# ra-model

Run: `python3 ra_model.py`

## Code

```python
#!/usr/bin/env python3
"""
RA-MODEL: Comprehensive Rheumatoid Arthritis Disease Model
DAS28-CRP/ESR, CDAI, SDAI, Boolean Remission, HAQ-DI, RAPID3, EQ-5D.
Treat-to-Target temporal milestones per ACR/EULAR 2023.

x402 Pricing (Base L2, USDC):
  Single assessment: $1.50
  Longitudinal (4 visits): $5.00
  Full study protocol (per patient): $12.00

Authors: Zamora-Tehozol EA (ORCID:0000-0002-7888-3961), DNAI
"""
import math
import numpy as np
from dataclasses import dataclass
from typing import List, Optional

@dataclass
class RAAssessment:
    visit: str
    tjc28: int = 0
    sjc28: int = 0
    crp: float = 0.0  # mg/L
    esr: float = 0.0  # mm/hr
    pga: float = 0.0  # patient global 0-100 VAS
    ega: float = 0.0  # evaluator global 0-100 VAS
    pain_vas: float = 0.0  # 0-100
    haq: float = 0.0  # 0-3
    eq5d_vas: int = 100
    morning_stiffness_min: int = 0

def das28_crp(a):
    s = 0.56*math.sqrt(a.tjc28) + 0.28*math.sqrt(a.sjc28) + 0.36*math.log(a.crp+1) + 0.014*a.pga + 0.96
    if s < 2.6: cat = "Remission"
    elif s < 3.2: cat = "Low activity"
    elif s < 5.1: cat = "Moderate activity"
    else: cat = "High activity"
    return {"score": round(s, 2), "category": cat}

def das28_esr(a):
    s = 0.56*math.sqrt(a.tjc28) + 0.28*math.sqrt(a.sjc28) + 0.70*math.log(max(1,a.esr)) + 0.014*a.pga
    if s < 2.6: cat = "Remission"
    elif s < 3.2: cat = "Low activity"
    elif s < 5.1: cat = "Moderate activity"
    else: cat = "High activity"
    return {"score": round(s, 2), "category": cat}

def cdai(a):
    s = a.tjc28 + a.sjc28 + a.pga/10 + a.ega/10
    if s <= 2.8: cat = "Remission"
    elif s <= 10: cat = "Low activity"
    elif s <= 22: cat = "Moderate activity"
    else: cat = "High activity"
    return {"score": round(s, 1), "category": cat}

def sdai(a):
    s = a.tjc28 + a.sjc28 + a.pga/10 + a.ega/10 + a.crp/10
    if s <= 3.3: cat = "Remission"
    elif s <= 11: cat = "Low activity"
    elif s <= 26: cat = "Moderate activity"
    else: cat = "High activity"
    return {"score": round(s, 1), "category": cat}

def boolean_remission(a):
    criteria = {
        "TJC28 <= 1": a.tjc28 <= 1,
        "SJC28 <= 1": a.sjc28 <= 1,
        "CRP <= 1 mg/dL": a.crp <= 10,  # 1 mg/dL = 10 mg/L
        "PGA <= 1 (0-10)": a.pga <= 10,
    }
    return {"remission": all(criteria.values()), "criteria": criteria}

def rapid3(a):
    """RAPID3 = HAQ-DI functional + pain VAS + patient global"""
    fn = min(10, a.haq * 3.33)
    pain = a.pain_vas / 10
    pga = a.pga / 10
    total = fn + pain + pga
    if total <= 3: cat = "Near remission"
    elif total <= 6: cat = "Low activity"
    elif total <= 12: cat = "Moderate activity"
    else: cat = "High activity"
    return {"score": round(total, 1), "category": cat, "max": 30}

def treat_to_target(visits: List[RAAssessment]):
    """ACR/EULAR T2T: assess every 3 months, target remission or LDA by 6 months"""
    results = []
    for v in visits:
        d28 = das28_crp(v)
        cd = cdai(v)
        sd = sdai(v)
        br = boolean_remission(v)
        r3 = rapid3(v)
        haq_cat = "Normal" if v.haq < 0.5 else "Mild" if v.haq < 1.0 else "Moderate" if v.haq < 2.0 else "Severe"
        
        results.append({
            "visit": v.visit,
            "composite_indices": {
                "DAS28-CRP": d28,
                "DAS28-ESR": das28_esr(v),
                "CDAI": cd,
                "SDAI": sd,
            },
            "remission": {
                "Boolean": br,
                "DAS28 remission": d28["score"] < 2.6,
                "CDAI remission": cd["score"] <= 2.8,
            },
            "PROs": {
                "HAQ-DI": {"score": v.haq, "category": haq_cat},
