Index

_

__add__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __call__() (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter method) (scistanpy.operations.Operation method) __get__() (scistanpy.model.components.parameters.ClassOrInstanceMethod method) __mul__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __neg__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __pow__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method)

__radd__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __rmul__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __rpow__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __rsub__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __rtruediv__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __sub__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method) __truediv__() (scistanpy.model.components.transformations.transformed_parameters.TransformableParameter method)

A

abs_() (in module scistanpy.operations) AbsParameter (class in scistanpy.model.components.transformations.transformed_parameters) AbstractModelComponent (class in scistanpy.model.components.abstract_model_component) AddParameter (class in scistanpy.model.components.transformations.transformed_parameters) aggregate_data() (in module scistanpy.plotting.plotting) all_model_components (scistanpy.model.model.Model property) all_model_components_dict (scistanpy.model.model.Model property) all_varnames (scistanpy.model.stan.stan_model.StanModel property) allow_interactive() (in module scistanpy.plotting.plotting)

allowed_index_names (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) ancestry (scistanpy.model.stan.stan_model.StanForLoop property) append() (scistanpy.model.stan.stan_model.StanForLoop method) (scistanpy.model.stan.stan_model.StanProgram method) as_observable() (scistanpy.model.components.parameters.Parameter method) assign_depth (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) autogathered_data (scistanpy.model.stan.stan_model.StanModel property) az_dask (class in scistanpy.utils)

B

BASE_STAN_DTYPE (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.DiscreteDistribution attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) BaseParameterType (in module scistanpy.custom_types) Beta (class in scistanpy.model.components.parameters) binary_exponential_growth() (in module scistanpy.operations)

binary_log_exponential_growth() (in module scistanpy.operations) BinaryExponentialGrowth (class in scistanpy.model.components.transformations.transformed_parameters) BinaryLogExponentialGrowth (class in scistanpy.model.components.transformations.transformed_parameters) BinaryTransformedParameter (class in scistanpy.model.components.transformations.transformed_parameters) Binomial (class in scistanpy.model.components.parameters) build_node_to_depth() (scistanpy.model.stan.stan_model.StanProgram method) build_operation() (in module scistanpy.operations) build_plotting_df() (in module scistanpy.plotting.plotting)

C

calculate_diagnostics() (scistanpy.model.results.hmc.SampleResults method) calculate_relative_quantiles() (in module scistanpy.plotting.plotting) calculate_summaries() (scistanpy.model.results.hmc.SampleResults method) (scistanpy.model.results.mle.MLEInferenceRes method) ccdf() (scistanpy.model.components.parameters.Parameter method) CDF (class in scistanpy.model.components.transformations.cdfs) cdf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) (scistanpy.model.components.parameters.Parameter method) CDFLike (class in scistanpy.model.components.transformations.cdfs) check_calibration() (scistanpy.model.results.mle.MLEInferenceRes method) check_parameters() (scistanpy.model.components.transformations.cdfs.CDFLike method) children (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) choose_module() (in module scistanpy.utils) choose_plotting_function() (in module scistanpy.plotting.plotting) ClassOrInstanceMethod (class in scistanpy.model.components.parameters) cmdstan_csv_to_netcdf() (in module scistanpy.model.results.hmc) CmdStanMCMCToNetCDFConverter (class in scistanpy.model.results.hmc) code (scistanpy.model.stan.stan_model.StanProgram property) code() (scistanpy.model.stan.stan_model.StanModel method)

coefficient (scistanpy.model.components.parameters.MultinomialLogTheta property) CombinableParameterType (in module scistanpy.custom_types) combine_lines() (scistanpy.model.stan.stan_model.StanCodeBase method) compile() (scistanpy.model.stan.stan_model.StanProgram method) Constant (class in scistanpy.model.components.constants) constant_dict (scistanpy.model.model.Model property) constants (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) (scistanpy.model.model.Model property) ContinuousDistribution (class in scistanpy.model.components.parameters) ContinuousParameterType (in module scistanpy.custom_types) convolve_sequence() (in module scistanpy.operations) ConvolveSequence (class in scistanpy.model.components.transformations.transformed_parameters) copy() (scistanpy.model.stan.stan_model.StanForLoop method) cov() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) cpu() (scistanpy.model.nn_module.PyTorchModel method) cuda() (scistanpy.model.nn_module.PyTorchModel method) CustomDirichlet (class in scistanpy.model.components.custom_distributions.custom_scipy_dists) CustomDistribution (class in scistanpy.model.components.custom_distributions.custom_torch_dists) CustomMultinomial (class in scistanpy.model.components.custom_distributions.custom_scipy_dists)

