RPANDA2.3 package

Geological time scale

Estimation of traits ancestral states.

Calculates paleodiversity dynamics with the probabilistic approach.

Identify modalities in a phylogeny

Build the interaction network in BipartiteEvol

Create class object

Create merged biogeography-by-class object

Create biogeography object

Create biogeography object using a stochastic map from BioGeoBEARS

Creation of a PhenotypicModel

Creation of a PhenotypicGMM

Build the phylogenies for BipartiteEvol

Automatic phylotypes delineation

Model comparison of diversification models

Diversification rates through time

Maximum likelihood fit of the general birth-death model

Maximum likelihood fit of the general birth-death model (backbone)

Maximum likelihood fit of the general birth-death model (backbone and ...

Fit ClaDS to a phylogeny

Infer ClaDS0's parameter on a phylogeny

Maximum likelihood fit of the equilibrium model

Fit birth-death model using a coalescent approch

Maximum likelihood fit of the environmental birth-death model

Maximum likelihood fit of the SGD model

Fits models of trait evolution incorporating competitive interactions

Fits models of trait evolution incorporating competitive interactions,...

Maximum likelihood fit of the environmental model of trait evolution

Maximum likelihood fit of the OU environmental model of trait evolutio...

High-dimensional phylogenetic models of trait evolution

Fits standard models of trait evolution incorporating known and nuisan...

~~ Methods for Function fitTipData ~~

Maximum likelihood estimators of a model's parameters

Combinations of shifts of diversification.

Sampling fractions of subclades

~~ Methods for Function getDataLikelihood ~~

Likelihood of tip trait values.

Gets the Maximum A Posteriori for each ClaDS parameter

Gets the Maximum A Posteriori for each ClaDS0 parameter

Distribution of tip trait values.

Distribution of tip trait values.

Generalized Information Criterion (GIC) to compare models fit by Maxim...

Generalized Information Criterion (GIC) to compare models fit by Maxim...

Clustering on the Jensen-Shannon distance between phylogenetic trait d...

Jensen-Shannon distance between phylogenies

Clustering of phylogenies

Likelihood of a phylogeny under the general birth-death model

Likelihood of a phylogeny under the general birth-death model (backbon...

Likelihood of a phylogeny under the equilibrium diversity model

Likelihood of a birth-death model using a coalescent approch

Likelihood of a phylogeny under the SGD model

Likelihood of a dataset under models with biogeography fit to a subgro...

Likelihood of a dataset under diversity-dependent models.

Likelihood of a dataset under diversity-dependent models with biogeogr...

Likelihood of a dataset under environmental models of trait evolution.

Likelihood of a dataset under the matching competition model.

Likelihood of a dataset under the matching competition model with biog...

Add to a plot line segments joining the phenotypic evolutionary rate t...

Add to a plot line segments joining the phenotypic evolutionary optimu...

Compute the genealogies for BipartiteEvol

Compute Mantel test

Compute Mantel test

~~ Methods for Function modelSelection ~~

Phenotypic model selection from tip trait data.

A class used internally to compute ClaDS's likelihood

Paleodiversity through time

Class "PhenotypicACDC"

Class "PhenotypicADiag"

Class "PhenotypicBM"

Class "PhenotypicDD"

Class "PhenotypicGMM"

Class "PhenotypicModel"

Class "PhenotypicOU"

Class "PhenotypicPM"

Regularized Phylogenetic Principal Component Analysis (PCA).

Compute phylogenetic signal in a bipartite interaction network

Compute clade-specific phylogenetic signals in a bipartite interaction...

Compute nucleotidic diversity (Pi estimator)

Plot the phenotypic evolutionary rate through time estimated by the **...

Plot the phenotypic evolutionary optimum through time estimated by the...

Display modalities on a phylogeny.

Plot the MCMC chains obtained when infering ClaDS parameters

Plot a phylogeny with branch-specific values

Plot the MCMC chains obtained when infering ClaDS0 parameters

Plot the output of BipartiteEvol

Plot diversity through time

Plot speciation, extinction & net diversification rate functions of a ...

Plot speciation, extinction & net diversification rate functions of a ...

Plot the output of BipartiteEvol

Plot shifts of diversifcation on a phylogeny

Plot clade-specific phylogenetic signals in a bipartite interaction ne...

Plot diversity through time with confidence intervals.

Spectral density plot of a phylogeny.

Positive definite symmetric matrices

Confidence intervals of diversity through time

Removing a model from shift.estimates output

RPANDA

Estimating clade-shifts of diversification

Simulation of the BipartiteEvol model

Simulation of trait data under the model of convergent character displ...

Simulation of trait data under the model of divergent character displa...

Simulation of the ClaDS model

Simulate birth-death tree dependent on an environmental curve

Simulation of macroevolutionary diversification under the integrated m...

Algorithm for simulating a phylogenetic tree under the SGD model

Recursive simulation (root-to-tip) of competition models

Recursive simulation (root-to-tip) of the environmental model

Recursive simulation (root-to-tip) of the OU environmental model

Recursive simulation (root-to-tip) of two-regime models

Simulating trees from shift.estimates() results to test model adequacy

~~ Methods for Function simulateTipData ~~

Tip trait simulation under a model of phenotypic evolution.

Spectral density plot of a phylogeny

Spectral density plot of phylogenetic trait data

Compute Watterson genetic diversity (Theta estimator)