Man pages for RPANDA
Phylogenetic ANalyses of DiversificAtion

Anolis.dataAnolis dataset
BalaenopteridaeBalaenopteridae phylogeny
BGB.examplesBioGeoBEARS stochastic maps
BICompareIdentify modalities in a phylogeny
CalomysCalomys phylogeny
CetaceaCetacean phylogeny
CreateGeoObjectCreate biogeography object
CreateGeoObject_BioGeoBEARSCreate biogeography object using a stochastic map from...
createModelCreation of a PhenotypicModel
createModelCoevolutionCreation of a PhenotypicGMM
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_envMaximum likelihood fit of the environmental model of trait...
fitTipDataMaximum likelihood estimators of a model's parameters
fitTipData-methods~~ Methods for Function 'fitTipData' ~~
getDataLikelihoodLikelihood of tip trait values.
getDataLikelihood-methods~~ Methods for Function 'getDataLikelihood' ~~
getTipDistributionDistribution of tip trait values.
getTipDistribution-methodsDistribution of tip trait values.
InfTempPaleotemperature data across the Cenozoic
JSDtreeJensen-Shannon distance between phylogenies
JSDtree_clusterClustering of phylogenies
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_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' ~~
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
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.
RPANDA-packageRPANDA
sim.convergence.geoSimulation of trait data under the model of convergent...
sim.divergence.geoSimulation of trait data under the model of divergent...
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 May 29, 2017, 3:34 p.m.