Index

A

add_data() (in module lyscripts.configs) add_distributions() (in module lyscripts.configs)

add_modalities() (in module lyscripts.configs) assemble_signature() (in module lyscripts.decorators)

B

binom_pmf() (in module lyscripts.utils)

burnin_steps (lyscripts.configs.SamplingConfig attribute)

C

cache_dir (lyscripts.compute.utils.BaseComputeCLI attribute) ceil_at_decimal() (in module lyscripts.plots) ceil_to_step() (in module lyscripts.plots) check_input_file_exists() (in module lyscripts.decorators) check_interval (lyscripts.configs.SamplingConfig attribute) check_output_dir_exists() (in module lyscripts.decorators) check_pattern() (in module lyscripts.configs) class_ (lyscripts.configs.DeprecatedModelConfig attribute) class_name (lyscripts.configs.ModelConfig attribute) clean_and_check() (in module lyscripts.plots) clean_header() (in module lyscripts.data.lyproxify) cli_cmd() (lyscripts.compute.ComputeCLI method) (lyscripts.compute.posteriors.PosteriorsCLI method) (lyscripts.compute.prevalences.PrevalencesCLI method) (lyscripts.compute.priors.PriorsCLI method) (lyscripts.compute.risks.RisksCLI method) (lyscripts.data.collect.CollectorCLI method) (lyscripts.data.DataCLI method) (lyscripts.data.enhance.EnhanceCLI method) (lyscripts.data.filter.FilterCLI method) (lyscripts.data.generate.GenerateCLI method) (lyscripts.data.join.JoinCLI method) (lyscripts.data.lyproxify.LyproxifyCLI method) (lyscripts.data.split.SplitCLI method) (lyscripts.LyscriptsCLI method) (lyscripts.sample.SampleCLI method) (lyscripts.schedule.ScheduleCLI method)

collect (lyscripts.data.DataCLI attribute) column (lyscripts.data.filter.FilterCLI attribute) comp_bic() (in module lyscripts.evaluate) complete_pattern() (in module lyscripts.compute.utils) CompletedItersColumn (class in lyscripts.sample) compute (lyscripts.LyscriptsCLI attribute) compute_evidence() (in module lyscripts.evaluate) compute_posteriors() (in module lyscripts.compute.posteriors) compute_prevalences() (in module lyscripts.compute.prevalences) compute_priors() (in module lyscripts.compute.priors) compute_risks() (in module lyscripts.compute.risks) compute_ti_results() (in module lyscripts.evaluate) configs (lyscripts.configs.BaseCLI attribute) construct_model() (in module lyscripts.configs) constructor (lyscripts.configs.ModelConfig attribute) contra (lyscripts.configs.DiagnosisConfig attribute) (lyscripts.configs.InvolvementConfig attribute) cores (lyscripts.configs.SamplingConfig attribute) cross_validation (lyscripts.data.split.SplitCLI attribute) (lyscripts.schema.SchemaSettings attribute)

D

data (lyscripts.compute.prevalences.PrevalencesCLI attribute) (lyscripts.LyscriptsCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute) dataset (lyscripts.compute.utils.HDF5FileStorage attribute) (lyscripts.configs.SamplingConfig attribute) delete_private_keys() (in module lyscripts.utils) diagnosis (lyscripts.configs.ScenarioConfig attribute) (lyscripts.schema.SchemaSettings attribute) distributions (lyscripts.compute.utils.BaseComputeCLI attribute) (lyscripts.data.generate.GenerateCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute)

draw() (in module lyscripts.plots) (lyscripts.plots.AbstractDistribution method) (lyscripts.plots.BetaPosterior method) (lyscripts.plots.Histogram method) drop_cols (lyscripts.data.lyproxify.LyproxifyCLI attribute) drop_rows (lyscripts.data.lyproxify.LyproxifyCLI attribute) DummyPool (class in lyscripts.sample) DynamicYamlConfigSettingsSource (class in lyscripts.configs)

E

enhance (lyscripts.data.DataCLI attribute) ensure_column_map() (in module lyscripts.data.lyproxify) ensure_history_table() (in module lyscripts.sample) ensure_initial_state() (in module lyscripts.sample) ensure_parent_dir() (in module lyscripts.compute.utils)

ensure_python_file() (in module lyscripts.data.lyproxify) evidence (lyscripts.compute.ComputeCLI attribute) exclude_patients() (in module lyscripts.data.lyproxify) external_file (lyscripts.configs.ModelConfig attribute) extract_modalities() (in module lyscripts.compute.utils)

