Phylogenetic ANalyses of DiversificAtion

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Documentation for package ‘RPANDA’ version 2.3

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A B C D F G I J L M O P R S T misc

RPANDA-package RPANDA

-- A --

add.gts Geological time scale
ancestral Estimation of traits ancestral states.
Anolis.data Anolis dataset
apply_prob_dtt Calculates paleodiversity dynamics with the probabilistic approach.

-- B --

Balaenopteridae Balaenopteridae phylogeny
BGB.examples BioGeoBEARS stochastic maps
BICompare Identify modalities in a phylogeny
build_network.BipartiteEvol Build the interaction network in BipartiteEvol

-- C --

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 BioGeoBEARS
createModel Creation of a PhenotypicModel
createModelCoevolution Creation of a PhenotypicGMM

-- D --

d13c d13c data since the Jurassic
define_species.BipartiteEvol Build the phylogenies for BipartiteEvol
delineate_phylotypes Automatic phylotypes delineation
div.models Model comparison of diversification models
div.rates Diversification rates through time

-- F --

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_bd_backbone Maximum likelihood fit of the general birth-death model (backbone)
fit_bd_backbone_c Maximum likelihood fit of the general birth-death model (backbone and constraints)
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 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_env_ou Maximum likelihood fit of the OU environmental model of trait evolution
fit_t_pl High-dimensional phylogenetic models of trait evolution
fit_t_standard Fits standard models of trait evolution incorporating known and nuisance measurement error
foraminifera Foraminifera diversity since the Jurassic

-- G --

get.comb.shift Combinations of shifts of diversification.
get.sampling.fractions Sampling fractions of subclades
getDataLikelihood Likelihood of tip trait values.
getDataLikelihood-method ~~ Methods for Function 'getDataLikelihood' ~~
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-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

-- I --

InfTemp Paleotemperature data across the Cenozoic

-- J --

JSDtree Jensen-Shannon distance between phylogenies
JSDtree_cluster Clustering of phylogenies
JSDt_cluster Clustering on the Jensen-Shannon distance between phylogenetic trait data

-- L --

landplant Land plant diversity since the Jurassic
likelihood_bd Likelihood of a phylogeny under the general birth-death model
likelihood_bd_backbone Likelihood of a phylogeny under the general birth-death model (backbone)
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
lines.fit_t.env.ou Add to a plot line segments joining the phenotypic evolutionary optimum through time estimated by the _fit_t_env_ou_ function

-- M --

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-method ~~ Methods for Function 'modelSelection' ~~
modelSelection-methods ~~ Methods for Function 'modelSelection' ~~
MPhiFFT A class used internally to compute ClaDS's likelihood
mycorrhizal_network Mycorrhizal network from La Réunion island

-- O --

ostracoda Ostracod diversity since the Jurassic

-- P --

paleodiv Paleodiversity through time
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
phylosignal_network Compute phylogenetic signal in a bipartite interaction network
phylosignal_sub_network Compute clade-specific phylogenetic signals in a bipartite interaction network
pi_estimator Compute nucleotidic diversity (Pi estimator)
plot.fit_t.env Plot the phenotypic evolutionary rate through time estimated by the _fit_t_env_ function
plot.fit_t.env.ou Plot the phenotypic evolutionary optimum through time estimated by the _fit_t_env_ou_ function
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 functions of a fitted model
plot_fit_env Plot speciation, extinction & net diversification rate functions of a fitted environmental model
plot_net.BipartiteEvol Plot the output of BipartiteEvol
plot_phylosignal_sub_network Plot clade-specific phylogenetic signals in a bipartite interaction network
plot_phylo_comb Plot shifts of diversifcation on a phylogeny
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

-- R --

radiolaria Radiolaria diversity since the Jurassic
redalgae Red algae diversity since the Jurassic
remove.model Removing a model from shift.estimates output
RPANDA RPANDA

-- S --

sealevel Sea level data since the Jurassic
shift.estimates Estimating clade-shifts of diversification
shifts_cetacea Cetacean shift.estimates results
show-method Class '"PhenotypicModel"'
silica Silica data across the Cenozoic
sim.BipartiteEvol Simulation of the BipartiteEvol model
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
simul.comb.shift Simulating trees from shift.estimates() results to test model adequacy
simulateTipData Tip trait simulation under a model of phenotypic evolution.
simulateTipData-method ~~ Methods for Function 'simulateTipData' ~~
simulateTipData-methods ~~ Methods for Function 'simulateTipData' ~~
sim_ClaDS Simulation of the ClaDS model
sim_env_bd Simulate birth-death tree dependent on an environmental curve
sim_MCBD Simulation of macroevolutionary diversification under the integrated model described in Aristide & Morlon 2019
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
sim_t_env_ou Recursive simulation (root-to-tip) of the OU environmental model
sim_t_tworegime Recursive simulation (root-to-tip) of two-regime models
spectR Spectral density plot of a phylogeny
spectR_t Spectral density plot of phylogenetic trait data

-- T --

taxo_cetacea Cetacean taxonomy
theta_estimator Compute Watterson genetic diversity (Theta estimator)

-- misc --

[-method Class '"PhenotypicModel"'
[<--method Class '"PhenotypicModel"'