Phylogenetic ANalyses of DiversificAtion

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Documentation for package ‘RPANDA’ version 1.2

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RPANDA-package RPANDA
Anolis.data Anolis dataset
Balaenopteridae Balaenopteridae phylogeny
BICompare Identify modalities in a phylogeny
Calomys Calomys phylogeny
Cetacea Cetacean phylogeny
CreateGeoObject Create blank geography object
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
fit_t_comp Fits models of trait evolution incorporating competitive interactions
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
likelihood_t_DD Likelihood of a dataset under diversity-dependent models.
likelihood_t_DD_geog Likelihood of a dataset under diversity-dependent models with biogeography.
likelihood_t_MC Likelihood of a dataset under the matching competition model.
likelihood_t_MC_geog Likelihood of a dataset under the matching competition model with biogeography.
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
sim_t_comp Recursive simulation (root-to-tip) of competition models
spectR Spectral density plot of a phylogeny