Package: BAMMtools 2.1.12

Pascal Title

BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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.

Authors:Dan Rabosky [aut], Michael Grundler [aut], Pascal Title [aut, cre], Carlos Anderson [aut], Jeff Shi [aut], Joseph Brown [aut], Huateng Huang [aut], Jon Mitchell [aut]

BAMMtools_2.1.12.tar.gz
BAMMtools_2.1.12.tar.gz(r-4.5-noble)BAMMtools_2.1.12.tar.gz(r-4.4-noble)
BAMMtools_2.1.12.tgz(r-4.4-emscripten)BAMMtools_2.1.12.tgz(r-4.3-emscripten)
BAMMtools.pdf |BAMMtools.html✨
BAMMtools/json (API)

# Install 'BAMMtools' in R:
install.packages('BAMMtools', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.05 score 2 packages 468 scripts 2.0k downloads 55 mentions 43 exports 10 dependencies

Last updated 2 months agofrom:6aae075d51. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-linux-x86_64OKNov 12 2024

Exports:addBAMMlegendaddBAMMshiftsassignColorBreaksBAMMlikelihoodcohortscomputeBayesFactorscredibleShiftSetcumulativeShiftProbsTreedistinctShiftConfigurationsdtRatesgenerateControlFilegetBestShiftConfigurationgetBranchShiftPriorsgetCladeRatesgetCohortMatrixgetEventDatagetJenksBreaksgetMarginalBranchRateMatrixgetMeanBranchLengthTreegetmrcagetRateThroughTimeMatrixgetShiftNodesFromIndexgetTipRatesmarginalOddsRatioBranchesmarginalShiftProbsTreemaximumShiftCredibilityplot.bammdataplot.bammshiftsplot.credibleshiftsetplotPriorplotRateThroughTimeratesHistogramrichColorssamplingProbssetBAMMpriorsspeciesByRatesMatrixstepBFsubsetEventDatasubtreeBAMMtestTimeVariableBranchestraitDependentBAMMtransparentColorwriteEventData

Dependencies:apebitopscaToolsdigestgplotsgtoolsKernSmoothlatticenlmeRcpp

Readme and manuals

Help Manual

Help pageTopics
Add a color legend to a phylo-rate plotaddBAMMlegend
Add 'BAMM'-inferred rate shifts to a phylogeny plotaddBAMMshifts
Map macroevolutionary rates to colorsassignColorBreaks
Calculate 'BAMM' likelihoodBAMMlikelihood
BAMMtoolsBAMMtools-package BAMMtools
BAMMtools datasetsBAMMtools-data events.fishes events.primates events.whales fishes mass.primates mcmc.primates mcmc.whales primates traits.fishes whales
Visualize macroevolutionary cohortscohorts
Compute Bayes FactorscomputeBayesFactors
Credible set of macroevolutionary rate shift configurations from 'BAMM' resultscredibleShiftSet
Branch-specific rate shift probabilitiescumulativeShiftProbsTree marginalShiftProbsTree
Identify distinct rate shift configurationsdistinctShiftConfigurations
Calculate macroevolutionary rate changes on a phylogeny from 'BAMM' outputdtRates
Generate control file for 'BAMM'generateControlFile
Get the best (sampled) rate shift configuration from a 'BAMM' analysisgetBestShiftConfiguration
Compute prior odds of a rate shift on each branch of a phylogeny from BAMM outputgetBranchShiftPriors
Compute clade-specific mean ratesgetCladeRates
Compute the pairwise correlation in rate regimes between all tips in a 'bammdata' objectgetCohortMatrix
Create 'bammdata' object from MCMC outputgetEventData
Jenks natural breaks classificationgetJenksBreaks
Compute mean branch rates for 'bammdata' objectgetMarginalBranchRateMatrix
Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimatesgetMeanBranchLengthTree
Find most recent common ancestorsgetmrca
Generate rate-through-time matrix from 'bammdata' objectgetRateThroughTimeMatrix
Identify nodes associated with rate shifts from 'bammdata' objectgetShiftNodesFromIndex
Compute tip-specific macroevolutionary rates from 'bammdata' objectgetTipRates
Ratio of (marginal) posterior-to-prior probabilities on individual branchesmarginalOddsRatioBranches
Estimate maximum shift credibility configurationmaximumShiftCredibility
Plot 'BAMM'-estimated macroevolutionary rates on a phylogenyplot.bammdata
Plot distinct rate shift configurations on a phylogenyplot.bammshifts
Plot credible set of rate shift configurations from 'BAMM' analysisplot.credibleshiftset
Plot the prior and posterior distribution of shiftsplotPrior
Plot rates through timeplotRateThroughTime
Histogram of 'BAMM' rate frequenciesratesHistogram
Rich color paletterichColors
Creates clade-specific sampling fractionssamplingProbs
Set BAMM PriorssetBAMMpriors
Compute species-specific rate through time trajectoriesspeciesByRatesMatrix
Identify the optimal number of shifts using Bayes factorsstepBF
Subset a 'bammdata' objectsubsetEventData
Pulls out a subtree from 'bammdata' objectsubtreeBAMM
Summary of rate shift results from 'BAMM' analysissummary.bammdata
Summary of credible set of shift configurations from a 'BAMM' analysisprint.credibleshiftset summary.credibleshiftset
Evaluate evidence for temporal rate variation across treetestTimeVariableBranches
STRAPP: STructured Rate Permutations on Phylogeniesstrapp traitDependentBAMM
Define colors with transparencytransparentColor
Write a 'bammdata' object to diskwriteEventData