Anolis.data             Anolis dataset
BGB.examples            BioGeoBEARS stochastic maps
BICompare               Identify modalities in a phylogeny
Balaenopteridae         Balaenopteridae phylogeny
Calomys                 Calomys phylogeny
Caprimulgidae           The _Caprimulgidae_ phylogeny.
Caprimulgidae_ClaDS2    An example run of ClaDS2.
Cetacea                 Cetacean phylogeny
Cetacea_clades          Stochastic map of clade membership in Cetacean
                        phylogeny
ClaDS0_example          An example run of ClaDS0.
CreateClassObject       Create class object
CreateGeoObject         Create biogeography object
CreateGeoObject_BioGeoBEARS
                        Create biogeography object using a stochastic
                        map from BioGeoBEARS
CreateGeobyClassObject
                        Create merged biogeography-by-class object
GIC.fit_pl.rpanda       Generalized Information Criterion (GIC) to
                        compare models fit by Maximum Likelihood (ML)
                        or Penalized Likelihood (PL).
InfTemp                 Paleotemperature data across the Cenozoic
JSDt_cluster            Clustering on the Jensen-Shannon distance
                        between phylogenetic trait data
JSDtree                 Jensen-Shannon distance between phylogenies
JSDtree_cluster         Clustering of phylogenies
MPhiFFT                 A class used internally to compute ClaDS's
                        likelihood
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
Posdef                  Positive definite symmetric matrices
RPANDA-package          RPANDA
add.gts                 Geological time scale
ancestral               Estimation of traits ancestral states.
apply_prob_dtt          Calculates paleodiversity dynamics with the
                        probabilistic approach.
build_network.BipartiteEvol
                        Build the interaction network in BipartiteEvol
co2                     co2 data since the Jurassic
co2_res                 co2 data since the beginning of the Cenozoic
coccolithophore         Coccolithophore diversity since the Jurassic
createModel             Creation of a PhenotypicModel
createModelCoevolution
                        Creation of a PhenotypicGMM
d13c                    d13c data since the Jurassic
define_species.BipartiteEvol
                        Build the phylogenies for BipartiteEvol
delineate_phylotypes    Automatic phylotypes delineation
div.models              Model comparison of diversification models
div.rates               Diversification rates through time
fitTipData              Maximum likelihood estimators of a model's
                        parameters
fitTipData-methods      ~~ Methods for Function 'fitTipData' ~~
fit_ClaDS               Fit ClaDS to a phylogeny
fit_ClaDS0              Infer ClaDS0's parameter on a phylogeny
fit_bd                  Maximum likelihood fit of the general
                        birth-death model
fit_bd_backbone         Maximum likelihood fit of the general
                        birth-death model (backbone)
fit_bd_backbone_c       Maximum likelihood fit of the general
                        birth-death model (backbone and constraints)
fit_bd_in_past          Maximum likelihood fit of the general
                        birth-death model excluding the recent past
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_env_in_past         Maximum likelihood fit of the environmental
                        birth-death model excluding the recent past
fit_t_comp              Fits models of trait evolution incorporating
                        competitive interactions
fit_t_comp_subgroup     Fits models of trait evolution incorporating
                        competitive interactions, restricting
                        competition to occur only between members of a
                        subgroup
fit_t_env               Maximum likelihood fit of the environmental
                        model of trait evolution
fit_t_env_ou            Maximum likelihood fit of the OU environmental
                        model of trait evolution
fit_t_pl                High-dimensional phylogenetic models of trait
                        evolution
fit_t_standard          Fits standard models of trait evolution
                        incorporating known and nuisance measurement
                        error
foraminifera            Foraminifera diversity since the Jurassic
get.comb.shift          Combinations of shifts of diversification.
get.sampling.fractions
                        Sampling fractions of subclades
getDataLikelihood       Likelihood of tip trait values.
getDataLikelihood-methods
                        ~~ Methods for Function 'getDataLikelihood' ~~
getMAPS_ClaDS           Gets the Maximum A Posteriori for each ClaDS
                        parameter
getMAPS_ClaDS0          Gets the Maximum A Posteriori for each ClaDS0
                        parameter
getTipDistribution      Distribution of tip trait values.
