Files in RPANDA
Phylogenetic ANalyses of DiversificAtion

MD5
README.md
NAMESPACE
DESCRIPTION
R/fit_env.R R/CreateGeoObject_BioGeoBEARS.R R/DDexpMulti_geo_ADiag.R R/DDlin.rescale.geog.R R/fit_coal_var.R R/createModel.R R/DDexpMulti_nogeo_ADiag.R R/MC_nogeo_ADiag_ME.R R/fit_t_pl.R R/fit_ClaDS0.R R/likelihood_coal_cst_mod.R R/spectR.R R/sim_ClaDS.R R/likelihood_coal_cst.R R/MC_geo_PM_ME.R R/CreateGeoObject.R R/prob_dtt.R R/print.fit.env.R R/sim_MCBD.R R/MPhiFFT.class.R R/getMAPS_ClaDS.R R/resortGeoObject.R R/print.fit_t.env.R R/base_sgd.R R/likelihood_t_DD_geog.R R/likelihood_t_MC.R R/Psi.R R/DDexp_geo_ADiag.R R/MC.rescale_geog.R R/modelSelection.R R/plot_BICompare.R R/DDexp.rescale.R R/fitTipData.R R/DDexp_geo_ADiag_ME.R R/stratified_BGB_to_tables.R R/getMAPS_ClaDS0.R R/DDlin.rescale.R R/sim.BipartiteEvol.R R/plot_ClaDS_chains.R R/likelihood_bd.R R/sim.divergence.geo.R R/phyl.pca_pl.R R/plot_fit_bd.R R/likelihood_subgroup_model.R R/fit_ClaDS.R R/JSDtree.R R/likelihood_sgd.R R/sim_t_tworegime.R R/fit_bd.R R/trimSimmap.R R/CreateGeobyClassObject.R R/DDlinMulti_nogeo_ADiag.R R/fit_t_comp.R R/fit_t_comp_subgroup.R R/CreateClassObject.R R/sim_env_bd.r R/plot_ClaDS_phylo.R R/getTipDistribution.R R/spectR_t.R R/DDexp.rescale.geog.R R/MC_twoS_PM_geo.R R/DDexpMulti_nogeo_ADiag_ME.R R/GIC.R R/likelihood_coal_exp_mod.R R/misc_functions.R R/sim.convergence.geo.R R/DDexp_nogeo_ADiag.R R/MC_twoS_PM.R R/DDlin_geo_ADiag.R R/MPhiAbstract.class.R R/aPhenotypicModel.class.R R/sim_t_comp.R R/DDlinMulti_geo_ADiag_ME.R R/sim_sgd.R R/print.fit_pl.R R/MC_nogeo_ADiag.R R/fit_t_standard.R R/BICompare.R R/Phi.R R/simulateTipData.R R/MC.rescale.R R/fit_t_env.R R/resortSMatrix.R R/DDlinMulti_nogeo_ADiag_ME.R R/CreateBioGeoB_Object_subclade.R R/DDexpMulti_geo_ADiag_ME.R R/CreateSMatrix.R R/fit_coal_cst.R R/sim_t_env.R R/MC_twoS_PM_ME.R R/DDlinMulti_geo_ADiag.R R/likelihood_t_MC_geog.R R/fit_sgd.R R/integrate.R R/print.fit.bd.R R/DDlin_nogeo_ADiag.R R/likelihood_coal_var.R R/MC_twoS_PM_geo_ME.R R/DDlin_nogeo_ADiag_ME.R R/getDataLikelihood.R R/plot_prob_dtt.R R/DDexp_nogeo_ADiag_ME.R R/DDlin_geo_ADiag_ME.R R/proposal.R R/plot_dtt.R R/MC_geo_PM.R R/likelihood_t_env.R R/JSDtree_cluster.R R/plot_BipartiteEvol.R R/likelihood_t_DD.R R/plot.fit_t.env.r R/plot_fit_env.R R/utils_BipartiteEvol.R R/plot_spectR.R R/utils.R R/JSDt_cluster.R R/ReconcileGeoObjectSMatrix.R R/plot_ClaDS0_chains.R
src/covar.h
src/fitness.c
src/C_panda-covar-ou.c
src/RPANDA_init.c
src/diversif_lognormal.c
inst/CITATION
tests/test-all.R tests/testthat/test-fit-env-bd.r tests/testthat/test-fit-coal.r tests/testthat/test-fit-bd.r
data/datalist
data/sealevel.rda
data/Cetacea_clades.rda
data/InfTemp.rda
data/d13c.rda
data/Phyllostomidae.rda
data/BGB.examples.rda
data/ostracoda.rda
data/landplant.rda
data/radiolaria.rda
data/foraminifera.rda
