[Feature] Pregnancy documentation

Doxyfile.in

@@ -1377,9 +1377,9 @@ HTML_STYLESHEET        =
 # documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = docs/doxygen-awesome-css/doxygen-awesome.css \
-                         docs/doxygen-awesome-css/doxygen-awesome-sidebar-only.css \
-                         docs/doxygen-awesome-css/doxygen-awesome-sidebar-only-darkmode-toggle.css \
+HTML_EXTRA_STYLESHEET  = @AWESOME_CSS_DIR@/doxygen-awesome.css \
+                         @AWESOME_CSS_DIR@/doxygen-awesome-sidebar-only.css \
+                         @AWESOME_CSS_DIR@/doxygen-awesome-sidebar-only-darkmode-toggle.css \
                          docs/src/custom.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or

docs/images/mermaid/pregnancy.mmd

@@ -0,0 +1,50 @@
+%%{init: {
+	"theme": "base",
+	"themeVariables": {
+		"background": "#000000",
+		"primaryColor": "#4299e1",
+		"primaryTextColor": "#ffffff",
+		"primaryBorderColor": "#1a365d",
+		"lineColor": "#4299e1",
+		"secondaryColor": "#4299e1",
+		"tertiaryColor": "#4299e1",
+		"edgeLabelBackground": "#000000",
+		"edgeLabelColor": "#4299e1"
+	}
+}}%%
+flowchart TD
+%% linkStyle default stroke:#4299e1,stroke-width:3px
+	start([Pregnancy::Execute]) ==> alive{"Is person alive, female, and older than 180 months?"}
+	alive == "No" ==> return([Return])
+	alive == "Yes" ==> old_age{"Is person older than 540 months and not pregnant/postpartum?"}
+	old_age == "Yes" ==> return_old_age([Return])
+	old_age == "No" ==> restricted_window{"Is person in a restricted postpartum (e.g. < 3 months since birth)?"}
+	restricted_window == "Yes" ==> return_restricted([Return])
+	restricted_window == "No" ==> pregnant{"Is person pregnant?"}
+	pregnant == "Yes" ==> gestation{"At least 9 months since conception?"}
+	gestation == "No" ==> return_gestation([Return])
+	gestation == "Yes" ==> stillbirth{"Is pregnancy a stillbirth?"}
+
+	stillbirth == "Yes" ==> stillbirth_action["Stillbirth: increment stillbirths; set restricted postpartum"]
+	stillbirth_action ==> return_stillbirth([Return])
+	stillbirth == "No" ==> delivery["Sample number of births: one or two"]
+	delivery ==> child_loop["For each child"]
+	child_loop ==> chronic_hcv{"Mother has chronic HCV?"}
+	chronic_hcv == "No" ==> make_child["Make child: no HCV, not tested"]
+	chronic_hcv == "Yes" ==> exposure["Add infant HCV exposure"]
+	exposure ==> tested{"Infant is tested?"}
+	tested == "Yes" ==> infection["Sample vertical HCV infection; make tested child"]
+	tested == "No" ==> no_test_infection["Sample vertical HCV infection; make untested child"]
+	make_child ==> birth["Birth: record child; state becomes restricted postpartum"]
+	infection ==> birth
+	no_test_infection ==> birth
+	birth ==> another_child{"More children?"}
+	another_child == "Yes" ==> child_loop
+	another_child == "No" ==> return_birth([Return])
+
+	pregnant == "No" ==> age_limit{"Age > 540 months?"}
+	age_limit == "Yes" ==> return_age([Return])
+	age_limit == "No" ==>  conception{"Is person impregnated?"}
+	conception == "No" ==> return_no_conception([Return])
+	conception == "Yes" ==> impregnate["Impregnate: increment pregnancy count; set pregnant"]
+	impregnate ==> return_conception([Return])

docs/src/events.md

@@ -117,6 +117,15 @@ HCV treatment focuses on actually treating patients for HCV. As such, it deals w
     src="hcv-treatment.png"
 />
 
+## Pregnancy
+
+Pregnancy is a new state to the original HEP-CE model. It accounts for confounding pregnancy details including pregnancy, post-partum, and infant HCV diagnoses.
+
+<img
+    class="flowchart"
+    src="pregnancy.png"
+/>
+
 ## Overdose
 
 Overdose focuses on all type overdoses for patients. We delegate the fatality functionality to the Death event, but instead focus exclusively on the impacts of all overdoses in this event. The primary function of this event loads data from the `overdose` table and then samples a decision based on the provided probability. If overdose occurs, then cost and utility is updated, if not nothing occurs.

