RPANDA: Phylogenetic ANalyses of DiversificAtion
Version 1.3

Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) , Morlon et al. (2011) , Condamine et al. (2013) , Morlon et al. (2014) , Manceau et al. (2015) , Lewitus & Morlon (2016) , Drury et al. (2016) , Manceau et al. (2016) , and Clavel & Morlon (2017) .

AuthorHélène Morlon [aut, cre, cph], Eric Lewitus [aut, cph], Fabien Condamine [aut, cph], Marc Manceau [aut, cph], Julien Clavel [aut, cph], Jonathan Drury [aut, cph]
Date of publication2017-04-11 21:21:39 UTC
MaintainerHélène Morlon <morlon@biologie.ens.fr>
LicenseGPL-2
Version1.3
URL https://github.com/hmorlon/PANDA
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RPANDA")

Getting started

Package overview
README.md

Popular man pages

fit_bd: Maximum likelihood fit of the general birth-death model
PhenotypicADiag-class: Class '"PhenotypicADiag"'
PhenotypicDD-class: Class '"PhenotypicDD"'
RPANDA-package: RPANDA
simulateTipData: Tip trait simulation under a model of phenotypic evolution.
simulateTipData-methods: ~~ Methods for Function 'simulateTipData' ~~
spectR: Spectral density plot of a phylogeny
See all...

All man pages Function index File listing

Man pages

Anolis.data: Anolis dataset
Balaenopteridae: Balaenopteridae phylogeny
BGB.examples: BioGeoBEARS stochastic maps
BICompare: Identify modalities in a phylogeny
Calomys: Calomys phylogeny
Cetacea: Cetacean phylogeny
CreateGeoObject: Create biogeography object
CreateGeoObject_BioGeoBEARS: Create biogeography object using a stochastic map from...
createModel: Creation of a PhenotypicModel
createModelCoevolution: Creation of a PhenotypicGMM
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...
fit_t_env: Maximum likelihood fit of the environmental model of trait...
fitTipData: Maximum likelihood estimators of a model's parameters
fitTipData-methods: ~~ Methods for Function 'fitTipData' ~~
getDataLikelihood: Likelihood of tip trait values.
getDataLikelihood-methods: ~~ Methods for Function 'getDataLikelihood' ~~
getTipDistribution: Distribution of tip trait values.
getTipDistribution-methods: Distribution of tip trait values.
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_env: Likelihood of a dataset under environmental models of trait...
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...
lines.fit_t.env: Add to a plot line segments joining the phenotypic...
modelSelection: Phenotypic model selection from tip trait data.
modelSelection-methods: ~~ Methods for Function 'modelSelection' ~~
PhenotypicACDC-class: Class '"PhenotypicACDC"'
PhenotypicADiag-class: Class '"PhenotypicADiag"'
PhenotypicBM-class: Class '"PhenotypicBM"'
PhenotypicDD-class: Class '"PhenotypicDD"'
PhenotypicGMM-class: Class '"PhenotypicGMM"'
PhenotypicModel-class: Class '"PhenotypicModel"'
PhenotypicOU-class: Class '"PhenotypicOU"'
PhenotypicPM-class: Class '"PhenotypicPM"'
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.fit_t.env: Plot the phenotypic evolutionary rate through time estimated...
plot_spectR: Spectral density plot of a phylogeny.
RPANDA-package: RPANDA
sim.convergence.geo: Simulation of trait data under the model of convergent...
sim.divergence.geo: Simulation of trait data under the model of divergent...
sim_sgd: Algorithm for simulating a phylogenetic tree under the SGD...
sim_t_comp: Recursive simulation (root-to-tip) of competition models
sim_t_env: Recursive simulation (root-to-tip) of the environmental model
simulateTipData: Tip trait simulation under a model of phenotypic evolution.
simulateTipData-methods: ~~ Methods for Function 'simulateTipData' ~~
spectR: Spectral density plot of a phylogeny

