Phylogenetic ANalyses of DiversificAtion


[Up] [Top]

Documentation for package ‘RPANDA’ version 1.5

Help Pages

RPANDA-package RPANDA
ancestral Estimation of traits ancestral states.
Anolis.data Anolis dataset
Balaenopteridae Balaenopteridae phylogeny
BGB.examples BioGeoBEARS stochastic maps
BICompare Identify modalities in a phylogeny
Calomys Calomys phylogeny
Cetacea Cetacean phylogeny
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 BioGeoBEARS
createModel Creation of a PhenotypicModel
createModelCoevolution Creation of a PhenotypicGMM
d13c d13c data since the Jurassic
fitTipData Maximum likelihood estimators of a model's parameters
fitTipData-method ~~ Methods for Function 'fitTipData' ~~
fitTipData-methods ~~ Methods for Function 'fitTipData' ~~
fit_bd Maximum likelihood fit of the general birth-death model
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 interactions
fit_t_comp_subgroup Fits models of trait evolution incorporating competitive interactions, restricting competition to occur only between members of a subgroup
fit_t_env Maximum likelihood fit of the environmental model of trait evolution
fit_t_pl High-dimensional phylogenetic models of trait evolution
foraminifera Foraminifera diversity since the Jurassic
getDataLikelihood Likelihood of tip trait values.
getDataLikelihood-method ~~ Methods for Function 'getDataLikelihood' ~~
getDataLikelihood-methods ~~ Methods for Function 'getDataLikelihood' ~~
getTipDistribution Distribution of tip trait values.
getTipDistribution-method Distribution of tip trait values.
getTipDistribution-methods Distribution of tip trait values.
GIC.fit_pl.rpanda Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).
gic_criterion Generalized Information Criterion (GIC) to compare models fit by Maximum Likelihood (ML) or Penalized Likelihood (PL).
greenalgae Green algae diversity since the Jurassic
InfTemp Paleotemperature data across the Cenozoic
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 model
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 a subgroup.
likelihood_t_DD Likelihood of a dataset under diversity-dependent models.
likelihood_t_DD_geog Likelihood of a dataset under diversity-dependent models with biogeography.
likelihood_t_env Likelihood of a dataset under environmental models of trait evolution.
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 with biogeography.
lines.fit_t.env Add to a plot line segments joining the phenotypic evolutionary rate through time estimated by the _fit_t_env_ function
modelSelection Phenotypic model selection from tip trait data.
modelSelection-method ~~ Methods for Function 'modelSelection' ~~
modelSelection-methods ~~ Methods for Function 'modelSelection' ~~
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
phyl.pca_pl Regularized Phylogenetic Principal Component Analysis (PCA).
Phyllostomidae Phyllostomidae phylogeny
Phyllostomidae_genera Phylogenies of Phyllostomidae genera
plot.fit_t.env Plot the phenotypic evolutionary rate through time estimated by the _fit_t_env_ function
plot_BICompare Display modalities on a phylogeny.
plot_dtt Plot diversity through time
plot_fit_bd Plot speciation, extinction & net diversification rate functions of a fitted model
plot_fit_env Plot speciation, extinction & net diversification rate functions of a fitted environmental model
plot_prob_dtt Plot diversity through time with confidence intervals.
plot_spectR Spectral density plot of a phylogeny.
Posdef Positive definite symmetric matrices
print-method Class '"PhenotypicModel"'
prob_dtt Confidence intervals of diversity through time
radiolaria Radiolaria diversity since the Jurassic
redalgae Red algae diversity since the Jurassic
RPANDA RPANDA
sealevel Sea level data since the Jurassic
show-method Class '"PhenotypicModel"'
silica Silica data across the Cenozoic
sim.convergence.geo Simulation of trait data under the model of convergent character displacement described in Drury et al. 2017
sim.divergence.geo Simulation of trait data under the model of divergent character displacement described in Drury et al. 2017
simulateTipData Tip trait simulation under a model of phenotypic evolution.
simulateTipData-method ~~ Methods for Function 'simulateTipData' ~~
simulateTipData-methods ~~ Methods for Function 'simulateTipData' ~~
sim_env_bd Simulate birth-death tree dependent on an environmental curve
sim_sgd Algorithm for simulating a phylogenetic tree under the SGD model
sim_t_comp Recursive simulation (root-to-tip) of competition models
sim_t_env Recursive simulation (root-to-tip) of the environmental model
spectR Spectral density plot of a phylogeny
[-method Class '"PhenotypicModel"'
[<--method Class '"PhenotypicModel"'