Package: RPANDA 2.3

Hélène Morlon

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>, Drury et al. (2016) <doi:10.1093/sysbio/syw020>, Manceau et al. (2016) <doi:10.1093/sysbio/syw115>, Morlon et al. (2016) <doi:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <doi:10.1073/pnas.1606868114>, Drury et al. (2017) <doi:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <doi:10.1093/sysbio/syx095>, Drury et al. (2018) <doi:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <doi:10.1093/sysbio/syy045>, Maliet et al. (2019) <doi:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <doi:10.1093/sysbio/syz057>, Lewitus et al. (2019) <doi:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <doi:10.1111/ele.13385>, Maliet et al. (2020) <doi:10.1111/ele.13592>, Drury et al. (2021) <doi:10.1371/journal.pbio.3001270>, Perez-Lamarque & Morlon (2022) <doi:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <doi:10.1101/2021.08.30.458192>, Mazet et al. (2023) <doi:10.1111/2041-210X.14195>, Drury et al. (2024) <doi:10.1016/j.cub.2023.12.055>.

Authors:Hélène Morlon [aut, cre, cph], Eric Lewitus [aut, cph], Fabien Condamine [aut, cph], Marc Manceau [aut, cph], Julien Clavel [aut, cph], Jonathan Drury [aut, cph], Olivier Billaud [aut, cph], Odile Maliet [aut, cph], Leandro Aristide [aut, cph], Benoit Perez-Lamarque [aut, cph], Nathan Mazet [aut, cph]

RPANDA_2.3.tar.gz
RPANDA_2.3.zip(r-4.5)RPANDA_2.3.zip(r-4.4)RPANDA_2.3.zip(r-4.3)
RPANDA_2.3.tgz(r-4.4-x86_64)RPANDA_2.3.tgz(r-4.4-arm64)RPANDA_2.3.tgz(r-4.3-x86_64)RPANDA_2.3.tgz(r-4.3-arm64)
RPANDA_2.3.tar.gz(r-4.5-noble)RPANDA_2.3.tar.gz(r-4.4-noble)
RPANDA_2.3.tgz(r-4.4-emscripten)RPANDA_2.3.tgz(r-4.3-emscripten)
RPANDA.pdf |RPANDA.html✨
RPANDA/json (API)

# Install 'RPANDA' in R:
install.packages('RPANDA', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hmorlon/panda/issues

Datasets:

On CRAN:

102 exports 23 stars 4.40 score 119 dependencies 24 mentions 242 scripts 472 downloads

Last updated 2 months agofrom:5d02681797. Checks:OK: 1 WARNING: 8. Indexed: no.

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Exports:add.gtsancestralapply_prob_dttBIComparebuild_network.BipartiteEvolCreateClassObjectCreateGeobyClassObjectCreateGeoObjectCreateGeoObject_BioGeoBEARScreateModelcreateModelCoevolutiondefine_species.BipartiteEvoldelineate_phylotypesdiv.modelsdiv.ratesfit_bdfit_bd_backbonefit_bd_backbone_cfit_bd_in_pastfit_ClaDSfit_ClaDS0fit_coal_cstfit_coal_varfit_envfit_env_in_pastfit_sgdfit_t_compfit_t_comp_subgroupfit_t_envfit_t_env_oufit_t_plfit_t_standardfitTipDataget.comb.shiftget.sampling.fractionsgetDataLikelihoodgetMAPS_ClaDSgetMAPS_ClaDS0getTipDistributiongic_criterionJSDt_clusterJSDtreeJSDtree_clusterlikelihood_bdlikelihood_bd_backbonelikelihood_coal_cstlikelihood_coal_varlikelihood_sgdlikelihood_subgroup_modellikelihood_t_DDlikelihood_t_DD_geoglikelihood_t_envlikelihood_t_MClikelihood_t_MC_geoglines.fit_t.envlines.fit_t.env.oumake_gen.BipartiteEvolmantel_testmantel_test_nbpartnersmodelSelectionpaleodivphyl.pca_plphylosignal_networkphylosignal_sub_networkpi_estimatorplot_BICompareplot_ClaDS_chainsplot_ClaDS_phyloplot_ClaDS0_chainsplot_div.BipartiteEvolplot_dttplot_fit_bdplot_fit_envplot_net.BipartiteEvolplot_phylo_combplot_phylosignal_sub_networkplot_prob_dttplot_spectRplot.fit_t.envplot.fit_t.env.ouPosdefprintprob_dttremove.modelshift.estimatesshowsim_ClaDSsim_env_bdsim_MCBDsim_sgdsim_t_compsim_t_envsim_t_env_ousim_t_tworegimesim.BipartiteEvolsim.convergence.geosim.divergence.geosimul.comb.shiftsimulateTipDataspectRspectR_ttheta_estimator

