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RPANDA

R: Phylogenetic ANalyses of DiversificAtion

Implements fits of diversification and phenotypic evolution models to phylogenetic data. See Morlon et al. PLoSB (2010), Morlon et al. PNAS (2011), Condamine et al. Eco Lett (2013), Morlon et al. Eco Lett (2014), Manceau et al. Eco Lett (2015), Lewitus & Morlon Syst Biol (2016), Drury et al. Syst Biol (2016), Manceau et al. Syst Biol (2016), Clavel & Morlon PNAS (2017), Drury et al. Syst Biol (2017), Lewitus & Morlon Syst Biol (2017), Drury et al. PLoSB (2018), Clavel et al. Syst Biol (2019), Maliet et al. Nature Ecol Evol (2019), Condamine et al. Eco Lett (2019), Aristide & Morlon Eco Lett (2019), Billaud et al. Syst Biol (2019), Lewitus & Morlon Syst Biol (2019), Maliet et al. Eco Lett (2020), Drury et al. PloS B (2021).

More information on the RPANDA package and worked examples can be found in Morlon et al. (2016)

The current stable version of the RPANDA package (2.0) is available on the CRAN repository. https://cran.r-project.org/package=RPANDA

Package Installation

From gitHub You can install RPANDA directly from gitHub with devtools:

library(devtools)

install_github("hmorlon/PANDA", dependencies = TRUE)

From the binaries

You can download the pre-released binaries for Windows and Mac OS X from the release page

From the source

Otherwise, you can install it directly from the source. Download the RPANDA folder and then, from the terminal console (linux, windows or mac):

R CMD build RPANDA

This will produce the RPANDA tarball.

Then, for compiling the binary:

R CMD INSTALL --build RPANDA_2.X.tar.gz

Report an issue

Any bugs encountered when using the package can be reported here

Continuous integration

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Version

Install

install.packages('RPANDA')

Monthly Downloads

460

Version

2.2

License

GPL-2

Issues

Pull Requests

Stars

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Repository

https://github.com/hmorlon/PANDA

Maintainer

H<c3><a9>l<c3><a8>ne Morlon

Last Published

October 24th, 2022

Functions in RPANDA (2.2)

Clustering on the Jensen-Shannon distance between phylogenetic trait data

JSDtree_cluster

Clustering of phylogenies

CreateGeoObject_BioGeoBEARS

Create biogeography object using a stochastic map from BioGeoBEARS

CreateGeoObject

Create biogeography object

GIC.fit_pl.rpanda

Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).

CreateClassObject

Create class object

Jensen-Shannon distance between phylogenies

CreateGeobyClassObject

Create merged biogeography-by-class object

Paleotemperature data across the Cenozoic

A class used internally to compute ClaDS's likelihood

Phocoenidae phylogeny

PhenotypicModel-class

Class "PhenotypicModel"

Phyllostomidae phylogeny

PhenotypicGMM-class

Class "PhenotypicGMM"

PhenotypicPM-class

Class "PhenotypicPM"

PhenotypicOU-class

Class "PhenotypicOU"

Estimation of traits ancestral states.

PhenotypicBM-class

Class "PhenotypicBM"

PhenotypicDD-class

Class "PhenotypicDD"

Positive definite symmetric matrices

Phyllostomidae_genera

Phylogenies of Phyllostomidae genera

build_network.BipartiteEvol

Build the interaction network in BipartiteEvol

co2 data since the Jurassic

Creation of a PhenotypicModel

createModelCoevolution

Creation of a PhenotypicGMM

PhenotypicACDC-class

Class "PhenotypicACDC"

d13c data since the Jurassic

Maximum likelihood estimators of a model's parameters

coccolithophore

Coccolithophore diversity since the Jurassic

PhenotypicADiag-class

Class "PhenotypicADiag"

delineate_phylotypes

Automatic phylotypes delineation

Fit ClaDS to a phylogeny

define_species.BipartiteEvol

Build the phylogenies for BipartiteEvol

co2 data since the beginning of the Cenozoic

fitTipData-methods

~~ Methods for Function fitTipData ~~

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 general birth-death model

Foraminifera diversity since the Jurassic

Fits standard models of trait evolution incorporating known and nuisance measurement error

getDataLikelihood

Likelihood of tip trait values.

fit_t_comp_subgroup

Fits models of trait evolution incorporating competitive interactions, restricting competition to occur only between members of a subgroup

Fits models of trait evolution incorporating competitive interactions

getDataLikelihood-methods

~~ Methods for Function getDataLikelihood ~~

Maximum likelihood fit of the environmental birth-death model

Maximum likelihood fit of the SGD model

High-dimensional phylogenetic models of trait evolution

Maximum likelihood fit of the environmental model of trait evolution

Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).

