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RPANDA  

Phylogenetic ANalyses of DiversificAtion
View on CRAN: Click here


Download and install RPANDA package within the R console
Install from CRAN:
install.packages("RPANDA")

Install from Github:
library("remotes")
install_github("cran/RPANDA")

Install by package version:
library("remotes")
install_version("RPANDA", "2.3")



Attach the package and use:
library("RPANDA")
Maintained by
Hélène Morlon
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-12-02
Latest Update: 2022-10-24
Description:
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) , Morlon et al. (2016) , Clavel & Morlon (2017) , Drury et al. (2017) , Lewitus & Morlon (2017) , Drury et al. (2018) , Clavel et al. (2019) , Maliet et al. (2019) , Billaud et al. (2019) , Lewitus et al. (2019) , Aristide & Morlon (2019) , Maliet et al. (2020) , Drury et al. (2021) , Perez-Lamarque & Morlon (2022) , Perez-Lamarque et al. (2022) , Mazet et al. (2023) , Drury et al. (2024) .
How to cite:
Hélène Morlon (2014). RPANDA: Phylogenetic ANalyses of DiversificAtion. R package version 2.3, https://cran.r-project.org/web/packages/RPANDA. Accessed 06 Nov. 2024.
Previous versions and publish date:
1.0 (2014-12-02 14:36), 1.1 (2015-09-15 00:15), 1.2 (2016-03-31 18:47), 1.3 (2017-04-11 23:21), 1.4 (2018-08-04 23:20), 1.5 (2019-01-30 17:50), 1.6 (2019-06-11 13:00), 1.7 (2020-01-09 13:30), 1.8 (2020-03-06 20:10), 1.9 (2020-09-15 19:10), 2.0 (2021-11-10 09:10), 2.1 (2022-07-18 10:40), 2.2 (2022-10-24 17:28)
Other packages that cited RPANDA R package
View RPANDA citation profile
Other R packages that RPANDA depends, imports, suggests or enhances
Complete documentation for RPANDA
Functions, R codes and Examples using the RPANDA R package
Some associated functions: Anolis.data . BGB.examples . BICompare . Balaenopteridae . Calomys . Caprimulgidae . Caprimulgidae_ClaDS2 . Cetacea . Cetacea_clades . ClaDS0_example . CreateClassObject . CreateGeoObject . CreateGeoObject_BioGeoBEARS . CreateGeobyClassObject . GIC . InfTemp . JSDt_cluster . JSDtree . JSDtree_cluster . MPhiFFT . PhenotypicACDC-class . PhenotypicADiag-class . PhenotypicBM-class . PhenotypicDD-class . PhenotypicGMM-class . PhenotypicModel-class . PhenotypicOU-class . PhenotypicPM-class . Phocoenidae . Phyllostomidae . Phyllostomidae_genera . Posdef . RPANDA-package . ancestral . build_network.BipartiteEvol . co2 . co2_res . coccolithophore . createModel . createModelCoevolution . d13c . define_species.BipartiteEvol . delineate_phylotypes . fitTipData-methods . fitTipData . fit_ClaDS . fit_ClaDS0 . fit_bd . fit_coal_cst . fit_coal_var . fit_env . fit_sgd . fit_t_comp . fit_t_comp_subgroup . fit_t_env . fit_t_pl . fit_t_standard . foraminifera . getDataLikelihood-methods . getDataLikelihood . getMAPS_ClaDS . getMAPS_ClaDS0 . getTipDistribution-methods . getTipDistribution . gic_criterion . greenalgae . landplant . likelihood_bd . likelihood_coal_cst . likelihood_coal_var . likelihood_sgd . likelihood_subgroup_model . likelihood_t_DD . likelihood_t_DD_geog . likelihood_t_MC . likelihood_t_MC_geog . likelihood_t_env . lines.fit_t.env . make_gen.BipartiteEvol . mantel_test . mantel_test_nbpartners . modelSelection-methods . modelSelection . mycorrhizal_network . ostracoda . phyl.pca_pl . phylosignal_network . phylosignal_sub_network . pi_estimator . plot.fit_t.env . plot_BICompare . plot_ClaDS0_chains . plot_ClaDS_chains . plot_ClaDS_phylo . plot_div.BipartiteEvol . plot_dtt . plot_fit_bd . plot_fit_env . plot_net.BipartiteEvol . plot_phylosignal_sub_network . plot_prob_dtt . plot_spectR . prob_dtt . radiolaria . redalgae . sealevel . silica . sim.BipartiteEvol . sim.convergence.geo . sim.divergence.geo . sim_ClaDS . sim_MCBD . sim_env_bd . sim_sgd . sim_t_comp . sim_t_env . sim_t_tworegime . simulateTipData-methods . simulateTipData . spectR . spectR_t . theta_estimator . 
Some associated R codes: BICompare.R . CreateBioGeoB_Object_subclade.R . CreateClassObject.R . CreateGeoObject.R . CreateGeoObject_BioGeoBEARS.R . CreateGeobyClassObject.R . CreateSMatrix.R . DDexp.rescale.R . DDexp.rescale.geog.R . DDexpMulti_geo_ADiag.R . DDexpMulti_geo_ADiag_ME.R . DDexpMulti_nogeo_ADiag.R . DDexpMulti_nogeo_ADiag_ME.R . DDexp_geo_ADiag.R . DDexp_geo_ADiag_ME.R . DDexp_nogeo_ADiag.R . DDexp_nogeo_ADiag_ME.R . DDlin.rescale.R . DDlin.rescale.geog.R . DDlinMulti_geo_ADiag.R . DDlinMulti_geo_ADiag_ME.R . DDlinMulti_nogeo_ADiag.R . DDlinMulti_nogeo_ADiag_ME.R . DDlin_geo_ADiag.R . DDlin_geo_ADiag_ME.R . DDlin_nogeo_ADiag.R . DDlin_nogeo_ADiag_ME.R . GIC.R . JSDt_cluster.R . JSDtree.R . JSDtree_cluster.R . MC.rescale.R . MC.rescale_geog.R . MC_geo_PM.R . MC_geo_PM_ME.R . MC_nogeo_ADiag.R . MC_nogeo_ADiag_ME.R . MC_twoS_PM.R . MC_twoS_PM_ME.R . MC_twoS_PM_geo.R . MC_twoS_PM_geo_ME.R . MPhiAbstract.class.R . MPhiFFT.class.R . Phi.R . Psi.R . ReconcileGeoObjectSMatrix.R . aPhenotypicModel.class.R . base_sgd.R . createModel.R . delineate_phylotypes.R . fitTipData.R . fit_ClaDS.R . fit_ClaDS0.R . fit_bd.R . fit_coal_cst.R . fit_coal_var.R . fit_env.R . fit_sgd.R . fit_t_comp.R . fit_t_comp_subgroup.R . fit_t_env.R . fit_t_pl.R . fit_t_standard.R . full.R . getDataLikelihood.R . getMAPS_ClaDS.R . getMAPS_ClaDS0.R . getTipDistribution.R . integrate.R . likelihood_bd.R . likelihood_coal_cst.R . likelihood_coal_cst_mod.R . likelihood_coal_exp_mod.R . likelihood_coal_var.R . likelihood_sgd.R . likelihood_subgroup_model.R . likelihood_t_DD.R . likelihood_t_DD_geog.R . likelihood_t_MC.R . likelihood_t_MC_geog.R . likelihood_t_env.R . mantel_test.R . mantel_test_nbpartners.R . misc_functions.R . modelSelection.R . pblm.R . phyl.pca_pl.R . phylosignal_network.R . phylosignal_sub_network.R . pi_estimator.R . pi_per_site.R . plot_BICompare.R . plot_BipartiteEvol.R . plot_ClaDS0_chains.R . plot_ClaDS_chains.R . plot_ClaDS_phylo.R . plot_dtt.R . plot_fit_bd.R . plot_fit_env.R . plot_phylosignal_sub_network.R . plot_prob_dtt.R . plot_spectR.R . print.fit.bd.R . print.fit.env.R . print.fit_pl.R . print.fit_t.env.R . prob_dtt.R . proposal.R . resortGeoObject.R . resortSMatrix.R . seg_sites_fasta.R . sim.BipartiteEvol.R . sim.convergence.geo.R . sim.divergence.geo.R . sim_ClaDS.R . sim_MCBD.R . sim_sgd.R . sim_t_comp.R . sim_t_env.R . sim_t_tworegime.R . simulateTipData.R . spectR.R . spectR_t.R . stratified_BGB_to_tables.R . theta_estimator.R . trimSimmap.R . utils.R . utils_BipartiteEvol.R .  Full RPANDA package functions and examples
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