F

fetch (lyscripts.data.DataCLI attribute) file (lyscripts.compute.utils.HDF5FileStorage attribute) filter (lyscripts.data.DataCLI attribute) first_binom_prob (lyscripts.configs.DeprecatedModelConfig attribute) flatten() (in module lyscripts.utils) floor_at_decimal() (in module lyscripts.plots) floor_to_step() (in module lyscripts.plots)

folds (lyscripts.configs.CrossValidationConfig attribute) from_hdf5() (lyscripts.plots.BetaPosterior class method) (lyscripts.plots.Histogram class method) from_hdf5_attrs() (in module lyscripts.compute.utils) from_model() (lyscripts.configs.GraphConfig class method) (lyscripts.configs.ModelConfig class method) func (lyscripts.configs.DistributionConfig attribute)

G

generate (lyscripts.data.DataCLI attribute) generate_markdown_docs() (in module lyscripts.data.lyproxify) generate_query_from_diagnosis() (in module lyscripts.compute.prevalences) geometric_schedule() (in module lyscripts.configs) get_attrs() (lyscripts.compute.utils.HDF5FileStorage method) get_cached() (in module lyscripts.compute.utils) get_dict_depth() (in module lyscripts.utils) get_hdf5_backend() (in module lyscripts.utils) get_instruction_depth() (in module lyscripts.data.lyproxify) get_label() (in module lyscripts.plots)

get_load_kwargs() (lyscripts.configs.DataConfig method) get_modalities_subset() (in module lyscripts.utils) get_pool() (in module lyscripts.sample) get_schedule() (lyscripts.configs.ScheduleConfig method) get_size() (in module lyscripts.plots) get_symmetry_kwargs() (in module lyscripts.configs) get_xlims() (in module lyscripts.plots) graph (lyscripts.compute.utils.BaseComputeCLI attribute) (lyscripts.data.generate.GenerateCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute)

H

has_model_symbol() (in module lyscripts.configs) HasParentPath (in module lyscripts.compute.utils)

history_file (lyscripts.configs.SamplingConfig attribute) hostname (lyscripts.data.collect.CollectorCLI attribute)

I

include (lyscripts.data.filter.FilterCLI attribute) init_sampler() (in module lyscripts.sample) input (lyscripts.data.enhance.EnhanceCLI attribute) (lyscripts.data.filter.FilterCLI attribute) (lyscripts.data.split.SplitCLI attribute) input_file (lyscripts.data.lyproxify.LyproxifyCLI attribute) inputs (lyscripts.data.join.JoinCLI attribute) integrate (lyscripts.LyscriptsCLI attribute)

interpolate() (lyscripts.configs.ScenarioConfig method) inverse_temp (lyscripts.configs.SamplingConfig attribute) involvement (lyscripts.configs.ScenarioConfig attribute) (lyscripts.schema.SchemaSettings attribute) ipsi (lyscripts.configs.DiagnosisConfig attribute) (lyscripts.configs.InvolvementConfig attribute) is_converged() (in module lyscripts.sample) is_hdf5_compatible() (in module lyscripts.compute.utils) ItersPerSecondColumn (class in lyscripts.sample)

J

join (lyscripts.data.DataCLI attribute)

K

kind (lyscripts.configs.DistributionConfig attribute) kwargs (lyscripts.configs.DeprecatedModelConfig attribute) (lyscripts.configs.ModelConfig attribute) (lyscripts.plots.AbstractDistribution attribute)

