad184a076355a1a409be23038f8e13 *R/dropTip.R
340ca6de11b7fbe53cc1b7fca0c1ab26 *R/geomStepRibbon.R
9757982d3b504dc73e7d2e40cbf5f833 *R/getMAP.R
e677de2beb9edb5d3cd6803a579f9de7 *R/global.R
7cefb30385753f3e365b86761c6eab5d *R/matchNodes.R
566096dfa128ad6465a2d71634ce8044 *R/plotAncStatesMAP.R
21a46420f35a2ace02fd8a1cf116a831 *R/plotAncStatesPie.R
74d45add2bc0c00f3d8f7de6f4456e5b *R/plotDivRates.R
10ac41b48681217e64d70956af3dd919 *R/plotFBDTree.R
c9809174e214cffe83aafeaca9b20906 *R/plotHiSSE.R
24f1c3d02ec0ad87488cec68540a59b1 *R/plotMassExtinctions.R
5b162397aca4a874d63ddef18e4a01b0 *R/plotMuSSE.R
56894ce4479aa22389b2e0e051c4d933 *R/plotPostPredStats.R
031c3efa93f9fbe8e4d9f7d3ffe69a09 *R/plotTrace.R
5c14e1702915a08515564efa96cda1b3 *R/plotTree.R
10e55a5ad2207007b8029332e4a16187 *R/plotTreeFull.R
ea2e64338e098ca34745442ad699bf3a *R/posteriorSamplesToParametricPrior.R
7ae683818fd171c9f7b7b70c456a2cfb *R/processAncStates.R
5d9de5b0de756b7e671c85b3a63d2b49 *R/processBranchData.R
682fb3a09b1e22b8c03b15c27458aa5a *R/processDivRates.R
b11cb8b94e9e99146de518fcdc59a2fa *R/processPostPredStats.R
6deed9b7f887267a80bad68d8ed1fcb1 *R/processSSE.R
a37023b36ce15ec9afcdb96d53276a83 *R/readTrace.R
6734f5f6e0f4dcdcd5a641cdf972e983 *R/readTrees.R
a0c86068ab25159e504c0906e9e218b3 *R/removeBurnin.R
f7c6b44abf9c184748a92b02fe50c4e0 *R/rerootPhylo.R
09ae159708c3091c15ce8f58c3011ef9 *R/setMRFGlobalScaleHyperpriorNShifts.R
d59ad30000ac9ff9c842d5d230db2a27 *R/simulateMRF.R
20ab574997348ae8c323f79103b17d1a *R/summarizeTrace.R
4054d75ecc23ec2648e2ad3eb7f9e388 *R/utils.R
0d55316fd392ff67eb37f242b0910789 *README.md
38a05c68df0bdf69781241cf42764fb2 *inst/extdata/PPS/empirical_data_pps_example.csv
c9a94fa87ed5a39f809ccf0400b5c8f0 *inst/extdata/PPS/simulated_data_pps_mini.csv
d3010cf3462f3ae0de16231eb256a7d1 *inst/extdata/bds/primates.tre
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f365a6bc197748fb51079ebc8d090ea7 *inst/extdata/beast2/msbd.rates.trees
2544808f0d1381e5bbca0af1286413f6 *inst/extdata/chromo/ChromEvol_simple_final.tree
e95072d00c8e8d91d4469c66b41b009f *inst/extdata/comp_method_disc/ase_freeK.tree
06849f1fd52226822ce718d0e73e5313 *inst/extdata/dec/simple.ase.tre
3b009e8a9726eab6ffef9d197eaa6e1f *inst/extdata/dec/small_dec.tre
18fd2261c961589bfeab5227ffbe16e7 *inst/extdata/epi_bd/primates_EBD_extinction_rates_mini.p
39554678d2b5cec4035b02e5ff66d252 *inst/extdata/epi_bd/primates_EBD_extinction_times_mini.p
523f9a0d58363239283f1e11544a81fa *inst/extdata/epi_bd/primates_EBD_speciation_rates_mini.p
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70a77e6bd620ef30fbd11d1cf3b9b55f *inst/extdata/fbd/bears.mcc.tre
