Package index

All functions

generateViridisColorScale()

Generate Scaled Viridis Color Palette for Rate Parameters

plot(<rateMap>)

Plot rateMap Objects

plot_ic_acceptance_matrix()

Plot IC Acceptance Matrix with Optional Rate-of-Improvement Overlay

print(<bifrost_search>)

Print method for bifrost search results

print(<rateMap>)

Print a rateMap Object

rateMap()

Compute Branchwise Rate Maps Across Runs

rateMapControl()

Control Advanced rateMap() Options

rateMapRateFlags()

Control Near-Zero and Tail Rate Diagnostics for rateMap()

rateMapView()

Create a Display View of a rateMap Object

searchOptimalConfiguration()

Search for an Optimal Multi-Regime (Shift) Configuration on a Phylogeny