Congruent Rate Analyses in Birth-Death Scenarios

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Documentation for package ‘CRABS’ version 1.2.0

• DESCRIPTION file.
• Package NEWS.

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