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Population Schema (#148)
* Adding in the population, death reason, and linking tables to the example schema * Addressing PR comments * Addressing other PR comment * lmao love how I literally created the descrepency you were asking about
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‎extras/examples/inputs.db.sql‎

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/*
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* Filename: /home/matt/Repos/hep-ce/extras/examples/inputs.db.sql
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* Path: /home/matt/Repos/hep-ce/extras/examples
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* Created Date: Thursday, June 12th 2025, 2:53:18 pm
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* Author: Matthew Carroll
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*
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* Copyright (c) 2025 Syndemics Lab
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*/
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BEGIN TRANSACTION;
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DROP TABLE IF EXISTS "population";
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CREATE TABLE "population" (
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"id" INTEGER NOT NULL UNIQUE,
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"sex" INTEGER NOT NULL DEFAULT 0, -- male
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"age" INTEGER NOT NULL DEFAULT 0, -- in months
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"is_alive" INTEGER NOT NULL DEFAULT 1 CHECK (is_alive IN (0, 1)), -- default alive
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"boomer_classification" INTEGER NOT NULL DEFAULT 0 CHECK (boomer_classification IN (0, 1)), -- default not boomer
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"death_reason" INTEGER NOT NULL DEFAULT -1, -- not dead
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"drug_behavior" INTEGER NOT NULL DEFAULT 0, -- never used
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"time_last_active_drug_use" INTEGER NOT NULL DEFAULT 0,
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"hcv" INTEGER NOT NULL DEFAULT 0, -- no hcv
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"fibrosis_state" INTEGER NOT NULL DEFAULT -1, -- no fibrosis
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"is_genotype_three" INTEGER NOT NULL DEFAULT 0 CHECK (is_genotype_three IN (0, 1)), -- not genotype 3
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"seropositive" INTEGER NOT NULL DEFAULT 0 CHECK (seropositive IN (0, 1)), -- not seropositive
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"time_hcv_changed" INTEGER NOT NULL DEFAULT -1,
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"time_fibrosis_state_changed" INTEGER NOT NULL DEFAULT -1,
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"times_hcv_infected" INTEGER NOT NULL DEFAULT 0,
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"times_acute_cleared" INTEGER NOT NULL DEFAULT 0,
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"svrs" INTEGER NOT NULL DEFAULT 0,
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"hiv" TEXT DEFAULT NULL, -- make foreign key
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"time_hiv_changed" INTEGER DEFAULT NULL,
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"low_cd4_months_count" INTEGER DEFAULT NULL,
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"hcc_state" TEXT DEFAULT NULL, -- make foreign key
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"hcc_diagnosed" INTEGER NOT NULL DEFAULT 0 CHECK (hcc_diagnosed IN (0, 1)),
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"currently_overdosing" INTEGER NOT NULL DEFAULT 0 CHECK (currently_overdosing IN (0, 1)), -- not overdosing
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"num_overdoses" INTEGER NOT NULL DEFAULT 0,
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"moud_state" INTEGER NOT NULL DEFAULT 0, -- not in moud
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"time_started_moud" INTEGER NOT NULL DEFAULT -1,
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"current_moud_state_concurrent_months" INTEGER NOT NULL DEFAULT 0,
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"total_moud_months" INTEGER NOT NULL DEFAULT 0,
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"pregnancy_state" INTEGER NOT NULL DEFAULT -1, -- NA
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"time_of_pregnancy_change" INTEGER NOT NULL DEFAULT -1,
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"pregnancy_count" INTEGER NOT NULL DEFAULT 0,
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"num_infants" INTEGER NOT NULL DEFAULT 0,
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"num_stillbirths" INTEGER NOT NULL DEFAULT 0,
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"num_infant_hcv_exposures" INTEGER NOT NULL DEFAULT 0,
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"num_infant_hcv_infections" INTEGER NOT NULL DEFAULT 0,
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"num_infant_hcv_tests" INTEGER NOT NULL DEFAULT 0,
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"measured_fibrosis_state" INTEGER NOT NULL DEFAULT 4, -- no staging
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"had_second_test" INTEGER NOT NULL DEFAULT 0 CHECK (had_second_test IN (0, 1)), -- no second test
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"time_of_last_staging" INTEGER NOT NULL DEFAULT -1,
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"hcv_link_state" INTEGER NOT NULL DEFAULT 0, -- never linked
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"time_of_hcv_link_change" INTEGER NOT NULL DEFAULT -1,
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"hcv_link_count" INTEGER NOT NULL DEFAULT 0,
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"hiv_link_state" TEXT DEFAULT NULL, -- make foreign key
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"time_of_hiv_link_change" INTEGER DEFAULT NULL,
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"hiv_link_count" INTEGER DEFAULT NULL,
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"time_of_last_hcv_screening" INTEGER NOT NULL DEFAULT -1,
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"num_hcv_ab_tests" INTEGER NOT NULL DEFAULT 0,
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"num_hcv_rna_tests" INTEGER NOT NULL DEFAULT 0,
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"hcv_antibody_positive" INTEGER NOT NULL DEFAULT 0 CHECK (hcv_antibody_positive IN (0, 1)), -- not AB positive
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"hcv_identified" INTEGER NOT NULL DEFAULT 0 CHECK (hcv_identified IN (0, 1)), -- not currently identified
