RPANDA
Phylogenetic ANalyses of DiversificAtion

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Functions
455
Source code
134
Man pages
122
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RPANDA: Phylogenetic ANalyses of DiversificAtion
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API

API for RPANDA
Phylogenetic ANalyses of DiversificAtion

Global functions
.CLIMtransform Source code
.CreateBioGeoB_Object_subclade Source code
.CreateSMatrix Source code
.Integrate Source code
.Phi Source code
.Psi Source code
.ReconcileGeoObjectSMatrix Source code
.VCV.rescale Source code
.VCV.rescale.DDexp_geog Source code
.VCV.rescale.DDlin_geog Source code
.VCV.rescale.geog Source code
.covPenalized Source code
.create.function.list.EB1 Source code
.create.function.list.EBmulti Source code
.createModel_DDexp Source code
.createModel_DDexp_ME Source code
.createModel_DDexp_geo Source code
.createModel_DDexp_geo_ME Source code
.createModel_DDexp_multi Source code
.createModel_DDexp_multi_ME Source code
.createModel_DDexp_multi_geo Source code
.createModel_DDexp_multi_geo_ME Source code
.createModel_DDlin Source code
.createModel_DDlin_ME Source code
.createModel_DDlin_geo Source code
.createModel_DDlin_geo_ME Source code
.createModel_DDlin_multi Source code
.createModel_DDlin_multi_ME Source code
.createModel_DDlin_multi_geo Source code
.createModel_DDlin_multi_geo_ME Source code
.createModel_MC Source code
.createModel_MC_ME Source code
.createModel_MC_geo Source code
.createModel_MC_geo_ME Source code
.createModel_MC_twoS Source code
.createModel_MC_twoS_ME Source code
.createModel_MC_twoS_geo Source code
.createModel_MC_twoS_geo_ME Source code
.event_txt_into_events_row Source code
.events_txt_into_events_table Source code
.events_txt_list_into_events_table Source code
.fit_t_EB Source code
.fit_t_general Source code
.likelihood_coal_cst_mod Source code
.likelihood_coal_exp_mod Source code
.makePenalty Source code
.phyOU Source code
.resortGeoObject Source code
.resortSMatrix Source code
.sqM Source code
.starting_val Source code
.stratified_BGB_to_tables Source code
.tr Source code
.transformTree Source code
.transformsqrt Source code
.trimSimmap Source code
.vcv.rescale.DDexp Source code
.vcv.rescale.DDlin Source code
.vcvPhyloInternal Source code
.vec Source code
Anolis.data Man page
BGB.examples Man page
BICompare Man page Source code
Balaenopteridae Man page
Calomys Man page
Caprimulgidae Man page
Caprimulgidae_ClaDS2 Man page
Cetacea Man page
Cetacea_clades Man page
ClaDS0_example Man page
CreateClassObject Man page Source code
CreateGeoObject Man page Source code
CreateGeoObject_BioGeoBEARS Man page Source code
CreateGeobyClassObject Man page Source code
GIC.fit_pl.rpanda Man page Source code
InfTemp Man page
InterpolatedKhi Source code
InterpolatedPhi Source code
Inverse_FB Source code
Inverse_FB2 Source code
JSDt_cluster Man page Source code
JSDtree Man page Source code
JSDtree_cluster Man page Source code
Khi_ClaDS1 Source code
Khi_ClaDS2 Source code
Lambert2Newick Source code
LikelihoodSGDFromLambert Source code
MPhiFFT Man page
MagnusExpansion_ClaDS1 Source code
MagnusExpansion_ClaDS2 Source code
PhenotypicACDC-class Man page
PhenotypicADiag-class Man page
PhenotypicBM-class Man page
PhenotypicDD-class Man page
PhenotypicGMM-class Man page
PhenotypicModel-class Man page
PhenotypicOU-class Man page
PhenotypicPM-class Man page
Phi_ClaDS1 Source code
Phi_ClaDS2 Source code
Phocoenidae Man page
Phyllostomidae Man page
Phyllostomidae_genera Man page
Phylo2Lambert Source code
Posdef Man page
RPANDA Man page
RPANDA-package Man page
Simulate_SGD_Phylogeny Source code
[,PhenotypicModel,ANY,ANY,ANY-method Man page
[<-,PhenotypicModel,ANY,ANY,ANY-method Man page
abs.to.rel Source code
add_iter_ClaDS Source code
ancestral Man page
ancestral.fit_pl.rpanda Source code
ancestral.fit_t.comp Source code
ancestral.fit_t.env Source code
autoMetropolisGibbs Source code
build_network.BipartiteEvol Man page Source code
co2 Man page
co2_res Man page
coccolithophore Man page
compute.dist Source code
createLikelihood_ClaDS0 Source code
createLikelihood_ClaDS1 Source code
createLikelihood_ClaDS2 Source code
createModel Man page Source code
createModelCoevolution Man page Source code
create_model Source code
d13c Man page
define_species.BipartiteEvol Man page Source code
delineate_phylotypes Man page Source code
dens Source code
derivative_edge Source code
derivative_leaf Source code
endOfPeriods Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
endOfPeriodsGMM Source code
fitTipData Man page
fitTipData,PhenotypicModel-method Man page
fitTipData-methods Man page
fit_ClaDS Man page Source code
fit_ClaDS0 Man page Source code
fit_bd Man page
fit_coal_cst Man page
fit_coal_var Man page
fit_env Man page
