Anolis.data             Anolis dataset
BGB.examples            BioGeoBEARS stochastic maps
BICompare               Identify modalities in a phylogeny
Balaenopteridae         Balaenopteridae phylogeny
Calomys                 Calomys phylogeny
Cetacea                 Cetacean phylogeny
CreateGeoObject         Create biogeography object
CreateGeoObject_BioGeoBEARS
                        Create biogeography object using a stochastic
                        map from BioGeoBEARS
InfTemp                 Paleotemperature data across the Cenozoic
JSDtree                 Jensen-Shannon distance between phylogenies
JSDtree_cluster         Clustering of phylogenies
PhenotypicACDC-class    Class '"PhenotypicACDC"'
PhenotypicADiag-class   Class '"PhenotypicADiag"'
PhenotypicBM-class      Class '"PhenotypicBM"'
PhenotypicDD-class      Class '"PhenotypicDD"'
PhenotypicGMM-class     Class '"PhenotypicGMM"'
PhenotypicModel-class   Class '"PhenotypicModel"'
PhenotypicOU-class      Class '"PhenotypicOU"'
PhenotypicPM-class      Class '"PhenotypicPM"'
Phocoenidae             Phocoenidae phylogeny
Phyllostomidae          Phyllostomidae phylogeny
Phyllostomidae_genera   Phylogenies of Phyllostomidae genera
RPANDA-package          RPANDA
createModel             Creation of a PhenotypicModel
createModelCoevolution
                        Creation of a PhenotypicGMM
fitTipData              Maximum likelihood estimators of a model's
                        parameters
fitTipData-methods      ~~ Methods for Function 'fitTipData' ~~
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
fit_t_env               Maximum likelihood fit of the environmental
                        model of trait evolution
getDataLikelihood       Likelihood of tip trait values.
getDataLikelihood-methods
                        ~~ Methods for Function 'getDataLikelihood' ~~
getTipDistribution      Distribution of tip trait values.
getTipDistribution-methods
                        Distribution of tip trait values.
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.
likelihood_t_env        Likelihood of a dataset under environmental
                        models of trait evolution.
lines.fit_t.env         Add to a plot line segments joining the
                        phenotypic evolutionary rate through time
                        estimated by the _fit_t_env_ function
modelSelection          Phenotypic model selection from tip trait data.
modelSelection-methods
                        ~~ Methods for Function 'modelSelection' ~~
plot.fit_t.env          Plot the phenotypic evolutionary rate through
                        time estimated by the _fit_t_env_ function
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.
sim.convergence.geo     Simulation of trait data under the model of
                        convergent character displacement described in
                        Drury et al. 2017
sim.divergence.geo      Simulation of trait data under the model of
                        divergent character displacement described in
                        Drury et al. 2017
sim_sgd                 Algorithm for simulating a phylogenetic tree
                        under the SGD model
sim_t_comp              Recursive simulation (root-to-tip) of
                        competition models
sim_t_env               Recursive simulation (root-to-tip) of the
                        environmental model
simulateTipData         Tip trait simulation under a model of
                        phenotypic evolution.
simulateTipData-methods
                        ~~ Methods for Function 'simulateTipData' ~~
spectR                  Spectral density plot of a phylogeny