getTipDistribution-methods
                        Distribution of tip trait values.
gic_criterion           Generalized Information Criterion (GIC) to
                        compare models fit by Maximum Likelihood (ML)
                        or Penalized Likelihood (PL).
greenalgae              Green algae diversity since the Jurassic
landplant               Land plant diversity since the Jurassic
likelihood_bd           Likelihood of a phylogeny under the general
                        birth-death model
likelihood_bd_backbone
                        Likelihood of a phylogeny under the general
                        birth-death model (backbone)
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_subgroup_model
                        Likelihood of a dataset under models with
                        biogeography fit to a subgroup.
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
lines.fit_t.env.ou      Add to a plot line segments joining the
                        phenotypic evolutionary optimum through time
                        estimated by the _fit_t_env_ou_ function
make_gen.BipartiteEvol
                        Compute the genealogies for BipartiteEvol
mantel_test             Compute Mantel test
mantel_test_nbpartners
                        Compute Mantel test
modelSelection          Phenotypic model selection from tip trait data.
modelSelection-methods
                        ~~ Methods for Function 'modelSelection' ~~
mycorrhizal_network     Mycorrhizal network from La Réunion island
ostracoda               Ostracod diversity since the Jurassic
paleodiv                Paleodiversity through time
phyl.pca_pl             Regularized Phylogenetic Principal Component
                        Analysis (PCA).
phylosignal_network     Compute phylogenetic signal in a bipartite
                        interaction network
phylosignal_sub_network
                        Compute clade-specific phylogenetic signals in
                        a bipartite interaction network
pi_estimator            Compute nucleotidic diversity (Pi estimator)
plot.fit_t.env          Plot the phenotypic evolutionary rate through
                        time estimated by the _fit_t_env_ function
plot.fit_t.env.ou       Plot the phenotypic evolutionary optimum
                        through time estimated by the _fit_t_env_ou_
                        function
plot_BICompare          Display modalities on a phylogeny.
plot_ClaDS0_chains      Plot the MCMC chains obtained when infering
                        ClaDS0 parameters
plot_ClaDS_chains       Plot the MCMC chains obtained when infering
                        ClaDS parameters
plot_ClaDS_phylo        Plot a phylogeny with branch-specific values
plot_div.BipartiteEvol
                        Plot the output of BipartiteEvol
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_net.BipartiteEvol
                        Plot the output of BipartiteEvol
plot_phylo_comb         Plot shifts of diversifcation on a phylogeny
plot_phylosignal_sub_network
                        Plot clade-specific phylogenetic signals in a
                        bipartite interaction network
plot_prob_dtt           Plot diversity through time with confidence
                        intervals.
plot_spectR             Spectral density plot of a phylogeny.
prob_dtt                Confidence intervals of diversity through time
radiolaria              Radiolaria diversity since the Jurassic
redalgae                Red algae diversity since the Jurassic
remove.model            Removing a model from shift.estimates output
sealevel                Sea level data since the Jurassic
shift.estimates         Estimating clade-shifts of diversification
shifts_cetacea          Cetacean shift.estimates results
silica                  Silica data across the Cenozoic
sim.BipartiteEvol       Simulation of the BipartiteEvol model
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_ClaDS               Simulation of the ClaDS model
sim_MCBD                Simulation of macroevolutionary diversification
                        under the integrated model described in
                        Aristide & Morlon 2019
sim_env_bd              Simulate birth-death tree dependent on an
                        environmental curve
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
sim_t_env_ou            Recursive simulation (root-to-tip) of the OU
                        environmental model
sim_t_tworegime         Recursive simulation (root-to-tip) of
                        two-regime models
simul.comb.shift        Simulating trees from shift.estimates() results
                        to test model adequacy
simulateTipData         Tip trait simulation under a model of
                        phenotypic evolution.
simulateTipData-methods
                        ~~ Methods for Function 'simulateTipData' ~~
spectR                  Spectral density plot of a phylogeny
spectR_t                Spectral density plot of phylogenetic trait
                        data
taxo_cetacea            Cetacean taxonomy
theta_estimator         Compute Watterson genetic diversity (Theta
                        estimator)