Dependencies:apeBBbipartiteclasscliclueclusterclusterGenerationcodacodetoolscolorspacecombinatcorpcorcpp11DEoptimDEoptimRdeSolvedigestdiptestdirmultdoParalleldotCall64expmfansifarverfastmatchfBasicsfieldsflexmixforeachfpcgeigergenericsggplot2ggrepelggseqlogoglassoFastgluegmpgssgtableGUniFracigraphinlineisobanditeratorsjsonlitekernlablabelinglatticelifecyclemagrittrmapsMASSMatrixmatrixStatsmclustmgcvmnormtmodeestmodeltoolsmunsellmvMORPHmvtnormncbitnetworknlmennetnumDerivoptimParallelParallelLoggerpbmcapplypermutephangornphytoolspicantepillarpkgconfigprabcluspracmapsplinepvclustquadprogR.methodsS3R.ooR.utilsR6rasterRColorBrewerRcpprlangRmpfrrmutilrobustbaserpartscalesscatterplot3dsnasnowspspamspatialstablestablediststatipstatmodstatnet.commonsubplexterraTESStibbletimeDatetimeSeriesutf8vctrsveganviridisLitewithrxml2

Readme and manuals

Help Manual

Help pageTopics
RPANDARPANDA-package RPANDA
Geological time scaleadd.gts
Estimation of traits ancestral states.ancestral
Anolis datasetAnolis.data
Calculates paleodiversity dynamics with the probabilistic approach.apply_prob_dtt
Balaenopteridae phylogenyBalaenopteridae
BioGeoBEARS stochastic mapsBGB.examples
Identify modalities in a phylogenyBICompare
Build the interaction network in BipartiteEvolbuild_network.BipartiteEvol
Calomys phylogenyCalomys
The _Caprimulgidae_ phylogeny.Caprimulgidae
An example run of ClaDS2.Caprimulgidae_ClaDS2
Cetacean phylogenyCetacea
Stochastic map of clade membership in Cetacean phylogenyCetacea_clades
An example run of ClaDS0.ClaDS0_example
co2 data since the Jurassicco2
co2 data since the beginning of the Cenozoicco2_res
Coccolithophore diversity since the Jurassiccoccolithophore
Create class objectCreateClassObject
Create merged biogeography-by-class objectCreateGeobyClassObject
Create biogeography objectCreateGeoObject
Create biogeography object using a stochastic map from BioGeoBEARSCreateGeoObject_BioGeoBEARS
Creation of a PhenotypicModelcreateModel
Creation of a PhenotypicGMMcreateModelCoevolution
d13c data since the Jurassicd13c
Build the phylogenies for BipartiteEvoldefine_species.BipartiteEvol
Automatic phylotypes delineationdelineate_phylotypes
Model comparison of diversification modelsdiv.models
Diversification rates through timediv.rates
Maximum likelihood fit of the general birth-death modelfit_bd
Maximum likelihood fit of the general birth-death model (backbone)fit_bd_backbone
Maximum likelihood fit of the general birth-death model (backbone and constraints)fit_bd_backbone_c
Maximum likelihood fit of the general birth-death model excluding the recent pastfit_bd_in_past
Fit ClaDS to a phylogenyfit_ClaDS
Infer ClaDS0's parameter on a phylogenyfit_ClaDS0
Maximum likelihood fit of the equilibrium modelfit_coal_cst
Fit birth-death model using a coalescent approchfit_coal_var
Maximum likelihood fit of the environmental birth-death modelfit_env
Maximum likelihood fit of the environmental birth-death model excluding the recent pastfit_env_in_past
Maximum likelihood fit of the SGD modelfit_sgd
Fits models of trait evolution incorporating competitive interactionsfit_t_comp
Fits models of trait evolution incorporating competitive interactions, restricting competition to occur only between members of a subgroupfit_t_comp_subgroup
Maximum likelihood fit of the environmental model of trait evolutionfit_t_env
Maximum likelihood fit of the OU environmental model of trait evolutionfit_t_env_ou
High-dimensional phylogenetic models of trait evolutionfit_t_pl
Fits standard models of trait evolution incorporating known and nuisance measurement errorfit_t_standard