D

dask_enabled_diagnostics() (in module scistanpy.model.results.hmc) dask_enabled_summary_stats() (in module scistanpy.model.results.hmc) data_block (scistanpy.model.stan.stan_model.StanProgram property) declare_stan_variable() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) DEFAULT_CPP_OPTIONS (in module scistanpy.defaults) default_data (scistanpy.model.model.Model property) DEFAULT_DIM_NAMES (in module scistanpy.defaults) DEFAULT_EARLY_STOP (in module scistanpy.defaults) DEFAULT_EBFMI_THRESH (in module scistanpy.defaults) DEFAULT_ESS_THRESH (in module scistanpy.defaults) DEFAULT_FORCE_COMPILE (in module scistanpy.defaults) DEFAULT_INDEX_ORDER (in module scistanpy.defaults) DEFAULT_LR (in module scistanpy.defaults) DEFAULT_MODEL_NAME (in module scistanpy.defaults) DEFAULT_N_EPOCHS (in module scistanpy.defaults) DEFAULT_RHAT_THRESH (in module scistanpy.defaults)

DEFAULT_USER_HEADER (in module scistanpy.defaults) depth (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) diagnose() (scistanpy.model.results.hmc.SampleResults method) Dirichlet (class in scistanpy.model.components.parameters) dirichlet (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) DiscreteDistribution (class in scistanpy.model.components.parameters) DiscreteParameterType (in module scistanpy.custom_types) display() (scistanpy.model.results.hmc.VariableAnalyzer method) (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) DISTCLASS (scistanpy.operations.Operation attribute) DivideParameter (class in scistanpy.model.components.transformations.transformed_parameters) draw() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.model.Model method) (scistanpy.model.results.mle.MLE method) (scistanpy.model.results.mle.MLEParam method)

E

end (scistanpy.model.stan.stan_model.StanForLoop property) enforce_uniformity (scistanpy.model.components.constants.Constant property) entropy() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) evaluate_sample_stats() (scistanpy.model.results.hmc.SampleResults method) evaluate_variable_diagnostic_stats() (scistanpy.model.results.hmc.SampleResults method) exp() (in module scistanpy.operations) ExpDirichlet (class in scistanpy.model.components.custom_distributions.custom_scipy_dists) (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) expdirichlet (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) ExpExponential (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters)

expexponential (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) ExpLomax (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) explomax (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) Exponential (class in scistanpy.model.components.parameters) exponential_growth() (in module scistanpy.operations) ExponentialGrowth (class in scistanpy.model.components.transformations.transformed_parameters) export_distributions() (scistanpy.model.nn_module.PyTorchModel method) export_params() (scistanpy.model.nn_module.PyTorchModel method) ExpParameter (class in scistanpy.model.components.transformations.transformed_parameters)

F

finalize_line() (scistanpy.model.stan.stan_model.StanCodeBase method) fit() (scistanpy.model.nn_module.PyTorchModel method) fit_from_csv_noload() (in module scistanpy.model.results.hmc) Float (in module scistanpy.custom_types) FORCE_LOOP_RESET (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.transformations.transformed_parameters.ConvolveSequence attribute) force_name (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) (scistanpy.model.components.transformations.transformed_parameters.IndexParameter property)

FORCE_PARENT_NAME (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.transformations.transformed_parameters.ConvolveSequence attribute) (scistanpy.model.components.transformations.transformed_parameters.IndexParameter attribute) forward() (scistanpy.model.nn_module.PyTorchModel method) from_disk() (scistanpy.model.results.hmc.SampleResults class method) (scistanpy.model.results.mle.MLEInferenceRes class method) functions_block (scistanpy.model.stan.stan_model.StanProgram property)

