Index

A

AbstractPrediction (class in graph) After (class in transformations) age (database.OMOP_Person property) age_parameter() (biomodel.biomodel.BioModel method) (biomodel.biomodel.CustomModel method) (biomodel.biomodel.RFunction method) AgeInt (class in biomodel.biomodel) Always (class in transformations) apply() (transformations.Group method) (transformations.Increase method) (transformations.IncreaseByPercentage method) (transformations.OnSubset method) (transformations.Reduce method) (transformations.ReduceByPercentage method) (transformations.RegressToValue method) (transformations.Set method) (transformations.TimeDelta method) (transformations.Transformation method) (transformations.WithProbability method)

apply_this_year() (transformations.After method) (transformations.Always method) (transformations.Before method) (transformations.BeforeAndThen method) (transformations.Every method) (transformations.Once method) (transformations.OnRange method) (transformations.ThenOnwards method) (transformations.TimeDelta method)

B

Before (class in transformations) BeforeAndThen (class in transformations) BioModel (class in biomodel.biomodel) biomodel.biomodel module biomodel.models module biomodel.models.clivd module biomodel.models.clivd.clivd module biomodel.models.clivd_points module biomodel.models.clivd_points.clivd module biomodel.models.covid module biomodel.models.covid.covid module biomodel.models.framingham module biomodel.models.framingham.model_fr module biomodel.models.framingham_gen module biomodel.models.framingham_gen.model_fr module biomodel.models.gail module

biomodel.models.gail.model_gail module biomodel.models.lifecrc module biomodel.models.lifecrc.model module biomodel.models.pim module biomodel.models.pim.pim module biomodel.models.prostate module biomodel.models.prostate.prostate module biomodel.models.qrisk module biomodel.models.qrisk.qrisk module biomodel.models.qrisk.qrisk_model module biomodel.models.score module biomodel.models.score.score module biomodel.models.score.score_model module birth_datetime (database.OMOP_Person attribute) Bool (class in biomodel.biomodel) BoolInt (class in biomodel.biomodel)

C

calc_global_95CI() (in module graph) calculate_survival_probabilities() (in module biomodel.models.score.score_model) calculate_sy() (in module biomodel.models.score.score_model) calculate_weighted_sum() (in module biomodel.models.score.score_model) care_site_id (database.OMOP_Person attribute) CATEGORICAL (biomodel.biomodel.ReturnCategory attribute) check_value_in_range() (in module gui) Clap (class in transformations) class_name (biomodel.biomodel.RFunction property) CLivD (class in biomodel.models) (class in biomodel.models.clivd.clivd) clivd_gui module CLivDPoints (class in biomodel.models) (class in biomodel.models.clivd_points.clivd) combined_cvd_risk() (in module biomodel.models.score.score_model) contains_distribution() (transformations.Clap method) (transformations.Distribution method) (transformations.Group method) (transformations.Increase method) (transformations.IncreaseByPercentage method) (transformations.LimitValue method) (transformations.OnSubset method) (transformations.Reduce method) (transformations.ReduceByPercentage method) (transformations.RegressToValue method) (transformations.Set method) (transformations.TimeDelta method) (transformations.Transformation method) (transformations.WithProbability method)

contains_distribution_in_variations() (in module biomodel.biomodel) CONTINUOUS (biomodel.biomodel.ReturnCategory attribute) Covid (class in biomodel.models) (class in biomodel.models.covid.covid) covid_gui module crc_graph module crc_gui module current_age (graph.Prediction attribute) CustomModel (class in biomodel.biomodel) cvd_female_raw() (in module biomodel.models.qrisk.qrisk_model) cvd_male_raw() (in module biomodel.models.qrisk.qrisk_model) cvd_raw() (in module biomodel.models.qrisk.qrisk_model)

D

database module Database (class in database) day_of_birth (database.OMOP_Person attribute) describe() (biomodel.biomodel.BioModel method) Distribution (class in transformations)

domain_info() (biomodel.biomodel.Enum method) (biomodel.biomodel.Float method) (biomodel.biomodel.Int method) (biomodel.biomodel.Parameter method) DoubleSlider (class in gui) doubleValueChanged (gui.DoubleSlider attribute)

