Files in RPANDA
Phylogenetic ANalyses of DiversificAtion
MD5
README.md
NAMESPACE
DESCRIPTION
R/fit_env.R
R/CreateGeoObject_BioGeoBEARS.R
R/plot_phylosignal_sub_network.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/seg_sites_fasta.R
R/DDexp.rescale.R
R/fitTipData.R
R/DDexp_geo_ADiag_ME.R
R/stratified_BGB_to_tables.R
R/pi_estimator.R
R/getMAPS_ClaDS0.R
R/DDlin.rescale.R
R/mantel_test_nbpartners.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/pi_per_site.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/mantel_test.R
R/resortSMatrix.R
R/phylosignal_network.R
R/DDlinMulti_nogeo_ADiag_ME.R
R/theta_estimator.R
R/CreateBioGeoB_Object_subclade.R
R/pblm.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/phylosignal_sub_network.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/delineate_phylotypes.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/full.R
R/plot_spectR.R
R/utils.R
R/JSDt_cluster.R
R/ReconcileGeoObjectSMatrix.R
R/plot_ClaDS0_chains.R
src/permute.c
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/mycorrhizal_network.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/theta_estimator.Rd
man/fit_ClaDS0.Rd
man/likelihood_bd.Rd
man/getMAPS_ClaDS.Rd
man/mantel_test_nbpartners.Rd
man/likelihood_subgroup_model.Rd
man/BGB.examples.Rd
man/sim_sgd.Rd
man/spectR_t.Rd
man/RPANDA-package.Rd
man/phylosignal_sub_network.Rd
man/PhenotypicOU-class.Rd
man/silica.Rd
man/plot_spectR.Rd
man/likelihood_sgd.Rd
man/delineate_phylotypes.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/plot_phylosignal_sub_network.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/phylosignal_network.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/mantel_test.Rd
man/mycorrhizal_network.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/pi_estimator.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