G

Gamma (class in scistanpy.model.components.parameters) gather_inputs() (scistanpy.model.stan.stan_model.StanModel method) generate_quantities() (scistanpy.model.stan.stan_model.StanModel method) generated_quantities_block (scistanpy.model.stan.stan_model.StanProgram property) generated_quantities_prefix (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) generated_varname (scistanpy.model.components.parameters.Parameter property) get_assign_depth() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.transformations.transformed_parameters.Reduction method) get_child_paramnames() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) get_dimname_map() (scistanpy.model.model.Model method) get_ecdf_kwargs() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) get_generated_quantities() (scistanpy.model.components.parameters.Parameter method) (scistanpy.model.stan.stan_model.StanCodeBase method) get_generated_quantity_declaration() (scistanpy.model.components.parameters.Parameter method) get_index_offset() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.transformations.transformed_parameters.Reduction method) get_indexed_varname() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) get_inference_obj() (scistanpy.model.results.mle.MLE method) get_kde_kwargs() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) get_parent_loop() (scistanpy.model.stan.stan_model.StanCodeBase method) (scistanpy.model.stan.stan_model.StanForLoop method) (scistanpy.model.stan.stan_model.StanProgram method) get_raw_stan_parameter_declaration() (scistanpy.model.components.parameters.Parameter method) get_relationship_kwargs() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method)

get_right_side() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.constants.Constant method) (scistanpy.model.components.parameters.Normal method) (scistanpy.model.components.parameters.Parameter method) (scistanpy.model.components.transformations.transformed_parameters.Transformation method) get_rng() (scistanpy.model.components.parameters.Parameter method) get_shared_leading() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) get_stan_dtype() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) get_stan_parameter_declaration() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) get_supporting_functions() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.parameters.ExpExponential method) get_target_incrementation() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.parameters.Normal method) (scistanpy.model.components.parameters.Parameter method) (scistanpy.model.stan.stan_model.StanCodeBase method) get_torch_logprob() (scistanpy.model.components.parameters.Parameter method) get_transformation_assignment() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) (scistanpy.model.components.parameters.Normal method) (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter method) (scistanpy.model.stan.stan_model.StanCodeBase method) get_transformed_data_assignment() (scistanpy.model.components.transformations.transformed_data.TransformedData method) (scistanpy.model.stan.stan_model.StanCodeBase method) get_transformed_data_declaration() (scistanpy.model.components.parameters.Parameter method) get_varnames() (scistanpy.model.stan.stan_model.StanProgram method) get_varnames_to_dimnames() (scistanpy.model.stan.stan_model.StanModel method) get_violin_kwargs() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method)

H

HalfNormal (class in scistanpy.model.components.parameters) has_default_data (scistanpy.model.model.Model property) HAS_RAW_VARNAME (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.Normal property) (scistanpy.model.components.parameters.Parameter attribute)

hexgrid_with_mean() (in module scistanpy.plotting.plotting) hyperparameter_dict (scistanpy.model.model.Model property) hyperparameters (scistanpy.model.model.Model property)

I

identify_failed_diagnostics() (scistanpy.model.results.hmc.SampleResults method) IndexParameter (class in scistanpy.model.components.transformations.transformed_parameters) IndexType (in module scistanpy.custom_types) init_pytorch() (scistanpy.model.components.parameters.Parameter method) Integer (in module scistanpy.custom_types) inverse_transform() (scistanpy.model.components.custom_distributions.custom_scipy_dists.LogUnivariateScipyTransform method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) InverseGamma (class in scistanpy.model.components.parameters)

is_hyperparameter (scistanpy.model.components.parameters.Parameter property) IS_LOG_SIMPLEX (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) is_named (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) is_noncentered (scistanpy.model.components.parameters.Normal property) IS_SIMPLEX (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) isf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method)