E

emitDoubleValueChanged() (gui.DoubleSlider method) end (transformations.OnRange attribute) Enum (class in biomodel.biomodel)

ethnicity_concept_id (database.OMOP_Person attribute) ethnicity_source_concept_id (database.OMOP_Person attribute) ethnicity_source_value (database.OMOP_Person attribute) Every (class in transformations)

F

false (biomodel.biomodel.BoolInt attribute) file_path (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute) filter_transformations() (in module biomodel.biomodel) Float (class in biomodel.biomodel) fr_describe module fr_graph module fr_gui module

fr_gui_genetics module fr_gui_trans module fr_gui_twin module Framingham (class in biomodel.models) (class in biomodel.models.framingham.model_fr) FraminghamGenetics (class in biomodel.models) (class in biomodel.models.framingham_gen.model_fr) function_name (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute)

G

Gail (class in biomodel.models) (class in biomodel.models.gail.model_gail) gail_ui module gender_concept_id (database.OMOP_Person attribute) gender_source_concept_id (database.OMOP_Person attribute) gender_source_value (database.OMOP_Person attribute) get_as_id() (in module transformations) get_coefficients() (in module biomodel.models.score.score_model) get_default_value() (biomodel.biomodel.Bool method) (biomodel.biomodel.BoolInt method) (biomodel.biomodel.Enum method) (biomodel.biomodel.Float method) (biomodel.biomodel.Int method) (biomodel.biomodel.Parameter method)

get_id_value() (in module transformations) get_intervals() (biomodel.biomodel.BioModel method) get_title() (biomodel.biomodel.BioModel method) get_value() (in module transformations) graph module Group (class in transformations) gui module

H

has_intervals() (biomodel.biomodel.BioModel method)

has_title() (biomodel.biomodel.BioModel method)

I

id (biomodel.biomodel.AgeInt attribute) (biomodel.biomodel.Bool attribute) (biomodel.biomodel.BoolInt attribute) (biomodel.biomodel.Enum attribute) (biomodel.biomodel.Float attribute) (biomodel.biomodel.Int attribute) (biomodel.biomodel.OMOPId attribute) (biomodel.biomodel.Parameter attribute) (transformations.Increase attribute) (transformations.IncreaseByPercentage attribute) (transformations.OnSubset attribute) (transformations.Reduce attribute) (transformations.ReduceByPercentage attribute) (transformations.RegressToValue attribute) (transformations.Set attribute) Increase (class in transformations) IncreaseByPercentage (class in transformations) Int (class in biomodel.biomodel) integrate_horizontals() (in module graph) InterfaceModel (class in gui) interpretation (biomodel.models.CLivD attribute) (biomodel.models.clivd.clivd.CLivD attribute) (biomodel.models.clivd_points.clivd.CLivDPoints attribute) (biomodel.models.CLivDPoints attribute) (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute) (biomodel.models.Gail attribute) (biomodel.models.gail.model_gail.Gail attribute) (biomodel.models.LifeCRC attribute) (biomodel.models.lifecrc.model.LifeCRC attribute) (biomodel.models.pim.pim.PIMModel attribute) (biomodel.models.PIMModel attribute) (biomodel.models.QRisk attribute) (biomodel.models.qrisk.qrisk.QRisk attribute) (biomodel.models.score.score.ScoreModel attribute) (biomodel.models.ScoreModel attribute)

intervals (biomodel.models.CLivD attribute) (biomodel.models.clivd.clivd.CLivD attribute) (biomodel.models.clivd_points.clivd.CLivDPoints attribute) (biomodel.models.CLivDPoints attribute) (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute) (biomodel.models.Gail attribute) (biomodel.models.gail.model_gail.Gail attribute) (biomodel.models.LifeCRC attribute) (biomodel.models.lifecrc.model.LifeCRC attribute) (biomodel.models.QRisk attribute) (biomodel.models.qrisk.qrisk.QRisk attribute) (biomodel.models.score.score.ScoreModel attribute) (biomodel.models.ScoreModel attribute) is_female (database.OMOP_Person property) is_male (database.OMOP_Person property) iterate_person() (database.Database method) (database.OMOP_DB method)

