# Phylogenetic ANalyses of DiversificAtion

## Documentation for package ‘RPANDA’ version 2.5

- DESCRIPTION file.

## Help Pages

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_bd_in_past | Maximum likelihood fit of the general birth-death model excluding the recent past
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_env_in_past | Maximum likelihood fit of the environmental birth-death model excluding the recent past
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
fit_t_thresh | Maximum likelihood fit of Felsenstein' threshold model of evolution for a binary character.
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_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
lines.threshML | Add to a plot line segments joining the evolutionary rate through time estimated by the "ClimExp" model in the _fit_t_thresh_ 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.threshML | Plot the rate of evolution through time estimated by the "ClimExp" model in the _fit_t_thresh_ 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"'