Update pharmacokinetic parameters/calculations, add advanced settings, add disclaimer/citations, many improvements

src/constants/defaults.ts

@@ -8,13 +8,27 @@
  * @license MIT
  */
 
-export const LOCAL_STORAGE_KEY = 'medPlanAssistantState_v6';
-export const LDX_TO_DAMPH_CONVERSION_FACTOR = 0.2948;
+export const LOCAL_STORAGE_KEY = 'medPlanAssistantState_v7';
+
+// Pharmacokinetic Constants (from research literature)
+// MW ratio: 135.21 (d-amphetamine) / 455.60 (LDX dimesylate) = 0.29677
+export const LDX_TO_DAMPH_SALT_FACTOR = 0.29677;
+// Oral bioavailability for LDX (FDA label, 96.4%)
+export const DEFAULT_F_ORAL = 0.96;
 
 // Type definitions
+export interface AdvancedSettings {
+  weightBasedVd: { enabled: boolean; bodyWeight: string }; // kg
+  foodEffect: { enabled: boolean; tmaxDelay: string }; // hours
+  urinePh: { enabled: boolean; phTendency: string }; // 5.5-8.0 range
+  fOral: string; // bioavailability fraction
+  steadyStateDays: string; // days of medication history to simulate
+}
+
 export interface PkParams {
   damph: { halfLife: string };
-  ldx: { halfLife: string; absorptionRate: string };
+  ldx: { halfLife: string; absorptionHalfLife: string }; // renamed from absorptionRate
+  advanced: AdvancedSettings;
 }
 
 export interface DayDose {
@@ -82,7 +96,17 @@ export interface ConcentrationPoint {
 export const getDefaultState = (): AppState => ({
   pkParams: {
     damph: { halfLife: '11' },
-    ldx: { halfLife: '0.8', absorptionRate: '1.5' },
+    ldx: {
+      halfLife: '0.8',
+      absorptionHalfLife: '0.9' // changed from 1.5, better reflects ~1h Tmax
+    },
+    advanced: {
+      weightBasedVd: { enabled: false, bodyWeight: '70' }, // kg, adult average
+      foodEffect: { enabled: false, tmaxDelay: '1.0' }, // hours delay
+      urinePh: { enabled: false, phTendency: '6.0' }, // pH scale (5.5-8.0)
+      fOral: String(DEFAULT_F_ORAL), // 0.96 bioavailability
+      steadyStateDays: '7' // days of prior medication history
+    }
   },
   days: [
     {
@@ -96,15 +120,15 @@ export const getDefaultState = (): AppState => ({
       ]
     }
   ],
-  steadyStateConfig: { daysOnMedication: '7' },
-  therapeuticRange: { min: '10.5', max: '11.5' },
+  steadyStateConfig: { daysOnMedication: '7' }, // kept for backwards compatibility, now sourced from pkParams.advanced
+  therapeuticRange: { min: '5', max: '25' }, // widened from 10.5-11.5 to general adult range
   doseIncrement: '2.5',
   uiSettings: {
     showDayTimeOnXAxis: '24h',
     showTemplateDay: true,
     chartView: 'damph',
-    yAxisMin: '8',
-    yAxisMax: '13',
+    yAxisMin: '',
+    yAxisMax: '',
     simulationDays: '5',
     displayedDays: '2',
     showTherapeuticRange: true,