Index

_

__init__() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) (protocols.config_parser.ConfigurationManager method) (protocols.config_parser.SimulationConfig method) (protocols.protocol_parser.ProtocolParser method) (protocols.protocol_parser.SimulationConfig method) (simulation.base.BaseSimulation method) (simulation.base.Event method) (simulation.base.ProtocolEvent method) (simulation.base.SimulationClock method) (simulation.base.SimulationEnvironment method) (simulation.config.SimulationConfig method) (simulation.discontinuation_manager.DiscontinuationManager method) (simulation.patient_state.PatientState method) (simulation.scheduler.ClinicScheduler method) (simulation.vision_models.LiteratureBasedVisionModel method) (simulation.vision_models.SimplifiedVisionModel method)

A

action (simulation.base.ProtocolEvent attribute) analysis.eylea_data_analysis module analysis.eylea_intervals_analysis module analysis.visualize_long_gap_patients module analysis.visualize_va_by_pca_cluster module

analysis.visualize_va_change_by_cluster module analyze_first_year_injections() (in module analysis.eylea_intervals_analysis) analyze_injection_intervals() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) analyze_intervals_by_group() (in module analysis.eylea_intervals_analysis) analyze_patient_cohort() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) analyze_treatment_courses() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) analyze_va_by_group() (in module analysis.eylea_intervals_analysis) analyze_va_trajectories() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) apply_sensitivity_variation() (simulation.config.SimulationConfig method)

B

BaseSimulation (class in simulation.base)

BaseVisionModel (class in simulation.vision_models)

C

calculate_vision_change() (simulation.vision_models.BaseVisionModel method) (simulation.vision_models.LiteratureBasedVisionModel method) (simulation.vision_models.SimplifiedVisionModel method) clean_data() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) clean_va_measurements() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) ClinicScheduler (class in simulation.scheduler) cluster_treatment_patterns() (in module analysis.eylea_intervals_analysis) COLUMN_MAPPINGS (analysis.eylea_data_analysis.EyleaDataAnalyzer attribute)

ConfigurationManager (class in protocols.config_parser) connect_to_db() (in module analysis.eylea_intervals_analysis) (in module analysis.visualize_long_gap_patients) (in module analysis.visualize_va_by_pca_cluster) (in module analysis.visualize_va_change_by_cluster) create_patient_id() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) create_protocol_event() (simulation.base.Event class method) create_vision_model() (in module simulation.vision_models) current_vision (simulation.patient_state.PatientState property)

D

data (simulation.base.Event attribute) DATA_VALIDATION (analysis.eylea_data_analysis.EyleaDataAnalyzer attribute) database (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) description (protocols.protocol_parser.SimulationConfig attribute)

DiscontinuationManager (class in simulation.discontinuation_manager) discontinue_treatment() (simulation.patient_state.PatientState method) duration_days (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute)

E

evaluate_discontinuation() (simulation.discontinuation_manager.DiscontinuationManager method) evaluate_retreatment() (simulation.discontinuation_manager.DiscontinuationManager method) Event (class in simulation.base)

event_type (simulation.base.Event attribute) export_interval_va_data() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) EyleaDataAnalyzer (class in analysis.eylea_data_analysis)

F

from_yaml() (simulation.config.SimulationConfig class method)

G

generate_data_quality_report() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) get_clinical_model_params() (simulation.config.SimulationConfig method) get_cost_parameters() (simulation.config.SimulationConfig method) get_decisions() (simulation.base.Event method) get_des_params() (simulation.config.SimulationConfig method) get_full_configuration() (protocols.config_parser.ConfigurationManager method) (protocols.protocol_parser.ProtocolParser method), [1] get_loading_phase_params() (simulation.config.SimulationConfig method) get_long_gap_patients() (in module analysis.visualize_long_gap_patients) get_maintenance_params() (simulation.config.SimulationConfig method) get_next_event() (simulation.base.SimulationClock method)

get_optional_actions() (simulation.base.Event method) get_output_params() (simulation.config.SimulationConfig method) get_protocol() (simulation.base.BaseSimulation method) get_required_actions() (simulation.base.Event method) get_resource_params() (simulation.config.SimulationConfig method) get_sensitivity_analysis_params() (simulation.config.SimulationConfig method) get_simulation_params() (simulation.config.SimulationConfig method) get_statistics() (simulation.discontinuation_manager.DiscontinuationManager method) get_treatment_discontinuation_params() (simulation.config.SimulationConfig method) get_vision_params() (simulation.config.SimulationConfig method) get_visit_type() (simulation.base.Event method)

H

handle_missing_values() (analysis.eylea_data_analysis.EyleaDataAnalyzer method)

handle_temporal_anomalies() (analysis.eylea_data_analysis.EyleaDataAnalyzer method)

I

identify_treatment_groups() (in module analysis.eylea_intervals_analysis)