K

kwarg_to_omop() (biomodel.biomodel.BioModel method) (biomodel.biomodel.CustomModel method) (biomodel.biomodel.RFunction method)

L

labels (graph.Prediction attribute) (graph.SinglePrediction attribute) LifeCRC (class in biomodel.models) (class in biomodel.models.lifecrc.model)

LimitValue (class in transformations) linear_points() (in module biomodel.models.clivd_points.clivd) location_id (database.OMOP_Person attribute) LogNormal (class in transformations)

M

main() (in module biomodel.models.score.score_model) max (transformations.Clap attribute) (transformations.Uniform attribute) maximum (biomodel.biomodel.AgeInt attribute) (biomodel.biomodel.Float attribute) (biomodel.biomodel.Int attribute) mean (transformations.LogNormal attribute) (transformations.Normal attribute) measurement_concept_id (database.OMOP_Measurement attribute) measurement_date (database.OMOP_Measurement attribute) measurement_datetime (database.OMOP_Measurement attribute) measurement_id (database.OMOP_Measurement attribute) measurement_source_concept_id (database.OMOP_Measurement attribute) measurement_source_value (database.OMOP_Measurement attribute) measurement_type_concept_id (database.OMOP_Measurement attribute) min (transformations.Clap attribute) (transformations.Uniform attribute) minimum (biomodel.biomodel.AgeInt attribute) (biomodel.biomodel.Float attribute) (biomodel.biomodel.Int attribute) model (graph.Prediction attribute) (graph.SinglePrediction attribute) (graph.SpreadPrediction attribute) module biomodel.biomodel biomodel.models biomodel.models.clivd biomodel.models.clivd.clivd biomodel.models.clivd_points biomodel.models.clivd_points.clivd biomodel.models.covid biomodel.models.covid.covid biomodel.models.framingham biomodel.models.framingham.model_fr biomodel.models.framingham_gen biomodel.models.framingham_gen.model_fr biomodel.models.gail biomodel.models.gail.model_gail biomodel.models.lifecrc biomodel.models.lifecrc.model biomodel.models.pim biomodel.models.pim.pim biomodel.models.prostate biomodel.models.prostate.prostate biomodel.models.qrisk biomodel.models.qrisk.qrisk biomodel.models.qrisk.qrisk_model biomodel.models.score biomodel.models.score.score biomodel.models.score.score_model clivd_gui covid_gui crc_graph crc_gui database fr_describe fr_graph fr_gui fr_gui_genetics fr_gui_trans fr_gui_twin gail_ui graph gui omop_csv omop_csv_filter omop_csv_language pim_gui prostate_gui qrisk_describe qrisk_gui score_gui transformations

month_of_birth (database.OMOP_Person attribute)

N

name (biomodel.biomodel.AgeInt attribute) (biomodel.biomodel.BioModel property) (biomodel.biomodel.Bool attribute) (biomodel.biomodel.BoolInt attribute) (biomodel.biomodel.Enum attribute) (biomodel.biomodel.Float attribute) (biomodel.biomodel.Int attribute) (biomodel.biomodel.Parameter attribute) (biomodel.biomodel.RiskInterval attribute) (biomodel.models.CLivD attribute) (biomodel.models.clivd.clivd.CLivD attribute) (biomodel.models.clivd_points.clivd.CLivDPoints attribute) (biomodel.models.CLivDPoints attribute) (biomodel.models.pim.pim.PIMModel attribute) (biomodel.models.PIMModel attribute) (biomodel.models.Prostate attribute) (biomodel.models.prostate.prostate.Prostate attribute) (biomodel.models.QRisk attribute) (biomodel.models.qrisk.qrisk.QRisk attribute) (biomodel.models.score.score.ScoreModel attribute) (biomodel.models.ScoreModel attribute)

Normal (class in transformations) Normal95IC() (in module transformations)

