Index

_

__init__() (binference.Basis method) (binference.Bins method) (binference.Density method) (binference.inference.Auto method) (binference.Likelihoods method) (binference.Measure method) (binference.PointEstimate method) (binference.PopulationEstimator method) (binference.PopulationModel method) (binference.PopulationResult method) (binference.priors.BoundPrior method) (binference.priors.Dirichlet method) (binference.priors.DirichletTree method) (binference.priors.Fixed method) (binference.priors.Gamma method) (binference.priors.GammaRates method) (binference.priors.GeneralizedDirichlet method) (binference.priors.HalfNormal method) (binference.priors.Hyperprior method) (binference.priors.InverseGamma method) (binference.priors.LogisticGP method) (binference.priors.LogisticNormal method) (binference.priors.LogisticRandomWalk method) (binference.priors.LogNormal method) (binference.priors.PolyaTree method) (binference.priors.PopulationPrior method) (binference.Response method) (binference.samplers.Bootstrap method) (binference.samplers.Engine method) (binference.samplers.Gibbs method) (binference.samplers.Laplace method) (binference.samplers.MAP method) (binference.samplers.MeanFieldVB method) (binference.samplers.NUTS method) (binference.Selection method) (binference.simulate.Mock method) (binference.simulate.Truth method) (binference.Summary method) (binference.validation.CoverageResult method) (binference.validation.ExactPosterior method) (binference.validation.SBCResult method)

A

approximate ApproximationWarning as_selection() (in module binference.selection) at_mean() (binference.Selection method) attach() (binference.PopulationResult method) auto

Auto (class in binference.inference) autocorr_function() (in module binference.diagnostics) autocorr_time() (in module binference.diagnostics) autocorrelation time average() (binference.validation.CoverageResult method) axis_masses() (binference.Basis method)

B

basis (binference.Likelihoods property) (binference.PopulationResult attribute) Basis (class in binference) best (binference.PointEstimate property) (binference.PopulationResult property) bin bin volume bin-averaged likelihood

BinferenceWarning binned measurement binning bias binning_bias() (binference.PopulationResult method) bins (binference.Likelihoods property) Bins (class in binference) bootstrap Bootstrap (class in binference.samplers) BoundPrior (class in binference.priors)

C

C (binference.Basis property) candidates() (binference.inference.Auto method) categories() (binference.Bins class method) cell_index (binference.Bins property) cells (binference.Bins property) centers (binference.Bins property) chain chains (binference.PopulationResult property) check() (binference.PointEstimate method) (binference.PopulationResult method) coarsen() (binference.Bins method) coerce() (binference.Density class method) (binference.Measure class method) combined() (binference.Selection class method)

component_draws (binference.PopulationResult property) compress() (binference.Likelihoods method) concentration conjugate prior contains() (binference.Bins method) ConvergenceWarning corr() (binference.PopulationResult method) counts (binference.Response property) cov() (binference.PopulationResult method) coverage coverage() (in module binference.validation) coverage_rates() (binference.validation.CoverageResult method) CoverageResult (class in binference.validation) credible interval

D

data support density Density (class in binference) density() (binference.Measure class method) (binference.PointEstimate method) (binference.PopulationResult method) describe() (binference.priors.Dirichlet method) (binference.priors.DirichletTree method) (binference.priors.GeneralizedDirichlet method) (binference.priors.PolyaTree method) diagnostics (binference.PopulationResult property)

DiagnosticsError dim (binference.PopulationModel property) Dirichlet (class in binference.priors) Dirichlet prior Dirichlet tree DirichletTree (class in binference.priors) divergence divergent transition draw draw() (binference.Response method) (binference.Selection method) draw_total() (binference.PopulationModel method)

E

E-BFMI edges (binference.Bins property) effective sample size effective_likelihoods() (binference.PopulationModel method) efficiency (binference.Response property) EM engine Engine (class in binference.samplers)

ESS ess() (in module binference.diagnostics) exact_posterior() (in module binference.validation) ExactPosterior (class in binference.validation) expectation-maximisation expected counts expected() (binference.validation.SBCResult method) expected_counts() (binference.PopulationModel method) exposure

F

fit() (binference.PopulationEstimator method) (binference.samplers.MeanFieldVB method) Fixed (class in binference.priors) fixed() (binference.Response method) flat() (binference.Density class method) flatten() (binference.Bins method) forward() (binference.Measure method) (binference.priors.BoundPrior method) fractions from_base_measure() (binference.priors.Dirichlet class method) from_binned() (binference.Likelihoods class method) from_centers() (binference.Bins class method) from_counts() (binference.priors.Dirichlet class method) (binference.Response class method) from_densities() (binference.Density class method)

from_density() (binference.Likelihoods class method) from_distribution() (binference.Density class method) from_function() (binference.Density class method) (binference.Selection class method) from_gaussian() (binference.Likelihoods class method) from_injections() (binference.Selection class method) from_labelled() (binference.Response class method) from_log() (binference.Likelihoods class method) from_masses() (binference.Density class method) from_quantiles() (binference.priors.InverseGamma class method) from_samples() (binference.Likelihoods class method) (binference.PopulationResult class method) from_simulation() (binference.Response class method) from_table() (binference.Likelihoods class method) from_value() (binference.PopulationModel method) functional() (binference.PopulationResult method)

