RPANDA: Phylogenetic ANalyses of DiversificAtion

Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, and Drury et al. (2016) <DOI:10.1093/sysbio/syw020>.

AuthorHélène Morlon [aut, cre, cph]
Date of publication2016-03-31 18:47:57
MaintainerHélène Morlon <morlon@biologie.ens.fr>
LicenseGPL-2
Version1.2
https://github.com/hmorlon/PANDA

View on CRAN

Man pages

Anolis.data: Anolis dataset

Balaenopteridae: Balaenopteridae phylogeny

BICompare: Identify modalities in a phylogeny

Calomys: Calomys phylogeny

Cetacea: Cetacean phylogeny

CreateGeoObject: Create blank geography object

fit_bd: Maximum likelihood fit of the general birth-death model

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_sgd: Maximum likelihood fit of the SGD model

fit_t_comp: Fits models of trait evolution incorporating competitive...

InfTemp: Paleotemperature data across the Cenozoic

JSDtree: Jensen-Shannon distance between phylogenies

JSDtree_cluster: Clustering of phylogenies

likelihood_bd: Likelihood of a phylogeny under the general birth-death model

likelihood_coal_cst: Likelihood of a phylogeny under the equilibrium diversity...

likelihood_coal_var: Likelihood of a birth-death model using a coalescent approch

likelihood_sgd: Likelihood of a phylogeny under the SGD model

likelihood_t_DD: Likelihood of a dataset under diversity-dependent models.

likelihood_t_DD_geog: Likelihood of a dataset under diversity-dependent models with...

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...

Phocoenidae: Phocoenidae phylogeny

Phyllostomidae: Phyllostomidae phylogeny

Phyllostomidae_genera: Phylogenies of Phyllostomidae genera

plot_BICompare: Display modalities on a phylogeny.

plot_dtt: Plot diversity through time

plot_fit_bd: Plot speciation, extinction & net diversification rate...

plot_fit_env: Plot speciation, extinction & net diversification rate...

plot_spectR: Spectral density plot of a phylogeny.

RPANDA-package: RPANDA

sim_sgd: Algorithm for simulating a phylogenetic tree under the SGD...

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

spectR: Spectral density plot of a phylogeny

Files in this package

RPANDA
RPANDA/inst
RPANDA/inst/CITATION
RPANDA/tests
RPANDA/tests/testthat
RPANDA/tests/testthat/test-fit-bd.r
RPANDA/tests/testthat/test-fit-coal.r
RPANDA/tests/testthat/test-fit-env-bd.r
RPANDA/tests/test-all.R
RPANDA/NAMESPACE
RPANDA/data
RPANDA/data/Phyllostomidae_genera.rda
RPANDA/data/Phocoenidae.rda
RPANDA/data/Calomys.rda
RPANDA/data/Anolis.data.rda
RPANDA/data/Cetacea.rda
RPANDA/data/Balaenopteridae.rda
RPANDA/data/Phyllostomidae.rda
RPANDA/data/InfTemp.rda
RPANDA/R
RPANDA/R/DDexp.rescale.R RPANDA/R/plot_fit_env.R RPANDA/R/likelihood_bd.R RPANDA/R/likelihood_coal_exp_mod.R RPANDA/R/MC.rescale.R RPANDA/R/plot_fit_bd.R RPANDA/R/JSDtree_cluster.R RPANDA/R/Phi.R RPANDA/R/Psi.R RPANDA/R/fit_sgd.R RPANDA/R/likelihood_coal_var.R RPANDA/R/print.fit.bd.R RPANDA/R/DDlin.rescale.R RPANDA/R/integrate.R RPANDA/R/base_sgd.R RPANDA/R/likelihood_t_DD_geog.R RPANDA/R/JSDtree.R RPANDA/R/fit_coal_cst.R RPANDA/R/print.fit.env.R RPANDA/R/sim_t_comp.R RPANDA/R/likelihood_coal_cst_mod.R RPANDA/R/BICompare.R RPANDA/R/spectR.R RPANDA/R/likelihood_t_MC.R RPANDA/R/plot_BICompare.R RPANDA/R/likelihood_sgd.R RPANDA/R/MC.rescale_geog.R RPANDA/R/plot_spectR.R RPANDA/R/fit_coal_var.R RPANDA/R/plot_dtt.R RPANDA/R/fit_t_comp.R RPANDA/R/CreateGeoObject.R RPANDA/R/fit_bd.R RPANDA/R/fit_env.R RPANDA/R/DDexp.rescale.geog.R RPANDA/R/sim_sgd.R RPANDA/R/DDlin.rescale.geog.R RPANDA/R/likelihood_t_MC_geog.R RPANDA/R/likelihood_t_DD.R RPANDA/R/likelihood_coal_cst.R
RPANDA/README.md
RPANDA/MD5
RPANDA/DESCRIPTION
RPANDA/man
RPANDA/man/plot_BICompare.Rd RPANDA/man/plot_fit_env.Rd RPANDA/man/Phyllostomidae.Rd RPANDA/man/JSDtree_cluster.Rd RPANDA/man/likelihood_t_DD_geog.Rd RPANDA/man/Anolis.data.Rd RPANDA/man/Cetacea.Rd RPANDA/man/Balaenopteridae.Rd RPANDA/man/plot_spectR.Rd RPANDA/man/plot_dtt.Rd RPANDA/man/spectR.Rd RPANDA/man/likelihood_coal_cst.Rd RPANDA/man/JSDtree.Rd RPANDA/man/Phocoenidae.Rd RPANDA/man/BICompare.Rd RPANDA/man/Phyllostomidae_genera.Rd RPANDA/man/likelihood_t_DD.Rd RPANDA/man/sim_sgd.Rd RPANDA/man/fit_bd.Rd RPANDA/man/Calomys.Rd RPANDA/man/fit_sgd.Rd RPANDA/man/likelihood_coal_var.Rd RPANDA/man/CreateGeoObject.Rd RPANDA/man/likelihood_bd.Rd RPANDA/man/plot_fit_bd.Rd RPANDA/man/InfTemp.Rd RPANDA/man/fit_env.Rd RPANDA/man/likelihood_t_MC.Rd RPANDA/man/likelihood_t_MC_geog.Rd RPANDA/man/fit_t_comp.Rd RPANDA/man/fit_coal_var.Rd RPANDA/man/sim_t_comp.Rd RPANDA/man/fit_coal_cst.Rd RPANDA/man/RPANDA-package.Rd RPANDA/man/likelihood_sgd.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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