Functions

Anolis.data Man page
BGB.examples Man page
BICompare Man page Source code
Balaenopteridae Man page
CLIMtransform Source code
Calomys Man page
Cetacea Man page
CreateBioGeoB_Object_subclade Source code
CreateGeoObject Man page Source code
CreateGeoObject_BioGeoBEARS Man page Source code
InfTemp Man page
Integrate Source code
Inverse_FB Source code
Inverse_FB2 Source code
JSDtree Man page Source code
JSDtree_cluster Man page Source code
Lambert2Newick Source code
LikelihoodSGDFromLambert Source code
PhenotypicACDC-class Man page
PhenotypicADiag-class Man page
PhenotypicBM-class Man page
PhenotypicDD-class Man page
PhenotypicGMM-class Man page
PhenotypicModel-class Man page
PhenotypicOU-class Man page
PhenotypicPM-class Man page
Phi Source code
Phocoenidae Man page
Phyllostomidae Man page
Phyllostomidae_genera Man page
Phylo2Lambert Source code
Psi Source code
RPANDA Man page
RPANDA-package Man page
Simulate_SGD_Phylogeny Source code
VCV.rescale Source code
VCV.rescale.DDexp_geog Source code
VCV.rescale.DDlin_geog Source code
VCV.rescale.geog Source code
[,PhenotypicModel,ANY,ANY,ANY-method Man page
[<-,PhenotypicModel,ANY,ANY,ANY-method Man page
createModel Man page Source code
createModelCoevolution Man page Source code
createModel_DDexp Source code
createModel_DDexp_geo Source code
createModel_DDlin Source code
createModel_DDlin_geo Source code
createModel_MC Source code
createModel_MC_geo Source code
dens Source code
derivative_edge Source code
derivative_leaf Source code
endOfPeriods Source code Source code Source code Source code Source code Source code Source code
endOfPeriodsGMM Source code
event_txt_into_events_row Source code
events_txt_into_events_table Source code
events_txt_list_into_events_table Source code
fitTipData Man page
fitTipData,PhenotypicModel-method Man page
fitTipData-methods Man page
fit_bd Man page Source code
fit_coal_cst Man page Source code
fit_coal_var Man page Source code
fit_env Man page Source code
fit_sgd Man page Source code
fit_t_comp Man page Source code
fit_t_env Man page Source code
g Source code
getDataLikelihood Man page
getDataLikelihood,PhenotypicModel-method Man page
getDataLikelihood-methods Man page
getLivingLineages Source code Source code Source code Source code Source code Source code Source code
getMatrixCoalescenceJ Source code Source code Source code Source code
getStartingTimes Source code Source code Source code
getTipDistribution Man page
getTipDistribution,PhenotypicACDC-method Man page
getTipDistribution,PhenotypicADiag-method Man page
getTipDistribution,PhenotypicBM-method Man page
getTipDistribution,PhenotypicDD-method Man page
getTipDistribution,PhenotypicGMM-method Man page
getTipDistribution,PhenotypicModel-method Man page
getTipDistribution,PhenotypicOU-method Man page
getTipDistribution,PhenotypicPM-method Man page
getTipDistribution-methods Man page
integr Source code
isATip Source code Source code Source code Source code Source code Source code Source code
likelihood_bd Man page Source code
likelihood_coal_cst Man page Source code
likelihood_coal_cst_mod Source code
likelihood_coal_exp_mod Source code
likelihood_coal_var Man page Source code
likelihood_sgd Man page Source code
likelihood_t_DD Man page Source code
likelihood_t_DD_geog Man page Source code
likelihood_t_MC Man page Source code
likelihood_t_MC_geog Man page Source code
likelihood_t_env Man page Source code
lines.fit_t.env Man page Source code
m Source code
modelSelection Man page
modelSelection,PhenotypicModel-method Man page
modelSelection-methods Man page
periodizeOneTree Source code Source code Source code Source code
periodizeOneTree_geo Source code Source code Source code
plot.fit_t.env Man page Source code
plot_BICompare Man page Source code
plot_dtt Man page Source code
plot_fit_bd Man page Source code
plot_fit_env Man page Source code
plot_spectR Man page Source code
print,PhenotypicModel-method Man page
print.fit.bd Source code
print.fit.env Source code
print.fit_t.env Source code
resortGeoObject Source code
rho_0to1 Source code
rho_0tofixe Source code
rho_1mute0 Source code
rho_1to1 Source code
show,PhenotypicModel-method Man page
sim.convergence.geo Man page Source code
sim.divergence.geo Man page Source code
sim_sgd Man page Source code
sim_t_comp Man page Source code
sim_t_env Man page Source code
simulateTipData Man page
simulateTipData,PhenotypicModel-method Man page
simulateTipData-methods Man page
spectR Man page Source code
stratified_BGB_to_tables Source code
updateBranchingMatrixSigma Source code
vcv.rescale.DDexp Source code
vcv.rescale.DDlin Source code

