Man pages for RPANDA
Phylogenetic ANalyses of DiversificAtion

ancestralEstimation of traits ancestral states.
Anolis.dataAnolis dataset
BalaenopteridaeBalaenopteridae phylogeny
BGB.examplesBioGeoBEARS stochastic maps
BICompareIdentify modalities in a phylogeny
build_network.BipartiteEvolBuild the interaction network in BipartiteEvol
CalomysCalomys phylogeny
CaprimulgidaeThe _Caprimulgidae_ phylogeny.
Caprimulgidae_ClaDS2An example run of ClaDS2.
CetaceaCetacean phylogeny
Cetacea_cladesStochastic map of clade membership in Cetacean phylogeny
ClaDS0_exampleAn example run of ClaDS0.
co2co2 data since the Jurassic
co2_resco2 data since the beginning of the Cenozoic
coccolithophoreCoccolithophore diversity since the Jurassic
CreateClassObjectCreate class object
CreateGeobyClassObjectCreate merged biogeography-by-class object
CreateGeoObjectCreate biogeography object
CreateGeoObject_BioGeoBEARSCreate biogeography object using a stochastic map from...
createModelCreation of a PhenotypicModel
createModelCoevolutionCreation of a PhenotypicGMM
d13cd13c data since the Jurassic
define_species.BipartiteEvolBuild the phylogenies for BipartiteEvol
fit_bdMaximum likelihood fit of the general birth-death model
fit_ClaDSFit ClaDS to a phylogeny
fit_ClaDS0Infer ClaDS0's parameter on a phylogeny
fit_coal_cstMaximum likelihood fit of the equilibrium model
fit_coal_varFit birth-death model using a coalescent approch
fit_envMaximum likelihood fit of the environmental birth-death model
fit_sgdMaximum likelihood fit of the SGD model
fit_t_compFits models of trait evolution incorporating competitive...
fit_t_comp_subgroupFits models of trait evolution incorporating competitive...
fit_t_envMaximum likelihood fit of the environmental model of trait...
fitTipDataMaximum likelihood estimators of a model's parameters
fitTipData-methods~~ Methods for Function 'fitTipData' ~~
fit_t_plHigh-dimensional phylogenetic models of trait evolution
fit_t_standardFits standard models of trait evolution incorporating known...
foraminiferaForaminifera diversity since the Jurassic
getDataLikelihoodLikelihood of tip trait values.
getDataLikelihood-methods~~ Methods for Function 'getDataLikelihood' ~~
getMAPS_ClaDSGets the Maximum A Posteriori for each ClaDS parameter
getMAPS_ClaDS0Gets the Maximum A Posteriori for each ClaDS0 parameter
getTipDistributionDistribution of tip trait values.
getTipDistribution-methodsDistribution of tip trait values.
GICGeneralized Information Criterion (GIC) to compare models fit...
gic_criterionGeneralized Information Criterion (GIC) to compare models fit...
greenalgaeGreen algae diversity since the Jurassic
InfTempPaleotemperature data across the Cenozoic
JSDt_clusterClustering on the Jensen-Shannon distance between...
JSDtreeJensen-Shannon distance between phylogenies
JSDtree_clusterClustering of phylogenies
landplantLand plant diversity since the Jurassic
likelihood_bdLikelihood of a phylogeny under the general birth-death model
likelihood_coal_cstLikelihood of a phylogeny under the equilibrium diversity...
likelihood_coal_varLikelihood of a birth-death model using a coalescent approch
likelihood_sgdLikelihood of a phylogeny under the SGD model
likelihood_subgroup_modelLikelihood of a dataset under models with biogeography fit to...
likelihood_t_DDLikelihood of a dataset under diversity-dependent models.
likelihood_t_DD_geogLikelihood of a dataset under diversity-dependent models with...
likelihood_t_envLikelihood of a dataset under environmental models of trait...
likelihood_t_MCLikelihood of a dataset under the matching competition model.
likelihood_t_MC_geogLikelihood of a dataset under the matching competition model...
lines.fit_t.envAdd to a plot line segments joining the phenotypic...
make_gen.BipartiteEvolCompute the genealogies for BipartiteEvol
modelSelectionPhenotypic model selection from tip trait data.
modelSelection-methods~~ Methods for Function 'modelSelection' ~~
MPhiFFTA class used internally to compute ClaDS's likelihood
ostracodaOstracod diversity since the Jurassic
PhenotypicACDC-classClass '"PhenotypicACDC"'
PhenotypicADiag-classClass '"PhenotypicADiag"'
PhenotypicBM-classClass '"PhenotypicBM"'
PhenotypicDD-classClass '"PhenotypicDD"'
PhenotypicGMM-classClass '"PhenotypicGMM"'
PhenotypicModel-classClass '"PhenotypicModel"'
PhenotypicOU-classClass '"PhenotypicOU"'
PhenotypicPM-classClass '"PhenotypicPM"'
PhocoenidaePhocoenidae phylogeny
PhyllostomidaePhyllostomidae phylogeny
Phyllostomidae_generaPhylogenies of Phyllostomidae genera
phyl.pca_plRegularized Phylogenetic Principal Component Analysis (PCA).
plot_BICompareDisplay modalities on a phylogeny.
plot_ClaDS0_chainsPlot the MCMC chains obtained when infering ClaDS0 parameters
plot_ClaDS_chainsPlot the MCMC chains obtained when infering ClaDS parameters
plot_ClaDS_phyloPlot a phylogeny with branch-specific values
plot_div.BipartiteEvolPlot the output of BipartiteEvol
plot_dttPlot diversity through time
plot_fit_bdPlot speciation, extinction & net diversification rate...
plot_fit_envPlot speciation, extinction & net diversification rate...
plot.fit_t.envPlot the phenotypic evolutionary rate through time estimated...
plot_net.BipartiteEvolPlot the output of BipartiteEvol
plot_prob_dttPlot diversity through time with confidence intervals.
plot_spectRSpectral density plot of a phylogeny.
PosdefPositive definite symmetric matrices
prob_dttConfidence intervals of diversity through time
radiolariaRadiolaria diversity since the Jurassic
redalgaeRed algae diversity since the Jurassic
RPANDA-packageRPANDA
sealevelSea level data since the Jurassic
silicaSilica data across the Cenozoic
sim.BipartiteEvolSimulation of the BipartiteEvol model
sim_ClaDSSimulation of the ClaDS model
sim.convergence.geoSimulation of trait data under the model of convergent...
sim.divergence.geoSimulation of trait data under the model of divergent...
sim_env_bdSimulate birth-death tree dependent on an environmental curve
sim_MCBDSimulation of macroevolutionary diversification under the...
sim_sgdAlgorithm for simulating a phylogenetic tree under the SGD...
sim_t_compRecursive simulation (root-to-tip) of competition models
sim_t_envRecursive simulation (root-to-tip) of the environmental model
sim_t_tworegimeRecursive simulation (root-to-tip) of two-regime models
simulateTipDataTip trait simulation under a model of phenotypic evolution.
simulateTipData-methods~~ Methods for Function 'simulateTipData' ~~
spectRSpectral density plot of a phylogeny
spectR_tSpectral density plot of phylogenetic trait data
RPANDA documentation built on Nov. 10, 2021, 9:08 a.m.