fit_sgd Man page Source code
fit_t_comp Man page Source code
fit_t_comp_subgroup Man page Source code
fit_t_env Man page Source code
fit_t_pl Man page Source code
fit_t_standard Man page Source code
foraminifera Man page
g Source code
getDataLikelihood Man page
getDataLikelihood,PhenotypicModel-method Man page
getDataLikelihood-methods Man page
getLivingLineages Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
getMAPS_ClaDS Man page Source code
getMAPS_ClaDS0 Man page Source code
getMatrixCoalescenceJ Source code Source code Source code Source code Source code Source code Source code
getStartingTimes Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
getTipDistribution Man page
getTipDistribution,PhenotypicACDC-method Man page
getTipDistribution,PhenotypicADiag-method Man page
getTipDistribution,PhenotypicBM-method Man page
getTipDistribution,PhenotypicDD-method Man page
getTipDistribution,PhenotypicGMM-method Man page
getTipDistribution,PhenotypicModel-method Man page
getTipDistribution,PhenotypicOU-method Man page
getTipDistribution,PhenotypicPM-method Man page
getTipDistribution-methods Man page
get_ancestors Source code
get_rates Source code
gic_criterion Man page Source code
greenalgae Man page
ifft_panda Source code
integr Source code
isATip Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
landplant Man page
likelihood_bd Man page Source code
likelihood_coal_cst Man page Source code
likelihood_coal_var Man page Source code
likelihood_sgd Man page Source code
likelihood_subgroup_model Man page Source code
likelihood_t_DD Man page Source code
likelihood_t_DD_geog Man page Source code
likelihood_t_MC Man page Source code
likelihood_t_MC_geog Man page Source code
likelihood_t_env Man page Source code
lines.fit_t.env Man page Source code
m Source code
make_gen.BipartiteEvol Man page Source code
mantel_test Man page Source code
mantel_test_nbpartners Man page Source code
mcmcSamplerDE_gibbs Source code
mean.rate Source code
modelSelection Man page
modelSelection,PhenotypicModel-method Man page
modelSelection-methods Man page
mult_rate Source code
mycorrhizal_network Man page
norm2 Source code
ostracoda Man page
pblm Source code
periodizeOneTree Source code Source code Source code Source code
periodizeOneTree_geo Source code Source code Source code Source code Source code Source code
periodizeOneTree_multigeo Source code Source code Source code Source code Source code Source code
periodizeOneTree_multinogeo Source code Source code Source code Source code
periodizeOneTree_multinogeo_geo Source code
periodizeOneTree_nogeo Source code Source code Source code
periodizeOneTree_smulti Source code
phyl.pca_pl Man page Source code
phylosignal_network Man page Source code
phylosignal_sub_network Man page Source code
pi_estimator Man page Source code
pi_per_site Source code
plot.fit_t.env Man page Source code
plot.network Source code
plot.species Source code
plot.with.trait Source code
plot_BICompare Man page Source code
plot_ClaDS0_chains Man page Source code
plot_ClaDS_chains Man page Source code
plot_ClaDS_phylo Man page Source code
plot_div.BipartiteEvol Man page Source code
plot_dtt Man page Source code
plot_fit_bd Man page Source code
plot_fit_env Man page Source code
plot_net.BipartiteEvol Man page Source code
plot_phylosignal_sub_network Man page Source code
plot_prob_dtt Man page
plot_spectR Man page Source code
prepare_ClaDS Source code
print,PhenotypicModel-method Man page
print.fit_pl.rpanda Source code
print.fit_t.env Source code
print.gic.rpanda Source code
prob_dtt Man page Source code
proposalGeneratorFactoryDE_gibbs Source code
proposal_kernel Source code
prune.with.traits Source code
prune_extinct.with.rates Source code
radiolaria Man page
rbactrian Source code
rbactrianLaplace Source code
rbactrianTriangle Source code
redalgae Man page
reflect Source code
rho_0to1 Source code
rho_0tofixe Source code
rho_1mute0 Source code
rho_1to1 Source code
rigth.order Source code
rigth.order.BE Source code
scalar Source code
sealevel Man page
show,PhenotypicModel-method Man page
silica Man page
sim.BipartiteEvol Man page Source code
sim.convergence.geo Man page Source code
sim.divergence.geo Man page Source code
sim_ClaDS Man page
sim_MCBD Man page
sim_env_bd Man page
sim_sgd Man page Source code
sim_t_comp Man page Source code
sim_t_env Man page Source code
sim_t_tworegime Man page Source code
simulateTipData Man page
simulateTipData,PhenotypicModel-method Man page
simulateTipData-methods Man page
sliding_rate Source code
spatial.plot Source code
spectR Man page
spectR_t Man page Source code
theta_estimator Man page
transform_EB Source code
updateBranchingMatrixSigma Source code
RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.

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