Man pages for RPANDA
Phylogenetic ANalyses of DiversificAtion
| ancestral | Estimation of traits ancestral states. |
| Anolis.data | Anolis dataset |
| Balaenopteridae | Balaenopteridae phylogeny |
| BGB.examples | BioGeoBEARS stochastic maps |
| BICompare | Identify modalities in a phylogeny |
| build_network.BipartiteEvol | Build the interaction network in BipartiteEvol |
| Calomys | Calomys phylogeny |
| Caprimulgidae | The _Caprimulgidae_ phylogeny. |
| Caprimulgidae_ClaDS2 | An example run of ClaDS2. |
| Cetacea | Cetacean phylogeny |
| Cetacea_clades | Stochastic map of clade membership in Cetacean phylogeny |
| ClaDS0_example | An example run of ClaDS0. |
| co2 | co2 data since the Jurassic |
| co2_res | co2 data since the beginning of the Cenozoic |
| coccolithophore | Coccolithophore diversity since the Jurassic |
| CreateClassObject | Create class object |
| CreateGeobyClassObject | Create merged biogeography-by-class object |
| CreateGeoObject | Create biogeography object |
| CreateGeoObject_BioGeoBEARS | Create biogeography object using a stochastic map from... |
| createModel | Creation of a PhenotypicModel |
| createModelCoevolution | Creation of a PhenotypicGMM |
| d13c | d13c data since the Jurassic |
| define_species.BipartiteEvol | Build the phylogenies for BipartiteEvol |
| delineate_phylotypes | Automatic phylotypes delineation |
| fit_bd | Maximum likelihood fit of the general birth-death model |
| fit_ClaDS | Fit ClaDS to a phylogeny |
| fit_ClaDS0 | Infer ClaDS0's parameter on a phylogeny |
| 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_comp_subgroup | 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' ~~ |
| fit_t_pl | High-dimensional phylogenetic models of trait evolution |
| fit_t_standard | Fits standard models of trait evolution incorporating known... |
| foraminifera | Foraminifera diversity since the Jurassic |
| getDataLikelihood | Likelihood of tip trait values. |
| getDataLikelihood-methods | ~~ Methods for Function 'getDataLikelihood' ~~ |
| getMAPS_ClaDS | Gets the Maximum A Posteriori for each ClaDS parameter |
| getMAPS_ClaDS0 | Gets the Maximum A Posteriori for each ClaDS0 parameter |
| getTipDistribution | Distribution of tip trait values. |
| getTipDistribution-methods | Distribution of tip trait values. |
| GIC | Generalized Information Criterion (GIC) to compare models fit... |
| gic_criterion | Generalized Information Criterion (GIC) to compare models fit... |
| greenalgae | Green algae diversity since the Jurassic |
| InfTemp | Paleotemperature data across the Cenozoic |
| JSDt_cluster | Clustering on the Jensen-Shannon distance between... |
| JSDtree | Jensen-Shannon distance between phylogenies |
| JSDtree_cluster | Clustering of phylogenies |
| landplant | Land plant diversity since the Jurassic |
| 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_subgroup_model | Likelihood of a dataset under models with biogeography fit to... |
| 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... |
| make_gen.BipartiteEvol | Compute the genealogies for BipartiteEvol |
| mantel_test | Compute Mantel test |
| mantel_test_nbpartners | Compute Mantel test |
| modelSelection | Phenotypic model selection from tip trait data. |
| modelSelection-methods | ~~ Methods for Function 'modelSelection' ~~ |
| MPhiFFT | A class used internally to compute ClaDS's likelihood |
| mycorrhizal_network | Mycorrhizal network from La Réunion island |
| ostracoda | Ostracod diversity since the Jurassic |
| 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 |
| phylosignal_network | Compute phylogenetic signal in a bipartite interaction... |
| phylosignal_sub_network | Compute clade-specific phylogenetic signals in a bipartite... |
| phyl.pca_pl | Regularized Phylogenetic Principal Component Analysis (PCA). |
| pi_estimator | Compute nucleotidic diversity (Pi estimator) |
| plot_BICompare | Display modalities on a phylogeny. |
| plot_ClaDS0_chains | Plot the MCMC chains obtained when infering ClaDS0 parameters |
| plot_ClaDS_chains | Plot the MCMC chains obtained when infering ClaDS parameters |
| plot_ClaDS_phylo | Plot a phylogeny with branch-specific values |
| plot_div.BipartiteEvol | Plot the output of BipartiteEvol |
| 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_net.BipartiteEvol | Plot the output of BipartiteEvol |
| plot_phylosignal_sub_network | Plot clade-specific phylogenetic signals in a bipartite... |
| plot_prob_dtt | Plot diversity through time with confidence intervals. |
| plot_spectR | Spectral density plot of a phylogeny. |
| Posdef | Positive definite symmetric matrices |
| prob_dtt | Confidence intervals of diversity through time |
| radiolaria | Radiolaria diversity since the Jurassic |
| redalgae | Red algae diversity since the Jurassic |
| RPANDA-package | RPANDA |
| sealevel | Sea level data since the Jurassic |
| silica | Silica data across the Cenozoic |
| sim.BipartiteEvol | Simulation of the BipartiteEvol model |
| sim_ClaDS | Simulation of the ClaDS model |
| 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_env_bd | Simulate birth-death tree dependent on an environmental curve |
| sim_MCBD | Simulation of macroevolutionary diversification under the... |
| 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 |
| sim_t_tworegime | Recursive simulation (root-to-tip) of two-regime models |
| simulateTipData | Tip trait simulation under a model of phenotypic evolution. |
| simulateTipData-methods | ~~ Methods for Function 'simulateTipData' ~~ |
| spectR | Spectral density plot of a phylogeny |
| spectR_t | Spectral density plot of phylogenetic trait data |
| theta_estimator | Compute Watterson genetic diversity (Theta estimator) |
