Phylogenetic ANalyses of DiversificAtion

Documentation for package ‘RPANDA’ version 1.1

RPANDA-package	RPANDA
Balaenopteridae	Balaenopteridae phylogeny
BICompare	Identify modalities in a phylogeny
Calomys	Calomys phylogeny
Cetacea	Cetacean phylogeny
fit_bd	Maximum likelihood fit of the general birth-death model
fit_coal_cst	Maximum likelihood fit of the equilibrium model
fit_coal_var	Fit birth-death model using a coalescent approch
fit_env	Maximum likelihood fit of the environmental birth-death model
fit_sgd	Maximum likelihood fit of the SGD model
InfTemp	Paleotemperature data across the Cenozoic
JSDtree	Jensen-Shannon distance between phylogenies
JSDtree_cluster	Clustering of phylogenies
likelihood_bd	Likelihood of a phylogeny under the general birth-death model
likelihood_coal_cst	Likelihood of a phylogeny under the equilibrium diversity model
likelihood_coal_var	Likelihood of a birth-death model using a coalescent approch
likelihood_sgd	Likelihood of a phylogeny under the SGD model
Phocoenidae	Phocoenidae phylogeny
Phyllostomidae	Phyllostomidae phylogeny
Phyllostomidae_genera	Phylogenies of Phyllostomidae genera
plot_BICompare	Display modalities on a phylogeny.
plot_dtt	Plot diversity through time
plot_fit_bd	Plot speciation, extinction & net diversification rate functions of a fitted model
plot_fit_env	Plot speciation, extinction & net diversification rate functions of a fitted environmental model
plot_spectR	Spectral density plot of a phylogeny.
RPANDA	RPANDA
sim_sgd	Algorithm for simulating a phylogenetic tree under the SGD model
spectR	Spectral density plot of a phylogeny