                "RAPID3": r3,
                "Pain VAS": v.pain_vas,
                "EQ-5D VAS": v.eq5d_vas,
                "Morning stiffness": f"{v.morning_stiffness_min} min",
            },
        })
    
    # T2T assessment
    if len(visits) >= 2:
        baseline_das = das28_crp(visits[0])["score"]
        latest_das = das28_crp(visits[-1])["score"]
        improvement = baseline_das - latest_das
        good_response = improvement > 1.2 and latest_das < 3.2
        moderate_response = improvement > 0.6
        
        t2t = {
            "DAS28 change": round(improvement, 2),
            "EULAR response": "Good" if good_response else "Moderate" if moderate_response else "No response",
            "Target met (remission or LDA)": latest_das < 3.2,
            "Action": "Continue current therapy" if latest_das < 3.2 else "Consider treatment escalation per ACR/EULAR T2T",
        }
    else:
        t2t = {"note": "Single visit — T2T requires longitudinal data"}
    
    return {"visits": results, "treat_to_target": t2t}


if __name__ == "__main__":
    print("=" * 70)
    print("RA-MODEL: Comprehensive Rheumatoid Arthritis Disease Model")
    print("DAS28 + CDAI + SDAI + Boolean + RAPID3 + HAQ + T2T")
    print("=" * 70)
    
    visits = [
        RAAssessment(visit="Baseline", tjc28=12, sjc28=8, crp=35, esr=48,
                     pga=72, ega=68, pain_vas=75, haq=1.6, eq5d_vas=35, morning_stiffness_min=90),
        RAAssessment(visit="Week 12", tjc28=6, sjc28=4, crp=12, esr=22,
                     pga=45, ega=40, pain_vas=48, haq=1.0, eq5d_vas=55, morning_stiffness_min=30),
        RAAssessment(visit="Week 24", tjc28=2, sjc28=1, crp=4, esr=10,
                     pga=18, ega=15, pain_vas=20, haq=0.5, eq5d_vas=72, morning_stiffness_min=10),
        RAAssessment(visit="Week 52", tjc28=1, sjc28=0, crp=2, esr=8,
                     pga=8, ega=5, pain_vas=10, haq=0.25, eq5d_vas=85, morning_stiffness_min=5),
    ]
    
    analysis = treat_to_target(visits)
    
    for v in analysis["visits"]:
        print(f"\n{'─' * 50}")
        print(f"  {v['visit']}")
        ci = v["composite_indices"]
        print(f"  DAS28-CRP: {ci['DAS28-CRP']['score']} ({ci['DAS28-CRP']['category']})")
        print(f"  DAS28-ESR: {ci['DAS28-ESR']['score']} ({ci['DAS28-ESR']['category']})")
        print(f"  CDAI: {ci['CDAI']['score']} ({ci['CDAI']['category']})")
        print(f"  SDAI: {ci['SDAI']['score']} ({ci['SDAI']['category']})")
        r = v["remission"]
        print(f"  Boolean Remission: {'✅' if r['Boolean']['remission'] else '❌'}")
        p = v["PROs"]
        print(f"  HAQ: {p['HAQ-DI']['score']} ({p['HAQ-DI']['category']}) | RAPID3: {p['RAPID3']['score']}")
        print(f"  Pain: {p['Pain VAS']} | EQ-5D: {p['EQ-5D VAS']} | Stiffness: {p['Morning stiffness']}")
    
    t = analysis["treat_to_target"]
    print(f"\n{'=' * 50}")
    print(f"  TREAT-TO-TARGET")
    print(f"  DAS28 change: -{t.get('DAS28 change', '?')}")
    print(f"  EULAR response: {t.get('EULAR response', '?')}")
    print(f"  Target met: {t.get('Target met (remission or LDA)', '?')}")
    print(f"  Action: {t.get('Action', '?')}")
    
    print(f"\n{'=' * 70}")
    print("x402 Pricing: Single $1.50 | Longitudinal $5.00 | Study $12.00 USDC")
    print("\nRefs:")
    print("  [1] Prevoo MLL et al. Arthritis Rheum 1995;38:44-8 (DAS28)")
    print("  [2] Aletaha D et al. Arthritis Rheum 2005;52:2625-36 (CDAI/SDAI)")
    print("  [3] Felson DT et al. Arthritis Rheum 2011;63:573-86 (Boolean)")
    print("  [4] Smolen JS et al. Ann Rheum Dis 2023;82:3-18 (EULAR T2T) DOI:10.1136/ard-2022-223356")
    print("  [5] Pincus T et al. J Rheumatol 2008;35:2136-47 (RAPID3)")
    print("=" * 70)