Maximum likelihood estimators of a model's parametersfitTipData
~~ Methods for Function 'fitTipData' ~~fitTipData,PhenotypicModel-method fitTipData-methods
Foraminifera diversity since the Jurassicforaminifera
Combinations of shifts of diversification.get.comb.shift
Sampling fractions of subcladesget.sampling.fractions
Likelihood of tip trait values.getDataLikelihood
~~ Methods for Function 'getDataLikelihood' ~~getDataLikelihood,PhenotypicModel-method getDataLikelihood-methods
Gets the Maximum A Posteriori for each ClaDS parametergetMAPS_ClaDS
Gets the Maximum A Posteriori for each ClaDS0 parametergetMAPS_ClaDS0
Distribution of tip trait values.getTipDistribution
Distribution of tip trait values.getTipDistribution,PhenotypicACDC-method getTipDistribution,PhenotypicADiag-method getTipDistribution,PhenotypicBM-method getTipDistribution,PhenotypicDD-method getTipDistribution,PhenotypicGMM-method getTipDistribution,PhenotypicModel-method getTipDistribution,PhenotypicOU-method getTipDistribution,PhenotypicPM-method getTipDistribution-methods
Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).gic_criterion
Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).GIC.fit_pl.rpanda
Green algae diversity since the Jurassicgreenalgae
Paleotemperature data across the CenozoicInfTemp
Clustering on the Jensen-Shannon distance between phylogenetic trait dataJSDt_cluster
Jensen-Shannon distance between phylogeniesJSDtree
Clustering of phylogeniesJSDtree_cluster
Land plant diversity since the Jurassiclandplant
Likelihood of a phylogeny under the general birth-death modellikelihood_bd
Likelihood of a phylogeny under the general birth-death model (backbone)likelihood_bd_backbone
Likelihood of a phylogeny under the equilibrium diversity modellikelihood_coal_cst
Likelihood of a birth-death model using a coalescent approchlikelihood_coal_var
Likelihood of a phylogeny under the SGD modellikelihood_sgd
Likelihood of a dataset under models with biogeography fit to a subgroup.likelihood_subgroup_model
Likelihood of a dataset under diversity-dependent models.likelihood_t_DD
Likelihood of a dataset under diversity-dependent models with biogeography.likelihood_t_DD_geog
Likelihood of a dataset under environmental models of trait evolution.likelihood_t_env
Likelihood of a dataset under the matching competition model.likelihood_t_MC
Likelihood of a dataset under the matching competition model with biogeography.likelihood_t_MC_geog
Add to a plot line segments joining the phenotypic evolutionary rate through time estimated by the _fit_t_env_ functionlines.fit_t.env
Add to a plot line segments joining the phenotypic evolutionary optimum through time estimated by the _fit_t_env_ou_ functionlines.fit_t.env.ou
Compute the genealogies for BipartiteEvolmake_gen.BipartiteEvol
Compute Mantel testmantel_test
Compute Mantel testmantel_test_nbpartners
Phenotypic model selection from tip trait data.modelSelection
~~ Methods for Function 'modelSelection' ~~modelSelection,PhenotypicModel-method modelSelection-methods
A class used internally to compute ClaDS's likelihoodMPhiFFT
Mycorrhizal network from La Réunion islandmycorrhizal_network
Ostracod diversity since the Jurassicostracoda
Paleodiversity through timepaleodiv
Class '"PhenotypicACDC"'PhenotypicACDC-class
Class '"PhenotypicADiag"'PhenotypicADiag-class
Class '"PhenotypicBM"'PhenotypicBM-class
Class '"PhenotypicDD"'PhenotypicDD-class
Class '"PhenotypicGMM"'PhenotypicGMM-class
