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BAMMtools  

Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
View on CRAN: Click here


Download and install BAMMtools package within the R console
Install from CRAN:
install.packages("BAMMtools")

Install from Github:
library("remotes")
install_github("cran/BAMMtools")

Install by package version:
library("remotes")
install_version("BAMMtools", "2.1.12")



Attach the package and use:
library("BAMMtools")
Maintained by
Pascal Title
[Scholar Profile | Author Map]
First Published: 2014-03-05
Latest Update: 2022-07-15
Description:
Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
How to cite:
Pascal Title (2014). BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees. R package version 2.1.12, https://cran.r-project.org/web/packages/BAMMtools. Accessed 29 Mar. 2025.
Previous versions and publish date:
1.0.1 (2014-03-07 13:52), 1.0 (2014-03-05 16:41), 2.0.2 (2014-07-10 05:11), 2.0.4 (2015-03-18 17:52), 2.0.5 (2015-03-23 13:51), 2.0.6 (2015-09-10 20:03), 2.1.0 (2015-11-10 09:41), 2.1.1 (2016-03-03 05:49), 2.1.3 (2016-05-24 14:49), 2.1.4 (2016-06-10 14:00), 2.1.5 (2016-10-03 22:47), 2.1.6 (2017-02-03 08:13), 2.1.7 (2019-12-05 23:50), 2.1.8 (2021-10-18 21:40), 2.1.9 (2022-04-23 22:50), 2.1.10 (2022-07-15 21:30), 2.1.11 (2023-12-19 06:50)
Other packages that cited BAMMtools R package
View BAMMtools citation profile
Other R packages that BAMMtools depends, imports, suggests or enhances
Complete documentation for BAMMtools
Functions, R codes and Examples using the BAMMtools R package
Some associated functions: BAMMlikelihood . BAMMtools-data . BAMMtools . ShiftProbsTree . addBAMMlegend . addBAMMshifts . assignColorBreaks . cohorts . computeBayesFactors . credibleShiftSet . distinctShiftConfigurations . dtRates . generateControlFile . getBestShiftConfiguration . getBranchShiftPriors . getCladeRates . getCohortMatrix . getEventData . getJenksBreaks . getMarginalBranchRateMatrix . getMeanBranchLengthTree . getRateThroughTimeMatrix . getShiftNodesFromIndex . getTipRates . getmrca . marginalOddsRatioBranches . maximumShiftCredibility . plot.bammshifts . plot.credibleshiftset . plot . plotPrior . plotRateThroughTime . ratesHistogram . richColors . samplingProbs . setBAMMpriors . speciesByRatesMatrix . stepBF . subsetEventData . subtreeBAMM . summary.bammdata . summary.credibleshiftset . testTimeVariableBranches . traitDependentBAMM . transparentColor . writeEventData . 
Some associated R codes: BAMMtools-data.R . BAMMtools-package.R . NU.branching.times.R . addBAMMlegend.R . addBAMMshifts.R . arc.R . areEventConfigurationsIdentical.R . areShiftSetsEqual.R . as.bammdata.R . as.phylo.bammdata.R . assignColorBreaks.R . bammLikelihood.R . bammcolors.R . barLegend.R . branchMeanRateExponential.R . cohorts.R . colorMap.R . computeBayesFactors.R . credibleShiftSet.R . cumulativeShiftProbsTree.R . distinctShiftConfigurations.R . dtRates.R . exponentialRate.R . fxnDeps.R . generateControlFile.R . getBestShiftConfiguration.R . getBranchShiftPriors.R . getCladeRates.R . getCohortMatrix.R . getDesc.R . getEventData.R . getJenksBreaks.R . getMarginalBranchRateMatrix.R . getMeanBranchLengthTree.R . getPathToRoot.R . getRateThroughTimeMatrix.R . getRecursiveSequence.R . getSequenceForwardTraversal.R . getShiftNodesFromIndex.R . getSpanningTaxonPair.R . getStartStopTimes.R . getTipRates.R . getmrca.R . inv.logit.R . logit.R . marginalOddsRatioBranches.R . marginalShiftProbsTree.R . maximumShiftCredibility.R . mkdtsegsPhylo.R . mkdtsegsPolar.R . phylogeneticMean.R . plot.bammdata.R . plot.bammshifts.R . plot.credibleshiftset.R . plotPrior.R . plotRateThroughTime.R . print.bammdata.R . rateLegend.R . ratesHistogram.R . recursivelySetNodeStates.R . samplingProbs.R . segMap.R . setBAMMpriors.R . setPhyloTreeCoords.R . setPolarTreeCoords.R . speciesByRatesMatrix.R . stepBF.R . subsetEventData.R . subtreeBAMM.R . summary.bammdata.R . summary.credibleshiftset.R . testTimeVariableBranches.R . timeIntegratedBranchRate.R . traitDependentBAMM.R . transparentColor.R . writeEventData.R .  Full BAMMtools package functions and examples
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