```

## Demo

```

DAS28 + CDAI + SDAI + Boolean + RAPID3 + HAQ + T2T
======================================================================

──────────────────────────────────────────────────
  Baseline
  DAS28-CRP: 5.99 (High activity)
  DAS28-ESR: 6.45 (High activity)
  CDAI: 34.0 (High activity)
  SDAI: 37.5 (High activity)
  Boolean Remission: ❌
  HAQ: 1.6 (Moderate) | RAPID3: 20.0
  Pain: 75 | EQ-5D: 35 | Stiffness: 90 min

──────────────────────────────────────────────────
  Week 12
  DAS28-CRP: 4.45 (Moderate activity)
  DAS28-ESR: 4.73 (Moderate activity)
  CDAI: 18.5 (Moderate activity)
  SDAI: 19.7 (Moderate activity)
  Boolean Remission: ❌
  HAQ: 1.0 (Moderate) | RAPID3: 12.6
  Pain: 48 | EQ-5D: 55 | Stiffness: 30 min

──────────────────────────────────────────────────
  Week 24
  DAS28-CRP: 2.86 (Low activity)
  DAS28-ESR: 2.94 (Low activity)
  CDAI: 6.3 (Low activity)
  SDAI: 6.7 (Low activity)
  Boolean Remission: ❌
  HAQ: 0.5 (Mild) | RAPID3: 5.5
  Pain: 20 | EQ-5D: 72 | Stiffness: 10 min

──────────────────────────────────────────────────
  Week 52
  DAS28-CRP: 2.03 (Remission)
  DAS28-ESR: 2.13 (Remission)
  CDAI: 2.3 (Remission)
  SDAI: 2.5 (Remission)
  Boolean Remission: ✅
  HAQ: 0.25 (Normal) | RAPID3: 2.6
  Pain: 10 | EQ-5D: 85 | Stiffness: 5 min

==================================================
  TREAT-TO-TARGET
  DAS28 change: -3.96
  EULAR response: Good
  Target met: True
  Action: Continue current therapy

======================================================================
x402 Pricing: Single $1.50 | Longitudinal $5.00 | Study $12.00 USDC

Refs:
  [1] Prevoo MLL et al. Arthritis Rheum 1995;38:44-8 (DAS28)
  [2] Aletaha D et al. Arthritis Rheum 2005;52:2625-36 (CDAI/SDAI)
  [3] Felson DT et al. Arthritis Rheum 2011;63:573-86 (Boolean)
  [4] Smolen JS et al. Ann Rheum Dis 2023;82:3-18 (EULAR T2T) DOI:10.1136/ard-2022-223356
  [5] Pincus T et al. J Rheumatol 2008;35:2136-47 (RAPID3)
======================================================================

```