L

label (lyscripts.plots.AbstractDistribution property) left_percentile() (lyscripts.plots.AbstractDistribution method) (lyscripts.plots.BetaPosterior method) (lyscripts.plots.Histogram method) leftright_to_ipsicontra() (in module lyscripts.data.lyproxify) linear_schedule() (in module lyscripts.configs) lnl (lyscripts.configs.GraphConfig attribute) lnl_subdivisions (lyscripts.data.enhance.EnhanceCLI attribute) load() (lyscripts.compute.utils.HDF5FileStorage method) (lyscripts.configs.DataConfig method) (lyscripts.configs.SamplingConfig method) load_model_samples() (in module lyscripts.utils) load_patient_data() (in module lyscripts.utils) load_yaml_params() (in module lyscripts.utils) log_level (lyscripts.LyscriptsCLI attribute) log_prob_fn() (in module lyscripts.sample) log_state() (in module lyscripts.decorators) lyproxify (lyscripts.data.DataCLI attribute) lyscripts module lyscripts.compute module lyscripts.compute.posteriors module lyscripts.compute.prevalences module lyscripts.compute.priors module lyscripts.compute.risks module lyscripts.compute.utils module lyscripts.configs module

lyscripts.data module lyscripts.data.collect module lyscripts.data.enhance module lyscripts.data.filter module lyscripts.data.generate module lyscripts.data.join module lyscripts.data.lyproxify module lyscripts.data.split module lyscripts.data.utils module lyscripts.decorators module lyscripts.evaluate module lyscripts.plots module lyscripts.sample module lyscripts.schedule module lyscripts.schema module lyscripts.utils module

M

main() (in module lyscripts.evaluate) (in module lyscripts.schema) map_to_optional_bool() (in module lyscripts.configs) mapping (lyscripts.configs.DataConfig attribute) mapping_file (lyscripts.data.lyproxify.LyproxifyCLI attribute) max_t (lyscripts.configs.DeprecatedModelConfig attribute) max_time (lyscripts.configs.ModelConfig attribute) method (lyscripts.configs.ScheduleConfig attribute) (lyscripts.data.enhance.EnhanceCLI attribute) midext (lyscripts.configs.ScenarioConfig attribute) modalities (lyscripts.compute.posteriors.PosteriorsCLI attribute) (lyscripts.compute.prevalences.PrevalencesCLI attribute) (lyscripts.compute.risks.RisksCLI attribute) (lyscripts.data.enhance.EnhanceCLI attribute) (lyscripts.data.generate.GenerateCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute) modalityconfig_from_model() (in module lyscripts.configs) mode (lyscripts.configs.ScenarioConfig attribute) model (lyscripts.compute.utils.BaseComputeCLI attribute) (lyscripts.data.generate.GenerateCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute) model_post_init() (lyscripts.configs.DeprecatedModelConfig method) (lyscripts.configs.ScenarioConfig method) (lyscripts.data.filter.FilterCLI method) (lyscripts.data.generate.GenerateCLI method)

module lyscripts lyscripts.compute lyscripts.compute.posteriors lyscripts.compute.prevalences lyscripts.compute.priors lyscripts.compute.risks lyscripts.compute.utils lyscripts.configs lyscripts.data lyscripts.data.collect lyscripts.data.enhance lyscripts.data.filter lyscripts.data.generate lyscripts.data.join lyscripts.data.lyproxify lyscripts.data.split lyscripts.data.utils lyscripts.decorators lyscripts.evaluate lyscripts.plots lyscripts.sample lyscripts.schedule lyscripts.schema lyscripts.utils

N

named_params (lyscripts.configs.ModelConfig attribute) new (lyscripts.sample.AcorTime attribute) (lyscripts.sample.NumAccepted attribute) newly_accepted (lyscripts.sample.NumAccepted property) normalize() (lyscripts.configs.ScenarioConfig method) num (lyscripts.configs.ScheduleConfig attribute)

num_fail (lyscripts.plots.BetaPosterior property) num_header_rows (lyscripts.data.lyproxify.LyproxifyCLI attribute) num_patients (lyscripts.data.generate.GenerateCLI attribute) num_steps (lyscripts.configs.SamplingConfig attribute) num_success (lyscripts.plots.BetaPosterior attribute) num_total (lyscripts.plots.BetaPosterior attribute)

O

observe_prevalence() (in module lyscripts.compute.prevalences) offset (lyscripts.plots.AbstractDistribution attribute) old (lyscripts.sample.AcorTime attribute) (lyscripts.sample.NumAccepted attribute) operator (lyscripts.data.filter.FilterCLI attribute)

output_dir (lyscripts.data.split.SplitCLI attribute) output_file (lyscripts.data.enhance.EnhanceCLI attribute) (lyscripts.data.filter.FilterCLI attribute) (lyscripts.data.generate.GenerateCLI attribute) (lyscripts.data.join.JoinCLI attribute) (lyscripts.data.lyproxify.LyproxifyCLI attribute)

