| alter.cols | Modify vectors of colors |
| anc.edges | Extract indices for edge ancestral to each edge in a... |
| check.ess | Check whether chains adequately sampled the posterior... |
| check.mix | Check whether chains of a fitted evorates model adequately... |
| combine.chains | Combine chains in a fitted evorates model |
| des.edges | Extract indices for edges descending from each edge in a... |
| drop.tips | Drop tips from objects with phylogenetic trees and... |
| edge.ranges | Extract start and end times for each edge in a phylogeny |
| evorates | evorates: Fitting continuously variable rate models to... |
| exclude.clade | Exclude edge indices for a nested subclade out of a larger... |
| exclude.warmup | Exclude warmup in a fitted evolving rates model |
| fit.evorates | Fit an Evolving Rates model |
| get.bg.rate | Extract background rate parameters from a fitted evorates... |
| get.clade.edges | Get all edge indices in a clade |
| get.post.traits | Sample posterior trait values at nodes given a fitted... |
| get.R | Extract branchwise rate parameters from a fitted evorates... |
| get.sd | Calculate Savage-Dickey ratio to test for significant rate... |
| grapes-chains-grapes | Extract posterior distribution samples from a fitted evorates... |
| grapes-diagnostics-grapes | Extract posterior distribution diagnostics from a fitted... |
| grapes-means-grapes | Extract posterior distribution means from a fitted evorates... |
| grapes-quantiles-grapes | Extract posterior distribution quantiles from a fitted... |
| grapes-select-grapes | Extract subsets from a parameter block |
| input.evorates | Prepare input data for an Evolving Rates model |
| ladder | Ladderize objects with phylogenetic trees and edgewise data |
| output.evorates | Process the output of an Evolving Rates model |
| param_block-class | Class 'param_block': parameter block arrays |
| par.c | Combine parameter blocks |
| plot.evorates | Plot simulated trait and/or rate data from a |
| plot.evorates_fit | Plot a fitted evorates model |
| prof.plot | Plot profiles of posterior samples from a fitted evorates... |
| pwc | Do pairwise comparison among parameter blocks |
| remove.trend | Extract detrended branchwise rate parameters from a fitted... |
| rnorm.par | Generate a parameter block of standard normal samples |
| root.edges | Extract indices for edges descending from root node |
| run.evorates | Run sampler for an Evolving Rates model |
| select.chains | Select chains in a fitted evorates model |
| sim.evorates | Simulate rate/trait data under an evorates model |
| sis.edges | Extract indices for edges sister to each edge in a phylogeny |
| thin.chains | Thin chains in a fitted evolving rates model |
| tip.edges | Extract indices for edges corresponding to tips in a... |
| trace.plot | Plot traces of posterior samples from a fitted evorates model |
