Files in revbayes/RevGadgets
Visualization and Post-Processing of 'RevBayes' Analyses

.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
CRAN-SUBMISSION
DESCRIPTION
NAMESPACE
NEWS.md R/RevGadgets.R R/calculateShiftBayesFactor.R R/colFun.R R/combineTrace.R R/densiTreeWithBranchData.R R/dropTip.R R/geomStepRibbon.R R/getMAP.R R/global.R R/matchNodes.R R/plotAncStatesMAP.R R/plotAncStatesPie.R R/plotDivRates.R R/plotDiversityOBDP.R R/plotFBDTree.R R/plotHiSSE.R R/plotMassExtinctions.R R/plotMuSSE.R R/plotPopSizes.R R/plotPostPredStats.R R/plotTrace.R R/plotTree.R R/plotTreeFull.R R/posteriorSamplesToParametricPrior.R R/processAncStates.R R/processBranchData.R R/processDivRates.R R/processPopSizes.R R/processPostPredStats.R R/processSSE.R R/readOBDP.R R/readTrace.R R/readTrees.R R/removeBurnin.R R/rerootPhylo.R R/setMRFGlobalScaleHyperpriorNShifts.R R/simulateMRF.R R/summarizeTrace.R R/utils.R README.md cran-comments.md inst/developers_guide.md
inst/extdata/PPS/empirical_data_pps_example.csv
inst/extdata/PPS/simulated_data_pps_mini.csv
inst/extdata/bds/primates.tre
inst/extdata/bds/primates_BDS_rates_truncated.p
inst/extdata/beast2/msbd.rates.trees
inst/extdata/chromo/ChromEvol_simple_final.tree
inst/extdata/comp_method_disc/ase_freeK.tree
inst/extdata/dec/simple.ase.tre
inst/extdata/dec/small_dec.tre
inst/extdata/epi_bd/primates_EBD_extinction_rates_mini.p
inst/extdata/epi_bd/primates_EBD_extinction_times_mini.p
inst/extdata/epi_bd/primates_EBD_speciation_rates_mini.p
inst/extdata/epi_bd/primates_EBD_speciation_times_mini.p
inst/extdata/fbd/bears.mcc.tre
inst/extdata/graphs/geomStepRibbon_df.rds
inst/extdata/graphs/plotAncStatesMAP_df.rds
inst/extdata/graphs/plotAncStatesPie_df.rds
inst/extdata/graphs/plotDivRates_df.rds
inst/extdata/graphs/plotDiversityOBDP_df.rds
inst/extdata/graphs/plotFBDTree_df.rds
inst/extdata/graphs/plotHiSSE_df.rds
inst/extdata/graphs/plotMassExtinctions_df.rds
inst/extdata/graphs/plotMuSSE_df.rds
inst/extdata/graphs/plotPopSizes.rds
inst/extdata/graphs/plotPostPredStats_df.rds
inst/extdata/graphs/plotTrace_df.rds
inst/extdata/graphs/plotTree_df.rds
inst/extdata/mass_extinction/crocs_mass_extinction_probabilities_mini.p
inst/extdata/obdp/Kt_trace.p
inst/extdata/obdp/mcmc_OBDP_trees.p
inst/extdata/obdp/start_time_trace.p
inst/extdata/pop_size/horses_CPP_popsizes_mini.p
inst/extdata/pop_size/horses_CPP_times_mini.p
inst/extdata/pop_size/horses_GMRF_popsizes_mini.p
inst/extdata/pop_size/horses_GMRF_times_mini.p
inst/extdata/pop_size/horses_constant_popsizes_mini.p
inst/extdata/relaxed_ou/relaxed_OU_MAP.tre
inst/extdata/sse/primates_BiSSE_activity_period_mini.p
inst/extdata/sse/primates_HiSSE_2_mini.p
inst/extdata/sub_models/primates_cytb_GTR_MAP.tre
inst/extdata/sub_models/primates_cytb_GTR_mini.p
inst/extdata/sub_models/primates_cytb_GTR_mini.trees
inst/hex_sticker.png
man/RevGadgets.Rd man/calculateShiftBayesFactor.Rd man/colFun.Rd man/combineTraces.Rd man/densiTreeWithBranchData.Rd man/dropTip.Rd man/geom_stepribbon.Rd man/getMAP.Rd man/matchNodes.Rd man/plotAncStatesMAP.Rd man/plotAncStatesPie.Rd man/plotDivRates.Rd man/plotDiversityOBDP.Rd man/plotFBDTree.Rd man/plotHiSSE.Rd man/plotMassExtinctions.Rd man/plotMuSSE.Rd man/plotPopSizes.Rd man/plotPostPredStats.Rd man/plotTrace.Rd man/plotTree.Rd man/plotTreeFull.Rd man/posteriorSamplesToParametricPrior.Rd man/processAncStates.Rd man/processBranchData.Rd man/processDivRates.Rd man/processPopSizes.Rd man/processPostPredStats.Rd man/processSSE.Rd man/readOBDP.Rd man/readTrace.Rd man/readTrees.Rd man/removeBurnin.Rd man/rerootPhylo.Rd man/setMRFGlobalScaleHyperpriorNShifts.Rd man/simulateMRF.Rd man/summarizeTrace.Rd
revdep/.gitignore
revdep/README.md revdep/cran.md revdep/failures.md revdep/problems.md tests/testthat.R tests/testthat/test_calculateShiftBayesFactor.R tests/testthat/test_colFun.R tests/testthat/test_densiTreeWithBranchData.R tests/testthat/test_dropTip.R tests/testthat/test_geomStepRibbon.R tests/testthat/test_getMAP.R tests/testthat/test_matchNodes.R tests/testthat/test_plotAncStatesMAP.R tests/testthat/test_plotAncStatesPie.R tests/testthat/test_plotDivRates.R tests/testthat/test_plotDiversityOBDP.R tests/testthat/test_plotFBDTree.R tests/testthat/test_plotHiSSE.R tests/testthat/test_plotMassExtinctions.R tests/testthat/test_plotMuSSE.R tests/testthat/test_plotPopSizes.R tests/testthat/test_plotPostPredStats.R tests/testthat/test_plotTrace.R tests/testthat/test_plotTree.R tests/testthat/test_posteriorSamplesToParametricPrior.R tests/testthat/test_processAncStates.R tests/testthat/test_processBranchData.R tests/testthat/test_processDivRates.R tests/testthat/test_processPopSizes.R tests/testthat/test_processPostPredStats.R tests/testthat/test_processSSE.R tests/testthat/test_readOBDP.R tests/testthat/test_readTrace.R tests/testthat/test_readTrees.R tests/testthat/test_removeBurnin.R tests/testthat/test_rerootPhylo.R tests/testthat/test_setMRFGlobalScaleHyperpriorNShifts.R tests/testthat/test_simulateMRF.R tests/testthat/test_summarizeTrace.R
revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.