G

Gamma (class in binference.priors) Gamma rates prior GammaRates (class in binference.priors) generalized Dirichlet GeneralizedDirichlet (class in binference.priors) get_params() (binference.PopulationEstimator method)

Gibbs (class in binference.samplers) grad_log_density() (binference.priors.BoundPrior method) grid() (binference.Bins class method) grid_index() (binference.Bins method) grid_masses (binference.Basis property)

H

HalfNormal (class in binference.priors) has_centering (binference.priors.BoundPrior attribute) height() (binference.Basis method) hierarchical posterior

histogram() (binference.validation.SBCResult method) hyperparameter hyperprior Hyperprior (class in binference.priors)

I

importance sampling importance_ess() (in module binference.diagnostics) index() (binference.Bins method) (binference.Response method) infer() (in module binference) init_from_value() (binference.priors.BoundPrior method) injections InputWarning

interim prior interval() (binference.PopulationResult method) inverse() (binference.Measure method) InverseGamma (class in binference.priors) is_categorical (binference.Bins property) is_identity (binference.Basis property) is_masked (binference.Bins property) is_named (binference.Measure property) is_sparse (binference.Likelihoods property)

J

joint (binference.inference.Auto attribute) (binference.PopulationModel property) (binference.samplers.Engine attribute) (binference.samplers.Gibbs attribute) (binference.samplers.Laplace attribute) (binference.samplers.MAP attribute) (binference.samplers.NUTS attribute)

K

K (binference.Basis property) (binference.Bins property) (binference.Likelihoods property) kind (binference.PopulationModel property) (binference.priors.GammaRates attribute) (binference.priors.PopulationPrior attribute)

KKT gap kkt_gap() (binference.PopulationModel method) (in module binference.diagnostics)

L

L-BFGS label label shift labels (binference.Bins property) Laplace (class in binference.samplers) laplace() (binference.PointEstimate method) leave-one-out likelihood function likelihood matrix Likelihoods (class in binference) linear() (binference.Bins class method) (binference.Measure class method) load() (binference.PopulationResult class method) load_result() (in module binference.io) log predictive density log() (binference.Bins class method) (binference.Measure class method)

log_density() (binference.priors.BoundPrior method) log_density_unconstrained (binference.PopulationResult attribute) log_density_unconstrained() (binference.PopulationModel method) log_density_unconstrained_and_grad() (binference.PopulationModel method) log_evidence_terms() (binference.Likelihoods method) log_jacobian() (binference.Measure method) log_likelihood() (binference.PopulationModel method) log_posterior() (binference.PopulationModel method) log_prior() (binference.PopulationModel method) log_prior_and_grad() (binference.priors.BoundPrior method) log_scale (binference.Likelihoods property) logistic prior LogisticGP (class in binference.priors) LogisticNormal (class in binference.priors) LogisticRandomWalk (class in binference.priors) LogNormal (class in binference.priors)

M

MAP (class in binference.samplers) markov (binference.samplers.Engine attribute) (binference.samplers.Gibbs attribute) (binference.samplers.NUTS attribute) mask (binference.Bins property) mass masses() (binference.Basis method) (binference.Density method) matrix (binference.Response property) MCSE mcse() (in module binference.diagnostics) mean (binference.PopulationResult property) mean-field VB MeanFieldVB (class in binference.samplers) measure Measure (class in binference)

measured_fractions() (binference.Response method) measures (binference.Bins property) median (binference.PopulationResult property) METHODS (in module binference.inference) missing information missing_information() (binference.PopulationModel method) (in module binference.diagnostics) mix-SQP Mock (class in binference.simulate) mock catalogue mock_1d() (in module binference.simulate) mock_2d() (in module binference.simulate) mock_categorical() (in module binference.simulate) mock_unfolding() (in module binference.simulate) mode (binference.Selection property) mode_and_covariance() (binference.samplers.Laplace method) Monte Carlo standard error

N

N (binference.Likelihoods property) n_draws (binference.PopulationResult property) ndim (binference.Bins property)

neighbors() (binference.Bins method) nnz (binference.Likelihoods property) NUTS (class in binference.samplers)

O

object

on_basis() (binference.Likelihoods method) ordered (binference.Bins property)