O

observation_concept_id (database.OMOP_Obsevation attribute) observation_date (database.OMOP_Obsevation attribute) observation_datetime (database.OMOP_Obsevation attribute) observation_id (database.OMOP_Obsevation attribute) observation_source_concept_id (database.OMOP_Obsevation attribute) observation_source_value (database.OMOP_Obsevation attribute) observation_type_concept_id (database.OMOP_Obsevation attribute) omop_csv module omop_csv_filter module omop_csv_language module

OMOP_DB (class in database) OMOP_Measurement (class in database) OMOP_Obsevation (class in database) OMOP_Person (class in database) OMOPId (class in biomodel.biomodel) on_parameter_changed() (gui.InterfaceModel method) Once (class in transformations) OnRange (class in transformations) OnSubset (class in transformations) operator (transformations.OnSubset attribute) operator_concept_id (database.OMOP_Measurement attribute) output_meaning() (biomodel.biomodel.BioModel method)

P

Parameter (class in biomodel.biomodel) ParameterChangedSignal (class in gui) parameters (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute) percentage (transformations.IncreaseByPercentage attribute) (transformations.ReduceByPercentage attribute) (transformations.RegressToValue attribute) person_id (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute) (database.OMOP_Person attribute) person_source_value (database.OMOP_Person attribute) pim_gui module PIMModel (class in biomodel.models) (class in biomodel.models.pim.pim) plot_change() (graph.AbstractPrediction method) (graph.Prediction method) (graph.SinglePrediction method) (graph.SpreadPrediction method) predict() (biomodel.biomodel.BioModel method) (biomodel.biomodel.CustomModel method) (biomodel.biomodel.RFunction method) (biomodel.models.CLivD method) (biomodel.models.clivd.clivd.CLivD method) (biomodel.models.clivd_points.clivd.CLivDPoints method) (biomodel.models.CLivDPoints method) (biomodel.models.Covid method) (biomodel.models.covid.covid.Covid method) (biomodel.models.Gail method) (biomodel.models.gail.model_gail.Gail method) (biomodel.models.LifeCRC method) (biomodel.models.lifecrc.model.LifeCRC method) (biomodel.models.pim.pim.PIMModel method) (biomodel.models.PIMModel method) (biomodel.models.Prostate method) (biomodel.models.prostate.prostate.Prostate method) (biomodel.models.QRisk method) (biomodel.models.qrisk.qrisk.QRisk method) (biomodel.models.score.score.ScoreModel method) (biomodel.models.ScoreModel method)

predict_over_time (biomodel.models.Gail attribute) (biomodel.models.gail.model_gail.Gail attribute) predict_person() (biomodel.biomodel.BioModel method) predict_person_once() (biomodel.biomodel.BioModel method) predict_person_time() (biomodel.biomodel.BioModel method) predict_person_time_variations() (biomodel.biomodel.BioModel method) predict_population_time() (biomodel.biomodel.BioModel method) Prediction (class in graph) prediction_years (graph.Prediction attribute) (graph.SpreadPrediction attribute) predictions (graph.Prediction attribute) (graph.SinglePrediction attribute) probability (transformations.WithProbability attribute) Prostate (class in biomodel.models) (class in biomodel.models.prostate.prostate) prostate_gui module provider_id (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute) (database.OMOP_Person attribute)

Q

QRisk (class in biomodel.models) (class in biomodel.models.qrisk.qrisk) qrisk_describe module

qrisk_gui module qualifier_concept_id (database.OMOP_Obsevation attribute) qualifier_source_value (database.OMOP_Obsevation attribute)

R

race_concept_id (database.OMOP_Person attribute) race_source_concept_id (database.OMOP_Person attribute) race_source_value (database.OMOP_Person attribute) range_high (database.OMOP_Measurement attribute) range_low (database.OMOP_Measurement attribute) Reduce (class in transformations) ReduceByPercentage (class in transformations) RegressToValue (class in transformations) resolved_path (biomodel.biomodel.RFunction property)

return_category (graph.Prediction attribute) (graph.SinglePrediction attribute) (graph.SpreadPrediction attribute) return_category() (biomodel.biomodel.BioModel method) (biomodel.biomodel.CustomModel method) (biomodel.biomodel.RFunction method) ReturnCategory (class in biomodel.biomodel) RFunction (class in biomodel.biomodel) RiskInterval (class in biomodel.biomodel) run() (gui.InterfaceModel method)

