Index

A

add_age_categories() (in module pearl.population) add_default_columns() (in module pearl.population) add_default_columns_new() (in module pearl.population) add_id() (in module pearl.population) add_multimorbidity() (in module pearl.population) AddNewUser (class in pearl.events) age_by_h1yy (pearl.parameters.Parameters attribute) AGE_CATS (pearl.parameters.Parameters attribute)

age_in_2009 (pearl.parameters.Parameters attribute) AGES (pearl.parameters.Parameters attribute) ALL_COMORBIDITIES (in module pearl.definitions) ALL_YEARS (pearl.parameters.Parameters attribute) append_new() (in module pearl.events) ApplyComorbidities (class in pearl.population) ART_NAIVE (in module pearl.definitions) ART_NONUSER (in module pearl.definitions) ART_USER (in module pearl.definitions)

B

BasePearl (class in pearl.base_model) BasePopulation (class in pearl.population) Bmi (class in pearl.population) bmi_intervention_coverage (pearl.parameters.Parameters attribute)

bmi_intervention_effectiveness (pearl.parameters.Parameters attribute) bmi_intervention_end_year (pearl.parameters.Parameters attribute) bmi_intervention_scenario (pearl.parameters.Parameters attribute) bmi_intervention_start_year (pearl.parameters.Parameters attribute)

C

calculate_cd4_decrease() (in module pearl.events) calculate_cd4_increase() (in module pearl.events) calculate_prob() (in module pearl.calculations) cast_type() (in module pearl.population) CD4_BINS (pearl.parameters.Parameters attribute) cd4_decrease (pearl.parameters.Parameters attribute) cd4_decrease_vcov (pearl.parameters.Parameters attribute) cd4_increase (pearl.parameters.Parameters attribute) cd4_increase_knots_age (pearl.parameters.Parameters attribute) cd4_increase_knots_cd4_init (pearl.parameters.Parameters attribute) cd4_increase_knots_time_from_h1yy (pearl.parameters.Parameters attribute)

cd4_increase_vcov (pearl.parameters.Parameters attribute) Cd4Increase (class in pearl.population) cd4n_by_h1yy (pearl.parameters.Parameters attribute) cd4n_by_h1yy_2009 (pearl.parameters.Parameters attribute) Comorbidity (class in pearl.population) comorbidity_coeff_dict (pearl.parameters.Parameters attribute) ComorbidityIncidence (class in pearl.events) create_comorbidity_pop_matrix() (in module pearl.multimorbidity) create_ltfu_pop_matrix() (in module pearl.events) create_mm_detail_stats() (in module pearl.multimorbidity) create_mortality_in_care_pop_matrix() (in module pearl.events) create_mortality_out_care_pop_matrix() (in module pearl.events)

D

DEAD_ART_NONUSER (in module pearl.definitions) DEAD_ART_USER (in module pearl.definitions) DecreaseCD4Count (class in pearl.events) DELAYED (in module pearl.definitions)

delta_bmi() (in module pearl.population) delta_bmi_dict (pearl.parameters.Parameters attribute) draw_from_trunc_norm() (in module pearl.sample) DYING_ART_NONUSER (in module pearl.definitions) DYING_ART_USER (in module pearl.definitions)

E

Event (class in pearl.engine)

EventGrouping (class in pearl.engine)

F

final_state (pearl.parameters.Parameters attribute)

final_year (pearl.parameters.Parameters attribute)

G

group_name (pearl.parameters.Parameters attribute)

H

H1yy (class in pearl.population)

h1yy_by_age_2009 (pearl.parameters.Parameters attribute) history (pearl.parameters.Parameters attribute)

I

idu_threshold (pearl.parameters.Parameters attribute) ignore_columns (pearl.parameters.Parameters attribute) IncreaseCD4Count (class in pearl.events)

IncrementYear (class in pearl.events) init_random_state (pearl.parameters.Parameters attribute) INITIAL_YEARS (pearl.parameters.Parameters attribute)

K

KillInCare (class in pearl.events)

KillOutCare (class in pearl.events)

L

linkage_to_care (pearl.parameters.Parameters attribute) LoseToFollowUp (class in pearl.events) loss_to_follow_up (pearl.parameters.Parameters attribute)

loss_to_follow_up_vcov (pearl.parameters.Parameters attribute) Ltfu (class in pearl.population) LTFU (in module pearl.definitions) ltfu_knots (pearl.parameters.Parameters attribute)