P

Pareto k-hat passed() (binference.validation.SBCResult method) plot() (binference.PopulationResult method) plot_corner() (binference.PopulationResult method) (in module binference.plotting) plot_individual() (in module binference.plotting) plot_population() (in module binference.plotting) plot_sbc() (in module binference.plotting) plot_trace() (binference.PopulationResult method) (in module binference.plotting) point estimate PointEstimate (class in binference) PolyaTree (class in binference.priors) population population fractions population() (in module binference.simulate)

PopulationEstimator (class in binference) PopulationModel (class in binference) PopulationPrior (class in binference.priors) PopulationResult (class in binference) posterior predictive p-value posterior samples Pólya tree predict() (binference.PopulationEstimator method) predict_proba() (binference.PopulationEstimator method) predictive_pvalue() (binference.Response method) prior_key (binference.PopulationResult attribute) prior_predictive() (in module binference.simulate) pseudocounts (binference.priors.BoundPrior attribute) psis() (in module binference.diagnostics) psis_threshold() (in module binference.diagnostics) pvalues() (binference.validation.SBCResult method)

Q

quantile() (binference.PopulationResult method) (binference.validation.ExactPosterior method)

R

R-hat range (binference.Bins property) rates (binference.PointEstimate property) (binference.PopulationResult property) realised histogram realised sample rebin() (binference.PopulationResult method) reference prior reference() (binference.priors.Dirichlet class method) refine() (binference.Bins method) representation response (binference.PopulationModel attribute) Response (class in binference)

response matrix response_at() (binference.PopulationModel method) responsibilities responsibilities() (binference.PopulationModel method) result (binference.samplers.NUTS property) result_to_dict() (in module binference.io) rhat() (in module binference.diagnostics) rho (binference.PointEstimate property) run() (binference.inference.Auto method) (binference.samplers.Bootstrap method) (binference.samplers.Gibbs method) (binference.samplers.Laplace method) (binference.samplers.MAP method) (binference.samplers.MeanFieldVB method) (binference.samplers.NUTS method)

S

sample() (binference.PopulationEstimator method) (binference.samplers.Gibbs method) (binference.samplers.NUTS method) SAMPLE_COLOR (in module binference.plotting) sample_prior() (binference.PopulationModel method) sample_variance() (binference.Likelihoods method) sample_within() (binference.Bins method) samples (binference.PopulationResult property) save() (binference.PopulationResult method) save_result() (in module binference.io) SBC sbc() (in module binference.validation) SBCResult (class in binference.validation) score() (binference.PopulationEstimator method) selected (binference.PointEstimate property) (binference.PopulationResult property) selected population selection (binference.Likelihoods property) (binference.PointEstimate property) (binference.PopulationModel attribute) (binference.PopulationResult property) Selection (class in binference)

selection function selection mode selection_at() (binference.PopulationModel method) SELECTION_MODES (in module binference.selection) selection_row (binference.PopulationModel attribute) SELECTION_SCALES (in module binference.selection) selection_uncertain (binference.PopulationModel property) set_params() (binference.PopulationEstimator method) shape (binference.Bins property) (binference.Likelihoods property) shares (binference.Basis property) shrinkage simplex simulation-based calibration smoothness prior SQUAREM stack() (binference.Likelihoods method) stacking std (binference.PopulationResult property) stderr() (binference.validation.CoverageResult method) subset() (binference.Likelihoods method) Summary (class in binference) summary() (binference.PopulationResult method) support() (binference.Basis method)

T

tabulated() (binference.Measure class method) to_bins() (binference.Basis method) to_datatree() (binference.PopulationResult method) (in module binference.io) to_dense() (binference.Likelihoods method) to_dict() (binference.PopulationResult method) to_rho() (binference.PopulationModel method) to_sparse() (binference.Likelihoods method) to_value() (binference.PopulationModel method)

toarray() (binference.Likelihoods method) total (binference.PointEstimate property) (binference.PopulationResult property) total_exposure (binference.PopulationModel property) transform() (binference.Measure class method) (binference.PopulationModel method) tree depth Truth (class in binference.simulate)

U

u_edges (binference.Bins property) u_volumes (binference.Bins property) unbounded_density() (binference.priors.BoundPrior method) uncertain (binference.Response property)

unconstrained coordinates unflatten() (binference.Bins method) unsupported() (binference.samplers.Engine class method) (binference.samplers.Gibbs class method) (binference.samplers.MeanFieldVB class method)

V

values (binference.Likelihoods property)

volumes (binference.Bins property)

W

W (binference.Likelihoods property) warm-up warmup() (binference.samplers.Gibbs method) (binference.samplers.NUTS method)

weights (binference.Likelihoods property) widths (binference.Bins property) with_selection() (binference.Likelihoods method) with_weights() (binference.Likelihoods method)