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"time_hcv_identified" INTEGER NOT NULL DEFAULT -1,
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"num_hcv_identifications" INTEGER NOT NULL DEFAULT 0,
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"hcv_screening_type" TEXT NOT NULL, -- make foreign key
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"num_hcv_false_negatives" INTEGER NOT NULL DEFAULT 0,
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"identifications_cleared" INTEGER NOT NULL DEFAULT 0,
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"time_of_last_hiv_screening" INTEGER DEFAULT NULL,
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"num_hiv_ab_tests" INTEGER DEFAULT NULL,
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"num_hiv_rna_tests" TEXT DEFAULT NULL,
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"hiv_antibody_positive" TEXT DEFAULT NULL,
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"hiv_identified" INTEGER DEFAULT NULL,
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"time_hiv_identified" INTEGER DEFAULT NULL,
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"num_hiv_identified" INTEGER DEFAULT NULL,
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"hiv_screening_type" TEXT DEFAULT NULL,
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"initiated_hcv_treatment" INTEGER NOT NULL DEFAULT 0 CHECK (initiated_hcv_treatment IN (0, 1)), -- not started hcv treatment
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"time_of_hcv_treatment_initiation" INTEGER NOT NULL DEFAULT -1,
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"num_hcv_treatment_starts" INTEGER NOT NULL DEFAULT 0,
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"num_hcv_treatment_withdrawals" INTEGER NOT NULL DEFAULT 0,
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"num_hcv_treatment_toxic_reactions" INTEGER NOT NULL DEFAULT 0,
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"num_completed_hcv_treatments" INTEGER NOT NULL DEFAULT 0,
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"num_hcv_salvages" INTEGER NOT NULL DEFAULT 0,
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"in_hcv_salvage_treatment" INTEGER NOT NULL DEFAULT 0 CHECK (in_hcv_salvage_treatment IN (0, 1)), -- not in hcv salvage treatment
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"initiated_hiv_treatment" INTEGER DEFAULT NULL,
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"time_of_hiv_treatment_initiation" INTEGER DEFAULT NULL,
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"num_hiv_treatment_starts" INTEGER DEFAULT NULL,
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"num_hiv_treatment_withdrawals" INTEGER DEFAULT NULL,
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"num_hiv_treatment_toxic_reactions" REAL DEFAULT NULL,
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"behavior_utility" REAL NOT NULL DEFAULT 1.0,
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"liver_utility" REAL NOT NULL DEFAULT 1.0,
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"treatment_utility" REAL NOT NULL DEFAULT 1.0,
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"background_utility" REAL NOT NULL DEFAULT 1.0,
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"moud_utility" REAL NOT NULL DEFAULT 1.0,
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"overdose_utility" REAL NOT NULL DEFAULT 1.0,
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"hiv_utility" REAL NOT NULL DEFAULT 1.0,
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"min_utility" REAL NOT NULL DEFAULT 0.0,
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"mult_utility" REAL NOT NULL DEFAULT 0.0,
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"discounted_min_utility" REAL NOT NULL DEFAULT 0.0,
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"discounted_mult_utility" REAL NOT NULL DEFAULT 0.0,
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"life_span" REAL NOT NULL DEFAULT 0.0,
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"discounted_life_span" REAL NOT NULL DEFAULT 0.0,
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"cost" REAL NOT NULL,
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"discount_cost" REAL NOT NULL DEFAULT 0.0,
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PRIMARY KEY("id"),
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FOREIGN KEY("sex") REFERENCES "sex"("id"),
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FOREIGN KEY("death_reasons") REFERENCES "death_reasons"("id"),
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FOREIGN KEY("drug_behavior") REFERENCES "drug_behaviors"("id"),
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FOREIGN KEY("hcv") REFERENCES "hcv_states"("id"),
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FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id"),
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FOREIGN KEY("moud_state") REFERENCES "moud"("id"),
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FOREIGN KEY("pregnancy_state") REFERENCES "pregnancy_states"("id"),
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FOREIGN KEY("measured_fibrosis_state") REFERENCES "fibrosis_diagnosis_states"("id"),
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FOREIGN KEY("hcv_link_state") REFERENCES "link_states"("id"),
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FOREIGN KEY("link_states") REFERENCES "link_states"("id")
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);
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DROP TABLE IF EXISTS "death_reasons";
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CREATE TABLE "death_reasons" (
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"id" INTEGER NOT NULL UNIQUE,
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"reason" TEXT NOT NULL UNIQUE,
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PRIMARY KEY ("id");
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);
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DROP TABLE IF EXISTS "link_states";
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CREATE TABLE "link_states" (
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"id" INTEGER NOT NULL UNIQUE,
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"state" TEXT NOT NULL UNIQUE,
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PRIMARY KEY ("id");
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);
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DROP TABLE IF EXISTS "antibody_testing";
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CREATE TABLE "antibody_testing" (
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"age_years" INTEGER NOT NULL,

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