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 from 'BAMM' results |
cumulativeShiftProbsTree |
Branch-specific rate shift probabilities |
distinctShiftConfigurations |
Identify distinct rate shift configurations |
dtRates |
Calculate macroevolutionary rate changes on a phylogeny from 'BAMM' output |
events.fishes |
BAMMtools datasets |
events.primates |
BAMMtools datasets |
events.whales |
BAMMtools datasets |
fishes |
BAMMtools datasets |
generateControlFile |
Generate control file for 'BAMM' |
getBestShiftConfiguration |
Get the best (sampled) rate shift configuration from a 'BAMM' analysis |
getBranchShiftPriors |
Compute prior odds of a rate shift on each branch of a phylogeny from BAMM output |
getCladeRates |
Compute clade-specific mean rates |
getCohortMatrix |
Compute the pairwise correlation in rate regimes between all tips in a 'bammdata' object |
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 macroevolutionary rate estimates |
getmrca |
Find most recent common ancestors |
getRateThroughTimeMatrix |
Generate rate-through-time matrix from 'bammdata' object |
getShiftNodesFromIndex |
Identify nodes associated with rate shifts from 'bammdata' object |
getTipRates |
Compute tip-specific macroevolutionary rates from 'bammdata' object |
marginalOddsRatioBranches |
Ratio of (marginal) posterior-to-prior probabilities on individual branches |
marginalShiftProbsTree |
Branch-specific rate shift probabilities |
mass.primates |
BAMMtools datasets |
maximumShiftCredibility |
Estimate maximum shift credibility configuration |
mcmc.primates |
BAMMtools datasets |
mcmc.whales |
BAMMtools datasets |
plot.bammdata |
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' analysis |
plotPrior |
Plot the prior and posterior distribution of shifts |
plotRateThroughTime |
Plot rates through time |
primates |
BAMMtools datasets |
print.credibleshiftset |
Summary of credible set of shift configurations from a 'BAMM' analysis |
ratesHistogram |
Histogram of 'BAMM' rate frequencies |
richColors |
Rich color palette |
samplingProbs |
Creates clade-specific sampling fractions |
setBAMMpriors |
Set BAMM Priors |
speciesByRatesMatrix |
Compute species-specific rate through time trajectories |
stepBF |
Identify the optimal number of shifts using Bayes factors |
strapp |
STRAPP: STructured Rate Permutations on Phylogenies |
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' analysis |
testTimeVariableBranches |
Evaluate evidence for temporal rate variation across tree |
traitDependentBAMM |
STRAPP: STructured Rate Permutations on Phylogenies |
traits.fishes |
BAMMtools datasets |
transparentColor |
Define colors with transparency |
whales |
BAMMtools datasets |
writeEventData |
Write a 'bammdata' object to disk |