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
CalomysCalomys phylogeny
CetaceaCetacean phylogeny
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
fit_bdMaximum likelihood fit of the general birth-death model
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
foraminiferaForaminifera diversity since the Jurassic
getDataLikelihoodLikelihood of tip trait values.
getDataLikelihood-methods~~ Methods for Function 'getDataLikelihood' ~~
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
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...
modelSelectionPhenotypic model selection from tip trait data.
modelSelection-methods~~ Methods for Function 'modelSelection' ~~
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_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_spectRSpectral density plot of a phylogeny.
PosdefPositive definite symmetric matrices
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.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_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
simulateTipDataTip trait simulation under a model of phenotypic evolution.
simulateTipData-methods~~ Methods for Function 'simulateTipData' ~~
spectRSpectral density plot of a phylogeny
RPANDA documentation built on Aug. 7, 2018, 9:04 a.m.