addBAMMlegend | Add a color legend to a phylo-rate plot |
addBAMMshifts | Add 'BAMM'-inferred rate shifts to a phylogeny plot |
assignColorBreaks | Map macroevolutionary rates to colors |
BAMMlikelihood | Calculate 'BAMM' likelihood |
BAMMtools | BAMMtools |
BAMMtools-data | BAMMtools datasets |
cohorts | Visualize macroevolutionary cohorts |
computeBayesFactors | Compute Bayes Factors |
credibleShiftSet | Credible set of macroevolutionary rate shift configurations... |
distinctShiftConfigurations | Identify distinct rate shift configurations |
dtRates | Calculate macroevolutionary rate changes on a phylogeny from... |
generateControlFile | Generate control file for 'BAMM' |
getBestShiftConfiguration | Get the best (sampled) rate shift configuration from a 'BAMM'... |
getBranchShiftPriors | Compute prior odds of a rate shift on each branch of a... |
getCladeRates | Compute clade-specific mean rates |
getCohortMatrix | Compute the pairwise correlation in rate regimes between all... |
getEventData | Create 'bammdata' object from MCMC output |
getJenksBreaks | Jenks natural breaks classification |
getMarginalBranchRateMatrix | Compute mean branch rates for 'bammdata' object |
getMeanBranchLengthTree | Compute phylogeny with branch lengths equal to corresponding... |
getmrca | Find most recent common ancestors |
getRateThroughTimeMatrix | Generate rate-through-time matrix from 'bammdata' object |
getShiftNodesFromIndex | Identify nodes associated with rate shifts from 'bammdata'... |
getTipRates | Compute tip-specific macroevolutionary rates from 'bammdata'... |
marginalOddsRatioBranches | Ratio of (marginal) posterior-to-prior probabilities on... |
maximumShiftCredibility | Estimate maximum shift credibility configuration |
plot | Plot 'BAMM'-estimated macroevolutionary rates on a phylogeny |
plot.bammshifts | Plot distinct rate shift configurations on a phylogeny |
plot.credibleshiftset | Plot credible set of rate shift configurations from 'BAMM'... |
plotPrior | Plot the prior and posterior distribution of shifts |
plotRateThroughTime | Plot rates through time |
ratesHistogram | Histogram of 'BAMM' rate frequencies |
richColors | Rich color palette |
samplingProbs | Creates clade-specific sampling fractions |
setBAMMpriors | Set BAMM Priors |
ShiftProbsTree | Branch-specific rate shift probabilities |
speciesByRatesMatrix | Compute species-specific rate through time trajectories |
stepBF | Identify the optimal number of shifts using Bayes factors |
subsetEventData | Subset a 'bammdata' object |
subtreeBAMM | Pulls out a subtree from 'bammdata' object |
summary.bammdata | Summary of rate shift results from 'BAMM' analysis |
summary.credibleshiftset | Summary of credible set of shift configurations from a 'BAMM'... |
testTimeVariableBranches | Evaluate evidence for temporal rate variation across tree |
traitDependentBAMM | STRAPP: STructured Rate Permutations on Phylogenies |
transparentColor | Define colors with transparency |
writeEventData | Write a 'bammdata' object to disk |
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