L

laplace_sample() (scistanpy.model.stan.stan_model.StanModel method) lazy_import() (in module scistanpy.utils) lazy_import_from() (in module scistanpy.utils) LazyObjectProxy (class in scistanpy.utils) log() (in module scistanpy.operations) log1p_exp() (in module scistanpy.operations) Log1pExpParameter (class in scistanpy.model.components.transformations.transformed_parameters) log_ccdf() (scistanpy.model.components.parameters.Parameter method) log_cdf() (scistanpy.model.components.custom_distributions.custom_torch_dists.LogNormal method) (scistanpy.model.components.custom_distributions.custom_torch_dists.Normal method) (scistanpy.model.components.parameters.Parameter method) log_exponential_growth() (in module scistanpy.operations) log_jacobian_correction() (scistanpy.model.components.custom_distributions.custom_scipy_dists.LogUnivariateScipyTransform method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) log_prob() (scistanpy.model.components.custom_distributions.custom_torch_dists.ExpDirichlet method) (scistanpy.model.components.custom_distributions.custom_torch_dists.Multinomial method) (scistanpy.model.stan.stan_model.StanModel method) log_sf() (scistanpy.model.components.custom_distributions.custom_torch_dists.LogNormal method) (scistanpy.model.components.custom_distributions.custom_torch_dists.Normal method) log_sigmoid() (in module scistanpy.operations) log_sigmoid_growth() (in module scistanpy.operations) log_sigmoid_growth_init_param() (in module scistanpy.operations) LOG_SIMPLEX_PARAMS (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) LogCDF (class in scistanpy.model.components.transformations.cdfs) LogExponentialGrowth (class in scistanpy.model.components.transformations.transformed_parameters) LogMultinomialCoefficient (class in scistanpy.model.components.transformations.transformed_data) LogNormal (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) LogParameter (class in scistanpy.model.components.transformations.transformed_parameters) logpdf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method)

logsf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) LogSigmoidGrowth (class in scistanpy.model.components.transformations.transformed_parameters) LogSigmoidGrowthInitParametrization (class in scistanpy.model.components.transformations.transformed_parameters) LogSigmoidParameter (class in scistanpy.model.components.transformations.transformed_parameters) logsumexp() (in module scistanpy.operations) LogSumExpParameter (class in scistanpy.model.components.transformations.transformed_parameters) LogSurvivalFunction (class in scistanpy.model.components.transformations.cdfs) LogUnivariateScipyTransform (class in scistanpy.model.components.custom_distributions.custom_scipy_dists) Lomax (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) loop_index (scistanpy.model.stan.stan_model.StanForLoop property) LOWER_BOUND (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.DiscreteDistribution attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.HalfNormal attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.transformations.transformed_parameters.AbsParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.ExpParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.LogSigmoidGrowth attribute) (scistanpy.model.components.transformations.transformed_parameters.LogSigmoidGrowthInitParametrization attribute) (scistanpy.model.components.transformations.transformed_parameters.NormalizeParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidGrowth attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidGrowthInitParametrization attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidParameter attribute)

M

mcmc() (scistanpy.model.model.Model method) mean() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) MetaOperation (class in scistanpy.operations) MLE (class in scistanpy.model.results.mle) mle() (scistanpy.model.model.Model method) MLEInferenceRes (class in scistanpy.model.results.mle) MLEParam (class in scistanpy.model.results.mle) Model (class in scistanpy.model.model) model_block (scistanpy.model.stan.stan_model.StanProgram property) model_components (scistanpy.model.stan.stan_model.StanCodeBase property) model_varname (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) (scistanpy.model.components.transformations.transformed_data.LogMultinomialCoefficient property) (scistanpy.model.components.transformations.transformed_data.TransformedData property) module scistanpy.custom_types scistanpy.defaults scistanpy.exceptions scistanpy.model scistanpy.model.components scistanpy.model.components.abstract_model_component scistanpy.model.components.constants scistanpy.model.components.custom_distributions scistanpy.model.components.custom_distributions.custom_scipy_dists scistanpy.model.components.custom_distributions.custom_torch_dists scistanpy.model.components.parameters scistanpy.model.components.transformations scistanpy.model.components.transformations.cdfs scistanpy.model.components.transformations.transformed_data scistanpy.model.components.transformations.transformed_parameters scistanpy.model.model scistanpy.model.nn_module scistanpy.model.results scistanpy.model.results.hmc scistanpy.model.results.mle scistanpy.model.stan scistanpy.model.stan.stan_model scistanpy.operations scistanpy.plotting scistanpy.plotting.plotting scistanpy.plotting.prior_predictive scistanpy.utils

