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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).

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 (1.9) 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_1.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

495

Version

1.9

License

GPL-2

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/hmorlon/PANDA

Maintainer

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

Last Published

September 15th, 2020

Functions in RPANDA (1.9)

Identify modalities in a phylogeny

Calomys phylogeny

The Caprimulgidae phylogeny.

An example run of ClaDS0.

CreateClassObject

Create class object

CreateGeoObject

Create biogeography object

CreateGeoObject_BioGeoBEARS

Create biogeography object using a stochastic map from BioGeoBEARS

BioGeoBEARS stochastic maps

Paleotemperature data across the Cenozoic

Clustering on the Jensen-Shannon distance between phylogenetic trait data

Jensen-Shannon distance between phylogenies

JSDtree_cluster

Clustering of phylogenies

PhenotypicADiag-class

Class "PhenotypicADiag"

Balaenopteridae

Balaenopteridae phylogeny

PhenotypicDD-class

Class "PhenotypicDD"

PhenotypicBM-class

Class "PhenotypicBM"

Phyllostomidae phylogeny

Caprimulgidae_ClaDS2

An example run of ClaDS2.

Cetacean phylogeny

CreateGeobyClassObject

Create merged biogeography-by-class object

coccolithophore

Coccolithophore diversity since the Jurassic

Phyllostomidae_genera

Phylogenies of Phyllostomidae genera

A class used internally to compute ClaDS's likelihood

define_species.BipartiteEvol

Build the phylogenies for BipartiteEvol

Foraminifera diversity since the Jurassic

Creation of a PhenotypicModel

fitTipData-methods

~~ Methods for Function fitTipData ~~

Estimation of traits ancestral states.

PhenotypicGMM-class

Class "PhenotypicGMM"

GIC.fit_pl.rpanda

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

PhenotypicModel-class

Class "PhenotypicModel"

build_network.BipartiteEvol

Build the interaction network in BipartiteEvol

PhenotypicOU-class

Class "PhenotypicOU"

Maximum likelihood estimators of a model's parameters

Fit ClaDS to a phylogeny

getDataLikelihood-methods

~~ Methods for Function getDataLikelihood ~~

co2 data since the Jurassic

co2 data since the beginning of the Cenozoic

createModelCoevolution

Creation of a PhenotypicGMM

getDataLikelihood

Likelihood of tip trait values.

Maximum likelihood fit of the general birth-death model

Infer ClaDS0's parameter on a phylogeny

PhenotypicACDC-class

Class "PhenotypicACDC"

d13c data since the Jurassic

likelihood_t_DD

Likelihood of a dataset under diversity-dependent models.

likelihood_subgroup_model

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

modelSelection-methods

~~ Methods for Function modelSelection ~~

likelihood_coal_var

Likelihood of a birth-death model using a coalescent approch

Gets the Maximum A Posteriori for each ClaDS parameter

Maximum likelihood fit of the environmental model of trait evolution

Fit birth-death model using a coalescent approch

Maximum likelihood fit of the equilibrium model

Phenotypic model selection from tip trait data.

plot_ClaDS_phylo

Plot a phylogeny with branch-specific values

Phocoenidae phylogeny

Positive definite symmetric matrices

PhenotypicPM-class

Class "PhenotypicPM"

Likelihood of a phylogeny under the SGD model

Maximum likelihood fit of the SGD model

Maximum likelihood fit of the environmental birth-death model

Regularized Phylogenetic Principal Component Analysis (PCA).

Ostracod diversity since the Jurassic

Likelihood of a phylogeny under the general birth-death model

Gets the Maximum A Posteriori for each ClaDS0 parameter

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

getTipDistribution-methods

Distribution of tip trait values.

Plot diversity through time

Green algae diversity since the Jurassic

plot_div.BipartiteEvol

Plot the output of BipartiteEvol

likelihood_coal_cst

Likelihood of a phylogeny under the equilibrium diversity model

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

Plot diversity through time with confidence intervals.

Spectral density plot of a phylogeny.

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

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

High-dimensional phylogenetic models of trait evolution

getTipDistribution

Distribution of tip trait values.

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.

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

Land plant diversity since the Jurassic

make_gen.BipartiteEvol

Compute the genealogies for BipartiteEvol

lines.fit_t.env

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

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

Confidence intervals of diversity through time

plot_ClaDS_chains

Plot the MCMC chains obtained when infering ClaDS parameters

plot_ClaDS0_chains

Plot the MCMC chains obtained when infering ClaDS0 parameters

Radiolaria diversity since the Jurassic

Simulation of the ClaDS model

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

plot_net.BipartiteEvol

Plot the output of BipartiteEvol

simulateTipData-methods

~~ Methods for Function simulateTipData ~~

sim.divergence.geo

Simulation of trait data under the model of divergent character displacement described in Drury et al. 2017

sim.convergence.geo

Simulation of trait data under the model of convergent character displacement described in Drury et al. 2017

simulateTipData

Tip trait simulation under a model of phenotypic evolution.

sim.BipartiteEvol

Simulation of the BipartiteEvol model

Silica data across the Cenozoic

likelihood_t_DD_geog

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

Simulate birth-death tree dependent on an environmental curve

Algorithm for simulating a phylogenetic tree under the SGD model

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

likelihood_t_MC

Likelihood of a dataset under the matching competition model.

Display modalities on a phylogeny.

Red algae diversity since the Jurassic

Spectral density plot of phylogenetic trait data

Sea level data since the Jurassic

Spectral density plot of a phylogeny