Files

inst
inst/CITATION
tests
tests/testthat
tests/testthat/test-fit-bd.r
tests/testthat/test-fit-coal.r
tests/testthat/test-fit-env-bd.r
tests/test-all.R
NAMESPACE
data
data/BGB.examples.rda
data/Phyllostomidae_genera.rda
data/Phocoenidae.rda
data/Calomys.rda
data/Anolis.data.rda
data/Cetacea.rda
data/Balaenopteridae.rda
data/Phyllostomidae.rda
data/InfTemp.rda
R
R/DDexp.rescale.R
R/plot_fit_env.R
R/likelihood_bd.R
R/likelihood_coal_exp_mod.R
R/MC.rescale.R
R/plot_fit_bd.R
R/JSDtree_cluster.R
R/Phi.R
R/Psi.R
R/fit_sgd.R
R/likelihood_coal_var.R
R/print.fit.bd.R
R/DDlin.rescale.R
R/stratified_BGB_to_tables.R
R/sim_t_env.R
R/integrate.R
R/events_txt_list_into_events_table.R
R/base_sgd.R
R/CreateGeoObject_BioGeoBEARS.R
R/fit_t_env.R
R/likelihood_t_DD_geog.R
R/events_txt_into_events_table.R
R/JSDtree.R
R/getTipDistribution.R
R/fit_coal_cst.R
R/print.fit.env.R
R/sim.convergence.geo.R
R/event_txt_into_events_row.R
R/sim_t_comp.R
R/likelihood_coal_cst_mod.R
R/BICompare.R
R/getDataLikelihood.R
R/spectR.R
R/likelihood_t_MC.R
R/print.fit_t.env.R
R/MC_nogeo_ADiag.R
R/plot_BICompare.R
R/likelihood_sgd.R
R/DDexp_geo_ADiag.R
R/PhenotypicModel.class.R
R/simulateTipData.R
R/MC.rescale_geog.R
R/plot_spectR.R
R/fit_coal_var.R
R/plot.fit_t.env.r
R/sim.divergence.geo.R
R/DDexp_nogeo_ADiag.R
R/modelSelection.R
R/createModel.R
R/plot_dtt.R
R/fitTipData.R
R/likelihood_t_env.R
R/resortGeoObject.R
R/fit_t_comp.R
R/CreateGeoObject.R
R/DDlin_nogeo_ADiag.R
R/fit_bd.R
R/fit_env.R
R/CreateBioGeoB_Object_subclade.R
R/DDexp.rescale.geog.R
R/MC_geo_PM.R
R/sim_sgd.R
R/DDlin.rescale.geog.R
R/DDlin_geo_ADiag.R
R/likelihood_t_MC_geog.R
R/likelihood_t_DD.R
R/likelihood_coal_cst.R
README.md
MD5
DESCRIPTION
man
man/plot_BICompare.Rd
man/sim.convergence.geo.Rd
man/plot_fit_env.Rd
man/PhenotypicDD-class.Rd
man/Phyllostomidae.Rd
man/fitTipData.Rd
man/getDataLikelihood.Rd
man/JSDtree_cluster.Rd
man/likelihood_t_DD_geog.Rd
man/Anolis.data.Rd
man/lines.fit_t.env.Rd
man/Cetacea.Rd
man/PhenotypicADiag-class.Rd
man/Balaenopteridae.Rd
man/plot_spectR.Rd
man/createModelCoevolution.Rd
man/plot_dtt.Rd
man/spectR.Rd
man/modelSelection.Rd
man/likelihood_coal_cst.Rd
man/JSDtree.Rd
man/Phocoenidae.Rd
man/PhenotypicPM-class.Rd
man/createModel.Rd
man/BICompare.Rd
man/fitTipData-methods.Rd
man/getTipDistribution.Rd
man/Phyllostomidae_genera.Rd
man/likelihood_t_DD.Rd
man/sim_sgd.Rd
man/PhenotypicGMM-class.Rd
man/fit_bd.Rd
man/Calomys.Rd
man/PhenotypicOU-class.Rd
man/simulateTipData.Rd
man/simulateTipData-methods.Rd
man/fit_sgd.Rd
man/likelihood_coal_var.Rd
man/PhenotypicModel-class.Rd
man/PhenotypicBM-class.Rd
man/CreateGeoObject.Rd
man/likelihood_bd.Rd
man/sim_t_env.Rd
man/plot_fit_bd.Rd
man/InfTemp.Rd
man/getTipDistribution-methods.Rd
man/fit_t_env.Rd
man/modelSelection-methods.Rd
man/fit_env.Rd
man/likelihood_t_MC.Rd
man/likelihood_t_MC_geog.Rd
man/getDataLikelihood-methods.Rd
man/PhenotypicACDC-class.Rd
man/sim.divergence.geo.Rd
man/fit_t_comp.Rd
man/fit_coal_var.Rd
man/sim_t_comp.Rd
man/fit_coal_cst.Rd
man/plot.fit_t.env.Rd
man/BGB.examples.Rd
man/RPANDA-package.Rd
man/CreateGeoObject_BioGeoBEARS.Rd
man/likelihood_t_env.Rd
man/likelihood_sgd.Rd
RPANDA documentation built on May 19, 2017, 1:21 p.m.

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