P

params (lyscripts.configs.DistributionConfig attribute) (lyscripts.data.generate.GenerateCLI attribute) ParsingError pdf() (lyscripts.plots.BetaPosterior method) port (lyscripts.data.collect.CollectorCLI attribute) posteriors (lyscripts.compute.ComputeCLI attribute) (lyscripts.compute.posteriors.PosteriorsCLI attribute)

power (lyscripts.configs.ScheduleConfig attribute) power_schedule() (in module lyscripts.configs) prevalences (lyscripts.compute.ComputeCLI attribute) (lyscripts.compute.prevalences.PrevalencesCLI attribute) priors (lyscripts.compute.ComputeCLI attribute) (lyscripts.compute.priors.PriorsCLI attribute) process() (in module lyscripts.data.collect)

R

raw_values (lyscripts.plots.Histogram attribute) reduce_pattern() (in module lyscripts.compute.utils) relative_diff (lyscripts.sample.AcorTime property) relative_thresh (lyscripts.configs.SamplingConfig attribute) render() (lyscripts.sample.CompletedItersColumn method) (lyscripts.sample.ItersPerSecondColumn method)

retrieve_graph_representation() (in module lyscripts.configs) right_percentile() (lyscripts.plots.AbstractDistribution method) (lyscripts.plots.BetaPosterior method) (lyscripts.plots.Histogram method) risks (lyscripts.compute.ComputeCLI attribute) (lyscripts.compute.risks.RisksCLI attribute) run_sampling() (in module lyscripts.sample)

S

sample (lyscripts.LyscriptsCLI attribute) sampling (lyscripts.compute.utils.BaseComputeCLI attribute) (lyscripts.sample.SampleCLI attribute) (lyscripts.schema.SchemaSettings attribute) save() (lyscripts.compute.utils.HDF5FileStorage method) save_figure() (in module lyscripts.plots) save_table_to_csv() (in module lyscripts.data.utils) scale (lyscripts.plots.AbstractDistribution attribute) scenarios (lyscripts.compute.utils.BaseComputeCLI attribute) (lyscripts.schema.SchemaSettings attribute) schedule (lyscripts.LyscriptsCLI attribute) (lyscripts.schema.SchemaSettings attribute)

seed (lyscripts.configs.CrossValidationConfig attribute) (lyscripts.configs.SamplingConfig attribute) (lyscripts.data.generate.GenerateCLI attribute) serve_collector_js() (in module lyscripts.data.collect) serve_index_html() (in module lyscripts.data.collect) serve_schema() (in module lyscripts.data.collect) set_attrs() (lyscripts.compute.utils.HDF5FileStorage method) side (lyscripts.configs.DataConfig attribute) source (lyscripts.configs.DataConfig attribute) split (lyscripts.data.DataCLI attribute) split_legends() (in module lyscripts.plots) storage_file (lyscripts.configs.SamplingConfig attribute)

T

t_stages (lyscripts.configs.DeprecatedModelConfig attribute) (lyscripts.configs.ScenarioConfig attribute) t_stages_dist (lyscripts.configs.ScenarioConfig attribute) (lyscripts.data.generate.GenerateCLI attribute) thin_by (lyscripts.configs.SamplingConfig attribute)

to_hdf5_attrs() (in module lyscripts.compute.utils) to_involvement() (lyscripts.configs.DiagnosisConfig method) transform_to_lyprox() (in module lyscripts.data.lyproxify) translate() (lyscripts.configs.DeprecatedModelConfig method) trust_factor (lyscripts.configs.SamplingConfig attribute) tumor (lyscripts.configs.GraphConfig attribute)

U

unflatten() (in module lyscripts.utils) update() (lyscripts.sample.AcorTime method) (lyscripts.sample.NumAccepted method)

update_history_table() (in module lyscripts.sample) use_mpl_stylesheet() (in module lyscripts.plots)

V

value (lyscripts.data.filter.FilterCLI attribute) values (lyscripts.configs.ScheduleConfig attribute) (lyscripts.plots.Histogram property)

version (lyscripts.LyscriptsCLI attribute) (lyscripts.schema.SchemaSettings attribute)

W

walkers_per_dim (lyscripts.configs.SamplingConfig attribute)