0241b75ca422c54744048df3ad88f4dc *inst/extdata/graphs/geomStepRibbon_df.rds
4577ae6e75edbc31f92f122ca2ce670f *inst/extdata/graphs/plotAncStatesMAP_df.rds
fb32bdbcae6a425d5d82bb991f5fbc5c *inst/extdata/graphs/plotAncStatesPie_df.rds
db44b3378b5f027a4985315d2af8faeb *inst/extdata/graphs/plotDivRates_df.rds
80c091298fcb66617c4eff49b1ca2f87 *inst/extdata/graphs/plotFBDTree_df.rds
8e175a398dc9f14ab4356277e5ef738f *inst/extdata/graphs/plotHiSSE_df.rds
6d0afec2cff49bc7c1dca8ca6b053f6d *inst/extdata/graphs/plotMassExtinctions_df.rds
2409f80ee835a9297629fe82818d294f *inst/extdata/graphs/plotMuSSE_df.rds
09cd2448e835c9fcb1850ca0532958e9 *inst/extdata/graphs/plotPostPredStats_df.rds
ef8138f2ebf9cfee930807f5412e67a4 *inst/extdata/graphs/plotTrace_df.rds
2691ec0a3698c9991a8fb97b2f5d7b15 *inst/extdata/graphs/plotTree_df.rds
348ac3148b2a6859e3c52ae2cafdea1d *inst/extdata/mass_extinction/crocs_mass_extinction_probabilities_mini.p
267e49a6f3cc6b2a987a9014157f8934 *inst/extdata/relaxed_ou/relaxed_OU_MAP.tre
cb1718d676fdb41dfb94f6819626e4a3 *inst/extdata/sse/primates_BiSSE_activity_period_mini.p
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acaaa1a91c3c3a210478525f6aafde69 *inst/extdata/sub_models/primates_cytb_GTR_MAP.tre
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0b0f53d58e10d7c74ec178f7e855cc07 *man/RevGadgets.Rd
34a4d93bf7fd5be7defa1cfc656a4cc7 *man/calculateShiftBayesFactor.Rd
b67649cc35e876038b6908fc45f1e513 *man/colFun.Rd
667660409002107f0c04a054eb254292 *man/combineTraces.Rd
43e644159ce45ea06bd1030805408a63 *man/densiTreeWithBranchData.Rd
a156f635bf635d0fdc08712cb24e74c1 *man/dropTip.Rd
d7434ce96b1bc68fc69a6f7512141c45 *man/geom_stepribbon.Rd
529a3a62c5cf54af8da568a7356362e1 *man/getMAP.Rd
a46775c6988894a92f254a59fa097d02 *man/matchNodes.Rd
16638867c3e5fc7afb4fd9841143e8a2 *man/plotAncStatesMAP.Rd
6fd080c6b91624b68d28a6968432d782 *man/plotAncStatesPie.Rd
22633cbb51d2134b8b79fefb7e8e7cd7 *man/plotDivRates.Rd
18870c2349749838d3ee3d73b44615a5 *man/plotFBDTree.Rd
1d794c147fe8d4f2847286e70dcbb4b0 *man/plotHiSSE.Rd
8433d5f30da97d7c1d1f310d83093cb4 *man/plotMassExtinctions.Rd
e5bd9c80e07f94cb2dfcf103aef5c15b *man/plotMuSSE.Rd
3eb84bc478bdb53079b783b9bbaefb8c *man/plotPostPredStats.Rd
7b4597fdf2c6736b96af78647134bad4 *man/plotTrace.Rd
4fe643dc1a9392cf87095d660a308efc *man/plotTree.Rd
33c227a458953414a7fa618eddfb6a01 *man/plotTreeFull.Rd
09685237b48fab1ca8646dab685f57a1 *man/posteriorSamplesToParametricPrior.Rd
65cdcac03c267fec06d86e157ac72c45 *man/processAncStates.Rd
327809a36f1bdc69110ae2aa4189558c *man/processBranchData.Rd
5fa37a6c98b934e35249d0c9e093c221 *man/processDivRates.Rd
b21ebedc6c486b7b6540ae81441b46c7 *man/processPostPredStats.Rd