S

sample() (transformations.Clap method) (transformations.LimitValue method) (transformations.LogNormal method) (transformations.Normal method) (transformations.Uniform method) score_gui module ScoreModel (class in biomodel.models) (class in biomodel.models.score.score) Set (class in transformations) set_minimum_value() (in module graph) setMaximum() (gui.DoubleSlider method) setMinimum() (gui.DoubleSlider method) setSingleStep() (gui.DoubleSlider method)

setValue() (gui.DoubleSlider method) sex (database.OMOP_Person property) should_have_meaning() (biomodel.biomodel.BioModel method) show_change() (graph.AbstractPrediction method) (graph.Prediction method) (graph.SpreadPrediction method) signal (gui.ParameterChangedSignal attribute) SinglePrediction (class in graph) singleStep() (gui.DoubleSlider method) source (transformations.Clap attribute) SpreadPrediction (class in graph) start (transformations.OnRange attribute) std (transformations.LogNormal attribute) (transformations.Normal attribute)

T

tables (graph.SpreadPrediction attribute) ten_year_risk() (in module biomodel.models.score.score_model) ten_year_survival_probability() (in module biomodel.models.score.score_model) ThenOnwards (class in transformations) TimeDelta (class in transformations) title (biomodel.models.CLivD attribute) (biomodel.models.clivd.clivd.CLivD attribute) (biomodel.models.clivd_points.clivd.CLivDPoints attribute) (biomodel.models.CLivDPoints attribute) (biomodel.models.Framingham attribute) (biomodel.models.framingham.model_fr.Framingham attribute) (biomodel.models.framingham_gen.model_fr.FraminghamGenetics attribute) (biomodel.models.FraminghamGenetics attribute) (biomodel.models.Gail attribute) (biomodel.models.gail.model_gail.Gail attribute) (biomodel.models.LifeCRC attribute) (biomodel.models.lifecrc.model.LifeCRC attribute) (biomodel.models.pim.pim.PIMModel attribute) (biomodel.models.PIMModel attribute) (biomodel.models.Prostate attribute) (biomodel.models.prostate.prostate.Prostate attribute) (biomodel.models.QRisk attribute) (biomodel.models.qrisk.qrisk.QRisk attribute) (biomodel.models.score.score.ScoreModel attribute) (biomodel.models.ScoreModel attribute)

Transformation (class in transformations) transformation (transformations.After attribute) (transformations.Always attribute) (transformations.Before attribute) (transformations.BeforeAndThen attribute) (transformations.Every attribute) (transformations.Once attribute) (transformations.OnRange attribute) (transformations.OnSubset attribute) (transformations.ThenOnwards attribute) (transformations.WithProbability attribute) transformations module transformations (transformations.Group attribute) true (biomodel.biomodel.BoolInt attribute) type_name() (biomodel.biomodel.Bool method) (biomodel.biomodel.BoolInt method) (biomodel.biomodel.Enum method) (biomodel.biomodel.Float method) (biomodel.biomodel.Int method) (biomodel.biomodel.Parameter method)

U

Uniform (class in transformations) unit_concept_id (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute)

unit_source_value (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute) update_graph() (gui.InterfaceModel method)

V

value (biomodel.biomodel.RiskInterval attribute) (transformations.Increase attribute) (transformations.OnSubset attribute) (transformations.Reduce attribute) (transformations.RegressToValue attribute) (transformations.Set attribute) value() (gui.DoubleSlider method) value_as_concept_id (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute)

value_as_number (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute) value_as_string (database.OMOP_Obsevation attribute) value_source_value (database.OMOP_Measurement attribute) values (biomodel.biomodel.Enum attribute) visit_occurrence_id (database.OMOP_Measurement attribute) (database.OMOP_Obsevation attribute)

W

WithProbability (class in transformations)

Y

year (transformations.After attribute) (transformations.Before attribute) (transformations.BeforeAndThen attribute) (transformations.Once attribute) (transformations.ThenOnwards attribute)

year_of_birth (database.OMOP_Person attribute) years (transformations.Every attribute)