data/Phyllostomidae_genera.rda
data/Calomys.rda
data/co2.rda
data/Cetacea.rda
data/ClaDS0_example.rda
data/redalgae.rda
data/Caprimulgidae.rda
data/coccolithophore.rda
data/co2_res.rda
data/greenalgae.rda
data/Balaenopteridae.rda
data/Caprimulgidae_ClaDS2.rda
data/silica.rda
data/Phocoenidae.rda
data/Anolis.data.rda
man/likelihood_t_MC_geog.Rd man/fit_ClaDS0.Rd man/likelihood_bd.Rd man/getMAPS_ClaDS.Rd man/likelihood_subgroup_model.Rd man/BGB.examples.Rd man/sim_sgd.Rd man/spectR_t.Rd man/RPANDA-package.Rd man/PhenotypicOU-class.Rd man/silica.Rd man/plot_spectR.Rd man/likelihood_sgd.Rd man/fit_t_env.Rd man/simulateTipData.Rd man/co2_res.Rd man/fitTipData-methods.Rd man/Cetacea.Rd man/createModel.Rd man/plot_ClaDS_phylo.Rd man/likelihood_t_env.Rd man/plot_dtt.Rd man/PhenotypicADiag-class.Rd man/sim.BipartiteEvol.Rd man/sim_env_bd.Rd man/sim_t_tworegime.Rd man/getTipDistribution.Rd man/getDataLikelihood.Rd man/sim_MCBD.Rd man/ClaDS0_example.Rd man/sim.convergence.geo.Rd man/plot_ClaDS0_chains.Rd man/PhenotypicGMM-class.Rd man/plot_fit_env.Rd man/Anolis.data.Rd man/CreateClassObject.Rd man/JSDt_cluster.Rd man/GIC.Rd man/fit_coal_var.Rd man/PhenotypicPM-class.Rd man/Phocoenidae.Rd man/redalgae.Rd man/InfTemp.Rd man/fit_sgd.Rd man/simulateTipData-methods.Rd man/CreateGeoObject_BioGeoBEARS.Rd man/foraminifera.Rd man/likelihood_coal_cst.Rd man/JSDtree_cluster.Rd man/fit_t_pl.Rd man/phyl.pca_pl.Rd man/Balaenopteridae.Rd man/PhenotypicBM-class.Rd man/ostracoda.Rd man/lines.fit_t.env.Rd man/sealevel.Rd man/fit_env.Rd man/likelihood_t_MC.Rd man/make_gen.BipartiteEvol.Rd man/fit_t_comp_subgroup.Rd man/plot_fit_bd.Rd man/fitTipData.Rd man/plot_div.BipartiteEvol.Rd man/PhenotypicModel-class.Rd man/plot_ClaDS_chains.Rd man/plot.fit_t.env.Rd man/fit_coal_cst.Rd man/sim_t_comp.Rd man/PhenotypicACDC-class.Rd man/CreateGeoObject.Rd man/BICompare.Rd man/coccolithophore.Rd man/likelihood_t_DD_geog.Rd man/modelSelection.Rd man/fit_t_standard.Rd man/sim.divergence.geo.Rd man/prob_dtt.Rd man/PhenotypicDD-class.Rd man/getTipDistribution-methods.Rd man/createModelCoevolution.Rd man/radiolaria.Rd man/fit_ClaDS.Rd man/build_network.BipartiteEvol.Rd man/CreateGeobyClassObject.Rd man/Caprimulgidae_ClaDS2.Rd man/sim_t_env.Rd man/sim_ClaDS.Rd man/landplant.Rd man/Phyllostomidae.Rd man/likelihood_t_DD.Rd man/fit_bd.Rd man/fit_t_comp.Rd man/Caprimulgidae.Rd man/plot_BICompare.Rd man/Calomys.Rd man/plot_net.BipartiteEvol.Rd man/gic_criterion.Rd man/d13c.Rd man/getDataLikelihood-methods.Rd man/greenalgae.Rd man/Phyllostomidae_genera.Rd man/likelihood_coal_var.Rd man/plot_prob_dtt.Rd man/modelSelection-methods.Rd man/MPhiFFT.Rd man/Cetacea_clades.Rd man/Posdef.Rd man/JSDtree.Rd man/getMAPS_ClaDS0.Rd man/define_species.BipartiteEvol.Rd man/ancestral.Rd man/spectR.Rd man/co2.Rd
RPANDA documentation built on Nov. 10, 2021, 9:08 a.m.