RPANDA: Phylogenetic ANalyses of DiversificAtion

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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>.

Author
Hélène Morlon [aut, cre, cph]
Date of publication
2016-03-31 18:47:57
Maintainer
Hélène Morlon <morlon@biologie.ens.fr>
License
GPL-2
Version
1.2
URLs

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