L

last_visit_date (simulation.patient_state.PatientState property) LiteratureBasedVisionModel (class in simulation.vision_models) load_cluster_assignments() (in module analysis.visualize_long_gap_patients) (in module analysis.visualize_va_by_pca_cluster) (in module analysis.visualize_va_change_by_cluster) load_data() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) load_interval_data() (in module analysis.eylea_intervals_analysis) (in module analysis.visualize_long_gap_patients) (in module analysis.visualize_va_by_pca_cluster) (in module analysis.visualize_va_change_by_cluster)

load_interval_summary() (in module analysis.eylea_intervals_analysis) load_parameter_file() (simulation.config.SimulationConfig method) load_protocol() (in module protocols.protocol_parser) load_simulation_config() (protocols.config_parser.ConfigurationManager method) (protocols.protocol_parser.ProtocolParser method), [1]

M

main() (in module analysis.eylea_data_analysis) (in module analysis.eylea_intervals_analysis) (in module analysis.visualize_long_gap_patients) (in module analysis.visualize_va_by_pca_cluster) (in module analysis.visualize_va_change_by_cluster) map_column_names() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) module analysis.eylea_data_analysis analysis.eylea_intervals_analysis analysis.visualize_long_gap_patients analysis.visualize_va_by_pca_cluster analysis.visualize_va_change_by_cluster protocols.config_parser protocols.protocol_parser simulation.base simulation.config simulation.discontinuation_manager simulation.patient_state simulation.scheduler simulation.vision_models visualization.acuity_viz

N

name (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) next_visit_interval (simulation.patient_state.PatientState property)

num_patients (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute)

P

parameter_set (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) parameters (protocols.protocol_parser.SimulationConfig attribute) (simulation.base.ProtocolEvent attribute) (simulation.config.SimulationConfig attribute) patient_id (simulation.base.Event attribute) PatientState (class in simulation.patient_state) perform_va_interval_pca() (in module analysis.eylea_intervals_analysis) phase (simulation.base.Event attribute) phase_type (simulation.base.ProtocolEvent attribute) plot_injection_intervals() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) plot_mean_acuity() (in module visualization.acuity_viz) plot_multiple_patients() (in module visualization.acuity_viz) plot_patient_acuity() (in module visualization.acuity_viz) plot_treatment_courses() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) plot_va_change_distribution() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) plot_va_trajectories() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) plots (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute)

prepare_va_interval_data_for_pca() (in module analysis.eylea_intervals_analysis) priority (simulation.base.Event attribute) process_event() (simulation.base.BaseSimulation method) process_monitoring_visit() (simulation.discontinuation_manager.DiscontinuationManager method) process_visit() (simulation.patient_state.PatientState method) protocol (protocols.protocol_parser.SimulationConfig attribute) (simulation.base.Event attribute) (simulation.config.SimulationConfig attribute) protocol_agent (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) protocol_event (simulation.base.Event attribute) protocol_type (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) ProtocolEvent (class in simulation.base) ProtocolParser (class in protocols.protocol_parser) protocols.config_parser module protocols.protocol_parser module

R

random_seed (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute) register_protocol() (simulation.base.BaseSimulation method) request_slot() (simulation.scheduler.ClinicScheduler method)

resources (protocols.config_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute) result (simulation.base.ProtocolEvent attribute) resume_treatment() (simulation.patient_state.PatientState method) run() (simulation.base.BaseSimulation method) run_analysis() (analysis.eylea_data_analysis.EyleaDataAnalyzer method)

S

save_results (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) schedule_event() (simulation.base.SimulationClock method) schedule_monitoring() (simulation.discontinuation_manager.DiscontinuationManager method) schedule_next_visit() (simulation.scheduler.ClinicScheduler method) schedule_protocol_event() (simulation.base.BaseSimulation method) sensitivity_analysis (simulation.config.SimulationConfig attribute) set_monitoring_schedule() (simulation.patient_state.PatientState method) set_next_visit_interval() (simulation.patient_state.PatientState method) SimplifiedVisionModel (class in simulation.vision_models) simulation.base module simulation.config module simulation.discontinuation_manager module

simulation.patient_state module simulation.scheduler module simulation.vision_models module simulation_type (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute) SimulationClock (class in simulation.base) SimulationConfig (class in protocols.config_parser) (class in protocols.protocol_parser) (class in simulation.config) SimulationEnvironment (class in simulation.base) start_date (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute)

T

time (simulation.base.Event attribute)

U

update_phase() (simulation.patient_state.PatientState method)

V

validate_data_structure() (analysis.eylea_data_analysis.EyleaDataAnalyzer method) verbose (protocols.config_parser.SimulationConfig attribute) (protocols.protocol_parser.SimulationConfig attribute) (simulation.config.SimulationConfig attribute) visit_history (simulation.patient_state.PatientState property)

visualization.acuity_viz module visualize_long_gap_patients() (in module analysis.visualize_long_gap_patients) visualize_va_change_by_cluster() (in module analysis.visualize_va_change_by_cluster) visualize_va_trajectories_by_cluster() (in module analysis.visualize_va_by_pca_cluster)