# Congruent Rate Analyses in Birth-Death Scenarios

## Documentation for package ‘CRABS’ version 1.2.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

CRABS-package | CRABS: Congruent Rate Analyses in Birth-death Scenarios
congruent.models | Create a set of congruent models
CRABS | CRABS: Congruent Rate Analyses in Birth-death Scenarios
crabs.loglikelihood | Compute likelihood
create.model | Computes the congruent class, i.e., the pulled rates.
full.plot.regularity.thresholds | Plots the rate functions after filtering them according to a given penalty and predefined thresholds.
joint.congruent.models | Create a set of congruent models
model2df | model2df
plot.CRABS | Plots the rate functions including the pulled rates.
plot.CRABSset | Plots the rate functions
primates | Primates phylogenetic tree
primates_ebd | RevBayes Primates birth-death model
primates_ebd_log | Primates birth-death model
primates_ebd_tess | TESS Primates birth-death model
primates_ebd_treepar | TreePar Primates birth-death model
print.CRABS | Print method for CRABS object
print.CRABSposterior | Title
print.CRABSset | Print method for CRABSset object
print.CRABSsets | print.CRABSsets
read.RevBayes | read RevBayes log file
sample.basic.models | Samples simple increase/decrease models through time with noise.
sample.basic.models.joint | Jointly samples speciation and extinction trajectories through time, with noise.
sample.congruence.class | Stochastic exploration of congruent models.
sample.congruence.class.posterior | Stochastic exploration of congruent models for all samples in the posterior
sample.rates | Sample custom functions through time.
summarize.posterior | Summarize trends in the posterior
summarize.trends | Summarize trends in the congruence class