Class '"PhenotypicModel"'PhenotypicModel-class print,PhenotypicModel-method show,PhenotypicModel-method [,PhenotypicModel,ANY,ANY,ANY-method [<-,PhenotypicModel,ANY,ANY,ANY-method
Class '"PhenotypicOU"'PhenotypicOU-class
Class '"PhenotypicPM"'PhenotypicPM-class
Phocoenidae phylogenyPhocoenidae
Regularized Phylogenetic Principal Component Analysis (PCA).phyl.pca_pl
Phyllostomidae phylogenyPhyllostomidae
Phylogenies of Phyllostomidae generaPhyllostomidae_genera
Compute phylogenetic signal in a bipartite interaction networkphylosignal_network
Compute clade-specific phylogenetic signals in a bipartite interaction networkphylosignal_sub_network
Compute nucleotidic diversity (Pi estimator)pi_estimator
Display modalities on a phylogeny.plot_BICompare
Plot the MCMC chains obtained when infering ClaDS parametersplot_ClaDS_chains
Plot a phylogeny with branch-specific valuesplot_ClaDS_phylo
Plot the MCMC chains obtained when infering ClaDS0 parametersplot_ClaDS0_chains
Plot the output of BipartiteEvolplot_div.BipartiteEvol
Plot diversity through timeplot_dtt
Plot speciation, extinction & net diversification rate functions of a fitted modelplot_fit_bd
Plot speciation, extinction & net diversification rate functions of a fitted environmental modelplot_fit_env
Plot the output of BipartiteEvolplot_net.BipartiteEvol
Plot shifts of diversifcation on a phylogenyplot_phylo_comb
Plot clade-specific phylogenetic signals in a bipartite interaction networkplot_phylosignal_sub_network
Plot diversity through time with confidence intervals.plot_prob_dtt
Spectral density plot of a phylogeny.plot_spectR
Plot the phenotypic evolutionary rate through time estimated by the _fit_t_env_ functionplot.fit_t.env
Plot the phenotypic evolutionary optimum through time estimated by the _fit_t_env_ou_ functionplot.fit_t.env.ou
Positive definite symmetric matricesPosdef
Confidence intervals of diversity through timeprob_dtt
Radiolaria diversity since the Jurassicradiolaria
Red algae diversity since the Jurassicredalgae
Removing a model from shift.estimates outputremove.model
Sea level data since the Jurassicsealevel
Estimating clade-shifts of diversificationshift.estimates
Cetacean shift.estimates resultsshifts_cetacea
Silica data across the Cenozoicsilica
Simulation of the ClaDS modelsim_ClaDS
Simulate birth-death tree dependent on an environmental curvesim_env_bd
Simulation of macroevolutionary diversification under the integrated model described in Aristide & Morlon 2019sim_MCBD
Algorithm for simulating a phylogenetic tree under the SGD modelsim_sgd
Recursive simulation (root-to-tip) of competition modelssim_t_comp
Recursive simulation (root-to-tip) of the environmental modelsim_t_env
Recursive simulation (root-to-tip) of the OU environmental modelsim_t_env_ou
Recursive simulation (root-to-tip) of two-regime modelssim_t_tworegime
Simulation of the BipartiteEvol modelsim.BipartiteEvol
Simulation of trait data under the model of convergent character displacement described in Drury et al. 2017sim.convergence.geo
Simulation of trait data under the model of divergent character displacement described in Drury et al. 2017sim.divergence.geo
Simulating trees from shift.estimates() results to test model adequacysimul.comb.shift
Tip trait simulation under a model of phenotypic evolution.simulateTipData
~~ Methods for Function 'simulateTipData' ~~simulateTipData,PhenotypicModel-method simulateTipData-methods
Spectral density plot of a phylogenyspectR
Spectral density plot of phylogenetic trait dataspectR_t
Cetacean taxonomytaxo_cetacea
Compute Watterson genetic diversity (Theta estimator)theta_estimator