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BAMMtools
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]
[Scholar Profile | Author Map]
All associated links for this package
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 22 Dec. 2024.
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
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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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