RPANDA-package	RPANDA-package
add.gts	add.gts
ancestral	ancestral
Anolis.data	Anolis.data
apply_prob_dtt	apply_prob_dtt
Balaenopteridae	Balaenopteridae
BGB.examples	BGB.examples
BICompare	BICompare
build_network.BipartiteEvol	build_network.BipartiteEvol
Calomys	Calomys
Caprimulgidae	Caprimulgidae
Caprimulgidae_ClaDS2	Caprimulgidae_ClaDS2
Cetacea	Cetacea
Cetacea_clades	Cetacea_clades
ClaDS0_example	ClaDS0_example
co2	co2
co2_res	co2_res
coccolithophore	coccolithophore
CreateClassObject	CreateClassObject
CreateGeobyClassObject	CreateGeobyClassObject
CreateGeoObject	CreateGeoObject
CreateGeoObject_BioGeoBEARS	CreateGeoObject_BioGeoBEARS
createModel	createModel
createModelCoevolution	createModelCoevolution
d13c	d13c
define_species.BipartiteEvol	define_species.BipartiteEvol
delineate_phylotypes	delineate_phylotypes
div.models	div.models
div.rates	div.rates
fitTipData	fitTipData
fitTipData,PhenotypicModel-method	fitTipData-methods
fitTipData-methods	fitTipData-methods
fit_bd	fit_bd
fit_bd_backbone	fit_bd_backbone
fit_bd_backbone_c	fit_bd_backbone_c
fit_bd_in_past	fit_bd_in_past
fit_ClaDS	fit_ClaDS
fit_ClaDS0	fit_ClaDS0
fit_coal_cst	fit_coal_cst
fit_coal_var	fit_coal_var
fit_env	fit_env
fit_env_in_past	fit_env_in_past
fit_t_comp	fit_t_comp
fit_t_comp_subgroup	fit_t_comp_subgroup
fit_t_env	fit_t_env
fit_t_env_ou	fit_t_env_ou
fit_t_pl	fit_t_pl
fit_t_standard	fit_t_standard
fit_t_thresh	fit_t_thresh
foraminifera	foraminifera
get.comb.shift	get.comb.shift
get.sampling.fractions	get.sampling.fractions
getDataLikelihood	getDataLikelihood
getDataLikelihood,PhenotypicModel-method	getDataLikelihood-methods
getDataLikelihood-methods	getDataLikelihood-methods
getMAPS_ClaDS	getMAPS_ClaDS
getMAPS_ClaDS0	getMAPS_ClaDS0
getTipDistribution	getTipDistribution
getTipDistribution,PhenotypicACDC-method	getTipDistribution-methods
getTipDistribution,PhenotypicADiag-method	getTipDistribution-methods
getTipDistribution,PhenotypicBM-method	getTipDistribution-methods
getTipDistribution,PhenotypicDD-method	getTipDistribution-methods
getTipDistribution,PhenotypicGMM-method	getTipDistribution-methods
getTipDistribution,PhenotypicModel-method	getTipDistribution-methods
getTipDistribution,PhenotypicOU-method	getTipDistribution-methods
getTipDistribution,PhenotypicPM-method	getTipDistribution-methods
getTipDistribution-methods	getTipDistribution-methods
GIC.fit_pl.rpanda	GIC
gic_criterion	gic_criterion
greenalgae	greenalgae
InfTemp	InfTemp
JSDtree	JSDtree
JSDtree_cluster	JSDtree_cluster
JSDt_cluster	JSDt_cluster
landplant	landplant
likelihood_bd	likelihood_bd
likelihood_bd_backbone	likelihood_bd_backbone
likelihood_coal_cst	likelihood_coal_cst
likelihood_coal_var	likelihood_coal_var
likelihood_subgroup_model	likelihood_subgroup_model
