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RPANDA

##R: Phylogenetic ANalyses of DiversificAtion

Implements fits of diversification 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), and Drury et al. Syst Biol (2016).

The current stable version of the RPANDA package (1.2) is available on the CRAN repository. https://cran.r-project.org/package=RPANDA

###Package Installation

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

Note: You must have gcc/gfortran, rtools... installed

###Report an issue Any bugs encountered when using the package can be reported here

###Continuous integration Travis-CI Build Status:

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Version

Install

install.packages('RPANDA')

Monthly Downloads

496

Version

1.2

License

GPL-2

Issues

Pull Requests

Stars

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Maintainer

Hlne Morlon

Last Published

March 31st, 2016

Functions in RPANDA (1.2)

Phocoenidae

Phocoenidae phylogeny
Cetacea

Cetacean phylogeny
RPANDA-package

RPANDA
Phyllostomidae_genera

Phylogenies of Phyllostomidae genera
Anolis.data

Anolis dataset
Balaenopteridae

Balaenopteridae phylogeny
fit_bd

Maximum likelihood fit of the general birth-death model
Phyllostomidae

Phyllostomidae phylogeny
plot_fit_env

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

Maximum likelihood fit of the environmental birth-death model
fit_coal_cst

Maximum likelihood fit of the equilibrium model
likelihood_coal_cst

Likelihood of a phylogeny under the equilibrium diversity model
sim_sgd

Algorithm for simulating a phylogenetic tree under the SGD model
fit_sgd

Maximum likelihood fit of the SGD model
likelihood_t_DD

Likelihood of a dataset under diversity-dependent models.
InfTemp

Paleotemperature data across the Cenozoic
JSDtree

Jensen-Shannon distance between phylogenies
Calomys

Calomys phylogeny
likelihood_bd

Likelihood of a phylogeny under the general birth-death model
JSDtree_cluster

Clustering of phylogenies
fit_t_comp

Fits models of trait evolution incorporating competitive interactions
likelihood_t_MC

Likelihood of a dataset under the matching competition model.
likelihood_sgd

Likelihood of a phylogeny under the SGD model
likelihood_t_MC_geog

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

Plot diversity through time
CreateGeoObject

Create blank geography object
likelihood_t_DD_geog

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

Fit birth-death model using a coalescent approch
likelihood_coal_var

Likelihood of a birth-death model using a coalescent approch
BICompare

Identify modalities in a phylogeny
plot_fit_bd

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

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

Spectral density plot of a phylogeny.
plot_BICompare

Display modalities on a phylogeny.
spectR

Spectral density plot of a phylogeny