d0bdc970c1c1fd1d1b9175be7dd01ff0 *man/processSSE.Rd
9721f50275afb463d139806961cb6820 *man/readTrace.Rd
07dfff23a1c4ba504c2dd2131cbd4e33 *man/readTrees.Rd
d939f6e7acbcd0d7df9e96dd19d448e4 *man/removeBurnin.Rd
0786c2af87dc854445156ba68e85651b *man/rerootPhylo.Rd
8ea461c974456705f31c2a2a073c45ff *man/setMRFGlobalScaleHyperpriorNShifts.Rd
609974228115c0f6a9308bfd7daa89ed *man/simulateMRF.Rd
3ea72449ab23a34ce0fcf8c2bd6aa400 *man/summarizeTrace.Rd
93da71c28efa4a6212f57a1e0d6697ae *tests/testthat.R
2a16e978aba10ebd326cc90d37027ba4 *tests/testthat/test_calculateShiftBayesFactor.R
95a8b2fa156d8fd9fde0ec98bad9cf0f *tests/testthat/test_colFun.R
5c955235b3a8dbcba1387a9f668406ed *tests/testthat/test_densiTreeWithBranchData.R
90a2b0ef9526adbbfc163202e8fd3a5a *tests/testthat/test_dropTip.R
e2562c265ced153acd3b251aa704c310 *tests/testthat/test_geomStepRibbon.R
1e922759adfb2d862f07d5d81f4209ba *tests/testthat/test_getMAP.R
53f3e9163821d514b480c886081e2ccd *tests/testthat/test_matchNodes.R
b1fe5c7f02771ecb8808d5f8b2b53ce1 *tests/testthat/test_plotAncStatesMAP.R
5c3116fc25410f30fdfdbb9f4d5b2f87 *tests/testthat/test_plotAncStatesPie.R
5a4c5a7b38b62f41a695a21e0865b395 *tests/testthat/test_plotDivRates.R
89471dc63001c912e31e01ffb3c3454d *tests/testthat/test_plotFBDTree.R
50f576e430c14427cf56d465e18b793e *tests/testthat/test_plotHiSSE.R
0252875588adb9aeb9b0dcbc8550793d *tests/testthat/test_plotMassExtinctions.R
361e8667bb39f6aea9e1a00795443815 *tests/testthat/test_plotMuSSE.R
1af99e5953f8cbb20df532bce3b0f5e7 *tests/testthat/test_plotPostPredStats.R
852ea780f4c69adb1fc06da272b8b65a *tests/testthat/test_plotTrace.R
a918f39fb3b1aa23be49e2354362cf5e *tests/testthat/test_plotTree.R
9e2c8b011a3671383eb39d41db87fad6 *tests/testthat/test_posteriorSamplesToParametricPrior.R
c71c80f88f4d748209c339ef48287fdb *tests/testthat/test_processAncStates.R
368c3ebddd329cc558243de47d9a570e *tests/testthat/test_processBranchData.R
1ecab71e86e5839319d7d94a15d58034 *tests/testthat/test_processDivRates.R
a252f440086e307143454709ccd049ca *tests/testthat/test_processPostPredStats.R
d72c7f59093648a948ba61b47b57df08 *tests/testthat/test_processSSE.R
50893975961f12f751beaae1512a2587 *tests/testthat/test_readTrace.R
0a6da5bba78f69170e59b4b6840308f1 *tests/testthat/test_readTrees.R
b2d264a2977e162bb302f39935fe9660 *tests/testthat/test_removeBurnin.R
4ba1ddcca55225dd85a64fc3c885e45d *tests/testthat/test_rerootPhylo.R
d89f7083aa0a40a6a40aa1ae7f1bd6cb *tests/testthat/test_setMRFGlobalScaleHyperpriorNShifts.R
78494d74077fe225a260402ae168364f *tests/testthat/test_simulateMRF.R
75694ac24054f1ed7ad12143d7bf95b0 *tests/testthat/test_summarizeTrace.R
