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Merged
MJC598 merged 4 commits into from
Nov 4, 2025
Merged

Population Schema #148

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4698dbe
Adding in the population, death reason, and linking tables to the exa…
MJC598 Nov 4, 2025
da0d2dd
Addressing PR comments
MJC598 Nov 4, 2025
77e32d5
Addressing other PR comment
MJC598 Nov 4, 2025
1d1f54c
lmao love how I literally created the descrepency you were asking about
MJC598 Nov 4, 2025
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126 changes: 117 additions & 9 deletions extras/examples/inputs.db.sql
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Original file line number Diff line number Diff line change
@@ -1,13 +1,121 @@
/*
* Filename: /home/matt/Repos/hep-ce/extras/examples/inputs.db.sql
* Path: /home/matt/Repos/hep-ce/extras/examples
* Created Date: Thursday, June 12th 2025, 2:53:18 pm
* Author: Matthew Carroll
*
* Copyright (c) 2025 Syndemics Lab
*/

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