likelihood_t_DD	likelihood_t_DD
likelihood_t_DD_geog	likelihood_t_DD_geog
likelihood_t_env	likelihood_t_env
likelihood_t_MC	likelihood_t_MC
likelihood_t_MC_geog	likelihood_t_MC_geog
lines.fit_t.env	lines.fit_t.env
lines.fit_t.env.ou	lines.fit_t_env.ou
lines.threshML	lines.fit_t_thresh
make_gen.BipartiteEvol	make_gen.BipartiteEvol
mantel_test	mantel_test
mantel_test_nbpartners	mantel_test_nbpartners
modelSelection	modelSelection
modelSelection,PhenotypicModel-method	modelSelection-methods
modelSelection-methods	modelSelection-methods
MPhiFFT	MPhiFFT
mycorrhizal_network	mycorrhizal_network
ostracoda	ostracoda
paleodiv	paleodiv
PhenotypicACDC-class	PhenotypicACDC-class
PhenotypicADiag-class	PhenotypicADiag-class
PhenotypicBM-class	PhenotypicBM-class
PhenotypicDD-class	PhenotypicDD-class
PhenotypicGMM-class	PhenotypicGMM-class
PhenotypicModel-class	PhenotypicModel-class
PhenotypicOU-class	PhenotypicOU-class
PhenotypicPM-class	PhenotypicPM-class
Phocoenidae	Phocoenidae
phyl.pca_pl	phyl.pca_pl
Phyllostomidae	Phyllostomidae
Phyllostomidae_genera	Phyllostomidae_genera
phylosignal_network	phylosignal_network
phylosignal_sub_network	phylosignal_sub_network
pi_estimator	pi_estimator
plot.fit_t.env	plot.fit_t.env
plot.fit_t.env.ou	plot.fit_t_env.ou
plot.threshML	plot.fit_t_thresh
plot_BICompare	plot_BICompare
plot_ClaDS0_chains	plot_ClaDS0_chains
plot_ClaDS_chains	plot_ClaDS_chains
plot_ClaDS_phylo	plot_ClaDS_phylo
plot_div.BipartiteEvol	plot_div.BipartiteEvol
plot_dtt	plot_dtt
plot_fit_bd	plot_fit_bd
plot_fit_env	plot_fit_env
plot_net.BipartiteEvol	plot_net.BipartiteEvol
plot_phylosignal_sub_network	plot_phylosignal_sub_network
plot_phylo_comb	plot_phylo_comb
plot_prob_dtt	plot_prob_dtt
plot_spectR	plot_spectR
Posdef	Posdef
print,PhenotypicModel-method	PhenotypicModel-class
prob_dtt	prob_dtt
radiolaria	radiolaria
redalgae	redalgae
remove.model	remove.model
RPANDA	RPANDA-package
sealevel	sealevel
shift.estimates	shift.estimates
shifts_cetacea	shifts_cetacea
show,PhenotypicModel-method	PhenotypicModel-class
silica	silica
sim.BipartiteEvol	sim.BipartiteEvol
sim.convergence.geo	sim.convergence.geo
sim.divergence.geo	sim.divergence.geo
simul.comb.shift	simul.comb.shift
simulateTipData	simulateTipData
simulateTipData,PhenotypicModel-method	simulateTipData-methods
simulateTipData-methods	simulateTipData-methods
sim_ClaDS	sim_ClaDS
sim_env_bd	sim_env_bd
sim_MCBD	sim_MCBD
sim_sgd	sim_sgd
sim_t_comp	sim_t_comp
sim_t_env	sim_t_env
sim_t_env_ou	sim_t_env_ou
sim_t_tworegime	sim_t_tworegime
spectR	spectR
spectR_t	spectR_t
taxo_cetacea	taxo_cetacea
theta_estimator	theta_estimator
[,PhenotypicModel,ANY,ANY,ANY-method	PhenotypicModel-class
[<-,PhenotypicModel,ANY,ANY,ANY-method	PhenotypicModel-class