Multinomial (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) multinomial (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) multinomial_log_theta (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) multinomial_logit (in module scistanpy.model.components.custom_distributions.custom_scipy_dists) MultinomialLogit (class in scistanpy.model.components.custom_distributions.custom_scipy_dists) (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) MultinomialLogTheta (class in scistanpy.model.components.custom_distributions.custom_scipy_dists) (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters) MultinomialProb (class in scistanpy.model.components.custom_distributions.custom_torch_dists) MultiplyParameter (class in scistanpy.model.components.transformations.transformed_parameters)

N

named_model_components (scistanpy.model.model.Model property) named_model_components_dict (scistanpy.model.model.Model property) ndim (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) neg_to_pos() (scistanpy.model.components.transformations.transformed_parameters.IndexParameter method) NegateParameter (class in scistanpy.model.components.transformations.transformed_parameters) NEGATIVE_PARAMS (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) nested_loops (scistanpy.model.stan.stan_model.StanCodeBase property) Normal (class in scistanpy.model.components.custom_distributions.custom_torch_dists) (class in scistanpy.model.components.parameters)

Normal.CDF (class in scistanpy.model.components.parameters) Normal.LOG_CDF (class in scistanpy.model.components.parameters) Normal.LOG_SF (class in scistanpy.model.components.parameters) Normal.SF (class in scistanpy.model.components.parameters) normalize() (in module scistanpy.operations) normalize_log() (in module scistanpy.operations) NormalizeLogParameter (class in scistanpy.model.components.transformations.transformed_parameters) NormalizeParameter (class in scistanpy.model.components.transformations.transformed_parameters) NP_FUNC (scistanpy.model.components.transformations.transformed_parameters.Reduction attribute) NumpySampleError (class in scistanpy.exceptions)

O

observable (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) (scistanpy.model.components.parameters.Parameter property) observable_dict (scistanpy.model.model.Model property)

observables (scistanpy.model.model.Model property) Operation (class in scistanpy.operations) optimize() (scistanpy.model.stan.stan_model.StanModel method)

P

Parameter (class in scistanpy.model.components.parameters) PARAMETER (scistanpy.model.components.parameters.Normal.CDF attribute) (scistanpy.model.components.parameters.Normal.LOG_CDF attribute) (scistanpy.model.components.parameters.Normal.LOG_SF attribute) (scistanpy.model.components.parameters.Normal.SF attribute) (scistanpy.model.components.parameters.Parameter.CDF attribute) (scistanpy.model.components.parameters.Parameter.LOG_CDF attribute) (scistanpy.model.components.parameters.Parameter.LOG_SF attribute) (scistanpy.model.components.parameters.Parameter.SF attribute) (scistanpy.model.components.transformations.cdfs.CDF attribute) (scistanpy.model.components.transformations.cdfs.CDFLike attribute) (scistanpy.model.components.transformations.cdfs.LogCDF attribute) (scistanpy.model.components.transformations.cdfs.LogSurvivalFunction attribute) (scistanpy.model.components.transformations.cdfs.SurvivalFunction attribute) Parameter.CDF (class in scistanpy.model.components.parameters) Parameter.LOG_CDF (class in scistanpy.model.components.parameters) Parameter.LOG_SF (class in scistanpy.model.components.parameters) Parameter.SF (class in scistanpy.model.components.parameters) parameter_dict (scistanpy.model.model.Model property) ParameterMeta (class in scistanpy.model.components.parameters) parameters (scistanpy.model.model.Model property) parameters_block (scistanpy.model.stan.stan_model.StanProgram property) parents (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) pathfinder() (scistanpy.model.stan.stan_model.StanModel method) pdf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) plot_calibration() (in module scistanpy.plotting.plotting) plot_distribution() (in module scistanpy.plotting.plotting)