Green algae diversity since the Jurassic

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

Gets the Maximum A Posteriori for each ClaDS parameter

Likelihood of a phylogeny under the general birth-death model

likelihood_t_MC

Likelihood of a dataset under the matching competition model.

Land plant diversity since the Jurassic

Likelihood of a phylogeny under the SGD model

Gets the Maximum A Posteriori for each ClaDS0 parameter

likelihood_t_DD

Likelihood of a dataset under diversity-dependent models.

getTipDistribution

Distribution of tip trait values.

getTipDistribution-methods

Distribution of tip trait values.

lines.fit_t.env

Add to a plot line segments joining the phenotypic evolutionary rate through time estimated by the fit_t_env function

likelihood_subgroup_model

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

likelihood_t_env

Likelihood of a dataset under environmental models of trait evolution.

likelihood_t_MC_geog

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

make_gen.BipartiteEvol

Compute the genealogies for BipartiteEvol

Compute nucleotidic diversity (Pi estimator)

Compute Mantel test

Plot the phenotypic evolutionary rate through time estimated by the fit_t_env function

phylosignal_sub_network

Compute clade-specific phylogenetic signals in a bipartite interaction network

phylosignal_network

Compute phylogenetic signal in a bipartite interaction network

mantel_test_nbpartners

Compute Mantel test

modelSelection-methods

~~ Methods for Function modelSelection ~~

Regularized Phylogenetic Principal Component Analysis (PCA).

Plot speciation, extinction & net diversification rate functions of a fitted model

Ostracod diversity since the Jurassic

plot_div.BipartiteEvol

Plot the output of BipartiteEvol

Display modalities on a phylogeny.

plot_ClaDS_chains

Plot the MCMC chains obtained when infering ClaDS parameters

Phenotypic model selection from tip trait data.

plot_net.BipartiteEvol

Plot the output of BipartiteEvol

likelihood_t_DD_geog

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

mycorrhizal_network

Mycorrhizal network from La Réunion island

Plot diversity through time

plot_phylosignal_sub_network

Plot clade-specific phylogenetic signals in a bipartite interaction network

plot_ClaDS_phylo

Plot a phylogeny with branch-specific values

Sea level data since the Jurassic

Plot speciation, extinction & net diversification rate functions of a fitted environmental model

Red algae diversity since the Jurassic

plot_ClaDS0_chains

Plot the MCMC chains obtained when infering ClaDS0 parameters

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.BipartiteEvol

Simulation of the BipartiteEvol model

Silica data across the Cenozoic

Plot diversity through time with confidence intervals.

Spectral density plot of a phylogeny.

Confidence intervals of diversity through time

Radiolaria diversity since the Jurassic

sim_t_tworegime

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

Spectral density plot of a phylogeny

Algorithm for simulating a phylogenetic tree under the SGD model

Simulate birth-death tree dependent on an environmental curve

simulateTipData

Tip trait simulation under a model of phenotypic evolution.

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

Simulation of macroevolutionary diversification under the integrated model described in Aristide & Morlon 2019

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

Simulation of the ClaDS model

simulateTipData-methods

~~ Methods for Function simulateTipData ~~

Spectral density plot of phylogenetic trait data

theta_estimator

Compute Watterson genetic diversity (Theta estimator)

Identify modalities in a phylogeny

An example run of ClaDS0.

BioGeoBEARS stochastic maps

Caprimulgidae_ClaDS2

An example run of ClaDS2.

Stochastic map of clade membership in Cetacean phylogeny

The Caprimulgidae phylogeny.

Balaenopteridae

Balaenopteridae phylogeny

Calomys phylogeny

Cetacean phylogeny