M

module pearl pearl.base_model pearl.calculations pearl.definitions pearl.engine pearl.events pearl.interpolate pearl.multimorbidity pearl.parameters pearl.population pearl.sample mortality_in_care (pearl.parameters.Parameters attribute)

mortality_in_care_age (pearl.parameters.Parameters attribute) mortality_in_care_co (pearl.parameters.Parameters attribute) mortality_in_care_post_art_bmi (pearl.parameters.Parameters attribute) mortality_in_care_sqrtcd4 (pearl.parameters.Parameters attribute) mortality_in_care_vcov (pearl.parameters.Parameters attribute) mortality_model (pearl.parameters.Parameters attribute) mortality_out_care (pearl.parameters.Parameters attribute) mortality_out_care_age (pearl.parameters.Parameters attribute) mortality_out_care_co (pearl.parameters.Parameters attribute) mortality_out_care_post_art_bmi (pearl.parameters.Parameters attribute) mortality_out_care_tv_sqrtcd4 (pearl.parameters.Parameters attribute) mortality_out_care_vcov (pearl.parameters.Parameters attribute) mortality_threshold (pearl.parameters.Parameters attribute) mortality_threshold_flag (pearl.parameters.Parameters attribute)

N

n_initial_nonusers (pearl.parameters.Parameters attribute) n_initial_users (pearl.parameters.Parameters attribute) n_new_agents (pearl.parameters.Parameters attribute) new_dx (pearl.parameters.Parameters attribute)

new_dx_val (pearl.parameters.Parameters attribute) NewAges (class in pearl.population) NewPopulation (class in pearl.population) NonUserPopInit (class in pearl.population)

O

on_art_2009 (pearl.parameters.Parameters attribute)

output_folder (pearl.parameters.Parameters attribute)

P

Parameters (class in pearl.parameters) parameters_path (pearl.parameters.Parameters attribute) pearl module Pearl (class in pearl.engine) pearl.base_model module pearl.calculations module pearl.definitions module pearl.engine module pearl.events module pearl.interpolate module pearl.multimorbidity module pearl.parameters module pearl.population module

pearl.sample module PearlEvents (class in pearl.events) PearlPopulation (class in pearl.population) POPULATION_TYPE_DICT (in module pearl.definitions) post_art_bmi (pearl.parameters.Parameters attribute) post_art_bmi_age_knots (pearl.parameters.Parameters attribute) post_art_bmi_cd4_knots (pearl.parameters.Parameters attribute) post_art_bmi_cd4_post_knots (pearl.parameters.Parameters attribute) post_art_bmi_dict (pearl.parameters.Parameters attribute) post_art_bmi_pre_art_bmi_knots (pearl.parameters.Parameters attribute) post_art_bmi_rse (pearl.parameters.Parameters attribute) PostArtBMI (class in pearl.population) pre_art_bmi (pearl.parameters.Parameters attribute) pre_art_bmi_age_knots (pearl.parameters.Parameters attribute) pre_art_bmi_h1yy_knots (pearl.parameters.Parameters attribute) pre_art_bmi_model (pearl.parameters.Parameters attribute) pre_art_bmi_rse (pearl.parameters.Parameters attribute) PreArtBMI (class in pearl.population) prev_inits_dict (pearl.parameters.Parameters attribute) prev_users_dict (pearl.parameters.Parameters attribute)

R

random_state (pearl.parameters.Parameters attribute) Reengage (class in pearl.events) REENGAGED (in module pearl.definitions)

replication (pearl.parameters.Parameters attribute) restricted_cubic_spline_var() (in module pearl.interpolate) restricted_quadratic_spline_var() (in module pearl.interpolate) run() (pearl.engine.Pearl method)

S

sa_scalars (pearl.parameters.Parameters attribute) sa_variables (pearl.parameters.Parameters attribute) save_parameters() (pearl.parameters.Parameters method) seed (pearl.parameters.Parameters attribute) simulate_new_dx() (pearl.parameters.Parameters method) SimulateAges (class in pearl.population) SIMULATION_YEARS (pearl.parameters.Parameters attribute) SMEARING (in module pearl.definitions)

sort_alphabetically() (in module pearl.population) SqrtCd4nInit (class in pearl.population) SqrtCd4nNew (class in pearl.population) STAGE0 (in module pearl.definitions) STAGE1 (in module pearl.definitions) STAGE2 (in module pearl.definitions) STAGE3 (in module pearl.definitions) start_year (pearl.parameters.Parameters attribute) Status (class in pearl.population)

U

update_mm() (in module pearl.events)

UserPopInit (class in pearl.population)

Y

year (pearl.parameters.Parameters attribute)

years_out_of_care (pearl.parameters.Parameters attribute) YearsOutCare (class in pearl.population)