plot_ecdf_kde() (in module scistanpy.plotting.plotting) plot_ecdf_violin() (in module scistanpy.plotting.plotting) plot_loss_curve() (scistanpy.model.results.mle.MLE method) plot_observed_quantiles() (scistanpy.model.results.mle.MLEInferenceRes method) plot_posterior_predictive_samples() (scistanpy.model.results.mle.MLEInferenceRes method) plot_relationship() (in module scistanpy.plotting.plotting) plot_sample_failure_quantile_traces() (scistanpy.model.results.hmc.SampleResults method) plot_variable_failure_quantile_traces() (scistanpy.model.results.hmc.SampleResults method) Poisson (class in scistanpy.model.components.parameters) POSITIVE_PARAMS (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.Binomial attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Poisson attribute) (scistanpy.model.components.transformations.transformed_parameters.LogParameter attribute) PowerParameter (class in scistanpy.model.components.transformations.transformed_parameters) ppf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) prior_predictive() (scistanpy.model.model.Model method) PriorPredictiveCheck (class in scistanpy.plotting.prior_predictive) ProcessedTestRes (in module scistanpy.custom_types) program (scistanpy.model.stan.stan_model.StanForLoop property) PyTorchModel (class in scistanpy.model.nn_module)

Q

quantile_plot() (in module scistanpy.plotting.plotting)

R

raw_varname (scistanpy.model.components.parameters.Parameter property) recurse_for_loops() (scistanpy.model.stan.stan_model.StanCodeBase method) (scistanpy.model.stan.stan_model.StanProgram method) recurse_model_components() (scistanpy.model.stan.stan_model.StanCodeBase method) Reduction (class in scistanpy.model.components.transformations.transformed_parameters) run_delayed_mcmc() (in module scistanpy.model.model) run_np_torch_op() (scistanpy.model.components.transformations.cdfs.CDF method) (scistanpy.model.components.transformations.cdfs.CDFLike method) (scistanpy.model.components.transformations.cdfs.LogCDF method) (scistanpy.model.components.transformations.cdfs.LogSurvivalFunction method) (scistanpy.model.components.transformations.cdfs.SurvivalFunction method) (scistanpy.model.components.transformations.transformed_parameters.BinaryTransformedParameter method) (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter method) (scistanpy.model.components.transformations.transformed_parameters.UnaryTransformedParameter method)

run_ppc() (scistanpy.model.results.mle.MLEInferenceRes method) rvs() (scistanpy.model.components.custom_distributions.custom_scipy_dists.CustomDirichlet method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.CustomMultinomial method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method)

S

sample() (scistanpy.model.components.custom_distributions.custom_torch_dists.Multinomial method) (scistanpy.model.stan.stan_model.StanModel method) SampleResults (class in scistanpy.model.results.hmc) SampleType (in module scistanpy.custom_types) save_netcdf() (scistanpy.model.results.mle.MLEInferenceRes method) SCIPY_DIST (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.Binomial attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.HalfNormal attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Multinomial attribute) (scistanpy.model.components.parameters.MultinomialLogit attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Parameter attribute) (scistanpy.model.components.parameters.Poisson attribute) SCIPY_FUNC (scistanpy.model.components.transformations.cdfs.CDF attribute) (scistanpy.model.components.transformations.cdfs.CDFLike attribute) (scistanpy.model.components.transformations.cdfs.LogCDF attribute) (scistanpy.model.components.transformations.cdfs.LogSurvivalFunction attribute) (scistanpy.model.components.transformations.cdfs.SurvivalFunction attribute) scistanpy.custom_types module scistanpy.defaults module scistanpy.exceptions module scistanpy.model module scistanpy.model.components module scistanpy.model.components.abstract_model_component module scistanpy.model.components.constants module scistanpy.model.components.custom_distributions module scistanpy.model.components.custom_distributions.custom_scipy_dists module scistanpy.model.components.custom_distributions.custom_torch_dists module scistanpy.model.components.parameters module scistanpy.model.components.transformations module scistanpy.model.components.transformations.cdfs module scistanpy.model.components.transformations.transformed_data module scistanpy.model.components.transformations.transformed_parameters module scistanpy.model.model module scistanpy.model.nn_module module scistanpy.model.results module scistanpy.model.results.hmc module scistanpy.model.results.mle module scistanpy.model.stan module scistanpy.model.stan.stan_model module scistanpy.operations module scistanpy.plotting module scistanpy.plotting.plotting module scistanpy.plotting.prior_predictive module scistanpy.utils module SciStanPyDistribution (in module scistanpy.custom_types) SciStanPyError (class in scistanpy.exceptions) set_group_dim_options() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) set_independent_var_options() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) set_plot_type_options() (scistanpy.plotting.prior_predictive.PriorPredictiveCheck method) sf() (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) shape (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) SHAPE_CHECK (scistanpy.model.components.transformations.transformed_data.LogMultinomialCoefficient attribute) (scistanpy.model.components.transformations.transformed_parameters.ConvolveSequence attribute) (scistanpy.model.components.transformations.transformed_parameters.IndexParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.Reduction attribute) (scistanpy.model.components.transformations.transformed_parameters.Transformation attribute) sigmoid() (in module scistanpy.operations) sigmoid_growth() (in module scistanpy.operations) sigmoid_growth_init_param() (in module scistanpy.operations)