extras/examples/inputs.db.sql

@@ -97,7 +97,7 @@ CREATE TABLE "population" (
     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_diagnosis_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"),
@@ -200,16 +200,16 @@ CREATE TABLE "fibrosis" (
 	"fib4"	REAL NOT NULL,
 	PRIMARY KEY("fibrosis_state","diagnosed_fibrosis"),
 	FOREIGN KEY("diagnosed_fibrosis") REFERENCES "fibrosis_diagnosis_states"("id"),
-	FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_real_states"("id")
+	FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id")
 );
 DROP TABLE IF EXISTS "fibrosis_diagnosis_states";
 CREATE TABLE "fibrosis_diagnosis_states" (
 	"id"	INTEGER NOT NULL UNIQUE,
 	"state"	TEXT NOT NULL,
 	PRIMARY KEY("id")
 );
-DROP TABLE IF EXISTS "fibrosis_real_states";
-CREATE TABLE "fibrosis_real_states" (
+DROP TABLE IF EXISTS "fibrosis_states";
+CREATE TABLE "fibrosis_states" (
 	"id"	INTEGER NOT NULL UNIQUE,
 	"state"	TEXT NOT NULL,
 	PRIMARY KEY("id")
@@ -221,7 +221,7 @@ CREATE TABLE "hcv_impacts" (
 	"cost"	REAL NOT NULL DEFAULT 0.0,
 	"utility"	REAL NOT NULL,
 	PRIMARY KEY("hcv_status","fibrosis_state"),
-	FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_real_states"("id"),
+	FOREIGN KEY("fibrosis_state") REFERENCES "fibrosis_states"("id"),
 	FOREIGN KEY("hcv_status") REFERENCES "bool_lookup"("id")
 );
 DROP TABLE IF EXISTS "hcv_states";
@@ -252,7 +252,8 @@ CREATE TABLE "init_cohort" (
 	"fibrosis_state"	INT,
 	"identified_as_hcv_positive"	INT,
 	"link_state"	INT,
-	"hcv_status"	INT
+	"hcv_status"	INT,
+    "pregnancy_state" INT
 );
 DROP TABLE IF EXISTS "link_states";
 CREATE TABLE "link_states" (
@@ -288,14 +289,18 @@ CREATE TABLE "pregnancy_states" (
 );
 DROP TABLE IF EXISTS "screening_and_linkage";
 CREATE TABLE "screening_and_linkage" (
-	"age_years"	INT,
-	"gender"	INT,
-	"drug_behavior"	INT,
-	"pregnancy"	INT,
-	"background_screen_probability"	REAL,
-	"background_link_probability"	REAL,
-	"intervention_screen_probability"	REAL,
-	"intervention_link_probability"	REAL
+	"age_years"	INT NOT NULL,
+	"gender"	INT NOT NULL,
+	"drug_behavior"	INT NOT NULL,
+	"pregnancy"	INT NOT NULL,
+	"background_screen_probability"	REAL NOT NULL,
+	"background_link_probability"	REAL NOT NULL,
+	"intervention_screen_probability"	REAL NOT NULL,
+	"intervention_link_probability"	REAL NOT NULL,
+    PRIMARY KEY("age_years", "gender", "drug_behavior", "pregnancy")
+    FOREIGN KEY("drug_behavior") REFERENCES "drug_behaviors"("id"),
+	FOREIGN KEY("gender") REFERENCES "sex"("id"),
+	FOREIGN KEY("pregnancy") REFERENCES "pregnancy_states"("id")
 );
 DROP TABLE IF EXISTS "sex";
 CREATE TABLE "sex" (
@@ -321,16 +326,15 @@ CREATE TABLE "treatment_initiations" (
 );
 DROP TABLE IF EXISTS "treatments";
 CREATE TABLE "treatments" (
-	"salvage"	INT,
-	"genotype_three"	INT,
-	"cirrhotic"	INT,
-	"course"	NUMERIC,
-	"duration"	INT,
-	"cost"	REAL,
-	"svr_prob_if_completed"	REAL,
-	"toxicity_prob_if_withdrawal"	REAL,
-	"withdrawal"	REAL,
-	"toxicity_prob"	REAL
+	"salvage" INT NOT NULL,
+	"genotype_three" INT NOT NULL,
+	"cirrhotic"	INT NOT NULL,
+	"course"	NUMERIC NOT NULL,
+	"duration"	INT NOT NULL,
+	"cost"	REAL NOT NULL,
+	"svr_prob_if_completed"	REAL NOT NULL,
+	"toxicity_prob_if_withdrawal"	REAL NOT NULL,
+	"withdrawal"	REAL NOT NULL
 );
 CREATE TABLE IF NOT EXISTS "moud_transitions" (
   "age_years" INTEGER NOT NULL,

extras/examples/sim.conf

@@ -13,10 +13,10 @@ use_population_table = true
 
 # A list of the discrete events to be used - order matters
 # Type: comma-separated strings
-# Default: Aging, BehaviorChanges, Clearance, FibrosisProgression, HCVInfection,
-# HCVScreening, HCVLinking, VoluntaryRelinking, FibrosisStaging, HCVTreatment,
-# Death
-events = Aging, BehaviorChanges, Clearance, FibrosisProgression, HCVInfection, HCVScreening, HCVLinking, FibrosisStaging, HCVTreatment, Death
+# Default: Aging, Pregnancy, BehaviorChanges, Clearance, FibrosisProgression, 
+# HCVInfection, HCVScreening, HCVLinking, VoluntaryRelinking, FibrosisStaging,
+# HCVTreatment, Death
+events = Aging, Pregnancy, BehaviorChanges, Clearance, FibrosisProgression, HCVInfection, HCVScreening, HCVLinking, FibrosisStaging, HCVTreatment, Death
 
 # The number of months for the simulation to run
 # Due to age restrictions, anything >=1200 is equivalent
@@ -345,6 +345,11 @@ tox_cost = 147.66
 # Type: float
 tox_utility = 0.21
 
+[pregnancy]
+multiple_delivery_probability = 0.03283
+infant_hcv_tested_probability = 0.4
+vertical_hcv_transition_probability = 0.08
+
 # This section governs general costing information throughout the simulation
 [cost]
 # The amount that costs are discounted in the model; scales such that earlier