SigmoidGrowth (class in scistanpy.model.components.transformations.transformed_parameters) SigmoidGrowthInitParametrization (class in scistanpy.model.components.transformations.transformed_parameters) SigmoidParameter (class in scistanpy.model.components.transformations.transformed_parameters) SIMPLEX_PARAMS (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Multinomial attribute) simulate_mcmc() (scistanpy.model.model.Model method) simulate_mle() (scistanpy.model.model.Model method) slider_end (scistanpy.model.components.constants.Constant property) slider_start (scistanpy.model.components.constants.Constant property) slider_step_size (scistanpy.model.components.constants.Constant property) squash() (scistanpy.model.stan.stan_model.StanForLoop method) stable_sigmoid() (in module scistanpy.utils) stan_bounds (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) STAN_DIST (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.Binomial attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.HalfNormal attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Multinomial attribute) (scistanpy.model.components.parameters.MultinomialLogit attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Parameter attribute) (scistanpy.model.components.parameters.Poisson attribute) (scistanpy.model.components.parameters.UnitNormal attribute) STAN_INCLUDE_PATHS (in module scistanpy.model.stan) stan_model_varname (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) STAN_OPERATOR (scistanpy.model.components.transformations.transformed_parameters.AddParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.DivideParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.MultiplyParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.NegateParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.PowerParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.SubtractParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter attribute) stan_program_path (scistanpy.model.stan.stan_model.StanModel property) STAN_SUFFIX (scistanpy.model.components.transformations.cdfs.CDF attribute) (scistanpy.model.components.transformations.cdfs.CDFLike attribute) (scistanpy.model.components.transformations.cdfs.LogCDF attribute) (scistanpy.model.components.transformations.cdfs.LogSurvivalFunction attribute) (scistanpy.model.components.transformations.cdfs.SurvivalFunction attribute) STAN_TO_SCIPY_NAMES (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.Binomial attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.HalfNormal attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Multinomial attribute) (scistanpy.model.components.parameters.MultinomialLogit attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Parameter attribute) (scistanpy.model.components.parameters.Poisson attribute) STAN_TO_SCIPY_TRANSFORMS (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Parameter attribute) STAN_TO_TORCH_NAMES (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.Binomial attribute) (scistanpy.model.components.parameters.Dirichlet attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.Exponential attribute) (scistanpy.model.components.parameters.Gamma attribute) (scistanpy.model.components.parameters.HalfNormal attribute) (scistanpy.model.components.parameters.InverseGamma attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Multinomial attribute) (scistanpy.model.components.parameters.MultinomialLogit attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Parameter attribute) (scistanpy.model.components.parameters.Poisson attribute) StanCodeBase (class in scistanpy.model.stan.stan_model) StanForLoop (class in scistanpy.model.stan.stan_model) StanModel (class in scistanpy.model.stan.stan_model) StanProgram (class in scistanpy.model.stan.stan_model) StrippedTestRes (in module scistanpy.custom_types) SubtractParameter (class in scistanpy.model.components.transformations.transformed_parameters) sum_() (in module scistanpy.operations) SumParameter (class in scistanpy.model.components.transformations.transformed_parameters) SurvivalFunction (class in scistanpy.model.components.transformations.cdfs)

T

target_inc_prefix (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) to() (scistanpy.model.nn_module.PyTorchModel method) to_pytorch() (scistanpy.model.model.Model method) to_stan() (scistanpy.model.model.Model method) TORCH_DIST (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.parameters.ExpExponential attribute) (scistanpy.model.components.parameters.ExpLomax attribute) (scistanpy.model.components.parameters.LogNormal attribute) (scistanpy.model.components.parameters.Lomax attribute) (scistanpy.model.components.parameters.Multinomial attribute) (scistanpy.model.components.parameters.MultinomialLogit attribute) (scistanpy.model.components.parameters.MultinomialLogTheta attribute) (scistanpy.model.components.parameters.Normal attribute) (scistanpy.model.components.parameters.Parameter attribute) torch_dist_instance (scistanpy.model.components.parameters.Parameter property) TORCH_FUNC (scistanpy.model.components.transformations.cdfs.CDF attribute) (scistanpy.model.components.transformations.cdfs.CDFLike attribute) (scistanpy.model.components.transformations.cdfs.LogCDF attribute) (scistanpy.model.components.transformations.cdfs.LogSurvivalFunction attribute) (scistanpy.model.components.transformations.cdfs.SurvivalFunction attribute) (scistanpy.model.components.transformations.transformed_parameters.Reduction attribute)

torch_parametrization (scistanpy.model.components.abstract_model_component.AbstractModelComponent property) (scistanpy.model.components.constants.Constant property) (scistanpy.model.components.parameters.Parameter property) (scistanpy.model.components.transformations.transformed_data.TransformedData property) (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter property) transform() (scistanpy.model.components.custom_distributions.custom_scipy_dists.LogUnivariateScipyTransform method) (scistanpy.model.components.custom_distributions.custom_scipy_dists.TransformedScipyDist method) TransformableParameter (class in scistanpy.model.components.transformations.transformed_parameters) Transformation (class in scistanpy.model.components.transformations.transformed_parameters) transformation_assi_prefix (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) transformed_data_block (scistanpy.model.stan.stan_model.StanProgram property) transformed_data_prefix (scistanpy.model.stan.stan_model.StanCodeBase property) (scistanpy.model.stan.stan_model.StanForLoop property) (scistanpy.model.stan.stan_model.StanProgram property) transformed_parameter_dict (scistanpy.model.model.Model property) transformed_parameters (scistanpy.model.model.Model property) transformed_parameters_block (scistanpy.model.stan.stan_model.StanProgram property) TransformedData (class in scistanpy.model.components.transformations.transformed_data) TransformedParameter (class in scistanpy.model.components.transformations.transformed_parameters) TransformedScipyDist (class in scistanpy.model.components.custom_distributions.custom_scipy_dists)

U

UnaryTransformedParameter (class in scistanpy.model.components.transformations.transformed_parameters) UnitNormal (class in scistanpy.model.components.parameters) UPPER_BOUND (scistanpy.model.components.abstract_model_component.AbstractModelComponent attribute) (scistanpy.model.components.parameters.Beta attribute) (scistanpy.model.components.parameters.ExpDirichlet attribute) (scistanpy.model.components.transformations.transformed_parameters.LogSigmoidGrowth attribute) (scistanpy.model.components.transformations.transformed_parameters.LogSigmoidGrowthInitParametrization attribute) (scistanpy.model.components.transformations.transformed_parameters.LogSigmoidParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.NormalizeLogParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.NormalizeParameter attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidGrowth attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidGrowthInitParametrization attribute) (scistanpy.model.components.transformations.transformed_parameters.SigmoidParameter attribute)

V

var() (scistanpy.model.components.custom_distributions.custom_scipy_dists.ExpDirichlet method)

VariableAnalyzer (class in scistanpy.model.results.hmc) variational() (scistanpy.model.stan.stan_model.StanModel method)

W

walk_tree() (scistanpy.model.components.abstract_model_component.AbstractModelComponent method) write_dist_args() (scistanpy.model.components.parameters.Parameter method) write_netcdf() (scistanpy.model.results.hmc.CmdStanMCMCToNetCDFConverter method) write_stan_operation() (scistanpy.model.components.transformations.cdfs.CDFLike method) (scistanpy.model.components.transformations.transformed_data.LogMultinomialCoefficient method) (scistanpy.model.components.transformations.transformed_parameters.BinaryTransformedParameter method) (scistanpy.model.components.transformations.transformed_parameters.Transformation method) (scistanpy.model.components.transformations.transformed_parameters.TransformedParameter method) (scistanpy.model.components.transformations.transformed_parameters.UnaryTransformedParameter method)

write_stan_program() (scistanpy.model.stan.stan_model.StanModel method)