# Read current.yaml for active medications, conditions, supplements
cat "{health_log_path}/current.yaml"

# Last 100 CSV entries from history.csv to identify recent patterns
tail -100 "{health_log_path}/history.csv"

# Recent narrative entries for context
tail -200 "{health_log_path}/health_log.md" | head -150

# From current.yaml (preferred - source of truth)
grep -A 100 "^conditions:" "{health_log_path}/current.yaml"

# From history.csv (for timeline analysis)
grep -E ",(condition|symptom)," "{health_log_path}/history.csv" | tail -50

# From current.yaml (preferred - source of truth)
grep -A 100 "^medications:" "{health_log_path}/current.yaml"
grep -A 100 "^supplements:" "{health_log_path}/current.yaml"

# From history.csv (for timeline analysis)
grep -E ",(medication|supplement)," "{health_log_path}/history.csv" | tail -50

# Health Log Augmentation Questionnaire
**Profile**: {name}
**Generated**: {YYYY-MM-DD}
**Purpose**: Systematic data collection to enrich existing health log entries

---

## Instructions

This questionnaire is designed to be completed iteratively...

[Instructions for use]

---

## Section 1: [Section Name]

### 1.1 [Subsection]

**[Question Category]:**
- [ ] Question 1
- [ ] Question 2

[Tables, forms, or structured data collection templates]

---

[Repeat for all sections]

---

## Next Steps

After completing relevant sections:

1. **Update health log entries** with new details
2. **Generate targeted analyses** using health-agent skills:
   - Use lab queries (see `analysis-patterns.md`) for markers with clarified patterns
   - Investigate episodes with enriched context
   - Identify cross-temporal correlations using data patterns
   - Run `investigate-root-cause` for conditions with new context
3. **Create provider reports** with augmented data (use `prepare-provider-visit`)
4. **Consider additional testing** based on gaps identified
5. **Set up prospective tracking** for patterns to monitor going forward

---

**Questionnaire Version**: 1.0
**Last Updated**: {YYYY-MM-DD}
**Status**: Initial draft for iterative completion

# Count entries by type
echo "=== Data Inventory ==="

# From current.yaml (current state)
echo "Current Medications: $(grep -c '^\s*-\s*name:' <(grep -A 100 '^medications:' "$current_yaml" 2>/dev/null) 2>/dev/null || echo 0)"
echo "Current Supplements: $(grep -c '^\s*-\s*name:' <(grep -A 100 '^supplements:' "$current_yaml" 2>/dev/null) 2>/dev/null || echo 0)"
echo "Current Conditions: $(grep -c '^\s*-\s*name:' <(grep -A 100 '^conditions:' "$current_yaml" 2>/dev/null) 2>/dev/null || echo 0)"

# From history.csv (timeline)
echo "Historical Medications: $(grep -c ',medication,' "$history_csv")"
echo "Historical Supplements: $(grep -c ',supplement,' "$history_csv")"
echo "Historical Symptoms: $(grep -c ',symptom,' "$history_csv")"
echo "Historical Conditions: $(grep -c ',condition,' "$history_csv")"
echo "Labs: $(wc -l < "$labs_csv" | tr -d ' ')"
echo "Exams: $(find "$exams_path" -name "*.summary.md" | wc -l | tr -d ' ')"
echo "Entities: $(grep -oE 'entity_[0-9]+' "$history_csv" | sort -u | wc -l | tr -d ' ')"

# Find medications without discontinuation reason (from history.csv)
grep ',medication,' "$history_csv" | \
  grep -iE 'stopped|discontinued|ended' | \
  grep -viE 'reason|because|due to|side effect' | \
  awk -F',' '{print $1, $2, $3, $5}'

# Find recurring symptoms without pattern info (from history.csv)
grep ',symptom,' "$history_csv" | \
  awk -F',' '{print $3}' | \
  sort | uniq -c | sort -rn | \
  awk '$1 > 3 {print $0}'
# These recurring symptoms need pattern questions

# Find abnormal labs not repeated (from all.csv)
awk -F',' 'NR>1 && ($5<$7 || $5>$8) {print $1, $4}' "$labs_csv" | \
  sort -t' ' -k2 | \
  uniq -f1 -c | \
  awk '$1 == 1 {print "Single abnormal:", $2, $3}'

Gap Score = Clinical_Value × Fillability × Urgency

Priority Score = Clinical_Value × Fillability × Urgency
Max score = 5 × 3 × 3 = 45

# Pseudocode for domain prioritization
domain_scores = {}
for gap in identified_gaps:
    domain = gap.domain  # e.g., "medications", "symptoms"
    score = gap.clinical_value * gap.fillability * gap.urgency
    domain_scores[domain] = domain_scores.get(domain, 0) + score

# Sort domains by total score
prioritized_domains = sorted(domain_scores.items(), key=lambda x: x[1], reverse=True)

### Family History: {Condition}

Your health log indicates {condition}. Family history is important for understanding your risk.

**First-degree relatives (parents, siblings, children):**
- [ ] Mother: {condition}? Age at diagnosis? Current status?
- [ ] Father: {condition}? Age at diagnosis? Current status?
- [ ] Siblings: Any with {condition}? Details:
- [ ] Children: Any with {condition}? Details:

**Second-degree relatives (grandparents, aunts/uncles):**
- [ ] Any known cases of {condition}?

### Medication: {Name}

You've been taking {medication}. Please fill in any missing details:

| Question | Your Answer |
|----------|-------------|
| Exact dose | |
| Frequency | |
| Date started | |
| Why prescribed | |
| How well does it work? (1-5) | |
| Any side effects? | |
| Have you ever missed doses? How often? | |

### Symptom: {Symptom Name}

This symptom has appeared {count} times in your records. Help us understand the pattern:

**Severity Scale** (use for each occurrence):
1 = Barely noticeable
2 = Mild, doesn't affect activities
3 = Moderate, somewhat limits activities
4 = Severe, significantly limits activities
5 = Extreme, incapacitating

**Pattern Questions**:
- Time of day most common: [ ] Morning [ ] Afternoon [ ] Evening [ ] Night [ ] No pattern
- Duration typically: [ ] Minutes [ ] Hours [ ] Days [ ] Constant
- What makes it better?:
- What makes it worse?:
- Associated symptoms:

**Occurrence Log** (fill in for recent episodes):
| Date | Severity (1-5) | Trigger (if known) | What helped |
|------|----------------|-------------------|-------------|
| | | | |

# Health Log Augmentation Questionnaire
**Profile**: Jane Doe
**Generated**: 2026-01-23
**Purpose**: Systematic data collection to enrich existing health log entries

---

## Instructions

This questionnaire targets specific gaps identified in your health records. You don't
need to complete everything at once—work through sections as you have time. For each
question, answer as completely as you can; if uncertain, mark with [UNCERTAIN].

**Priority indicators**:
- 🔴 CRITICAL: Important for upcoming care decisions
- 🟡 HIGH: Significantly improves health understanding
- 🟢 MEDIUM: Helpful context

---

## Section 1: Family History 🔴 CRITICAL

*Gap detected: Your records show elevated bilirubin and suspected Gilbert syndrome,
but no family history is documented. Gilbert syndrome is genetic.*

### 1.1 Gilbert Syndrome / Jaundice

Do any blood relatives have:
- [ ] Gilbert syndrome (diagnosed)
- [ ] History of jaundice (yellowing of eyes/skin)
- [ ] Unexplained elevated bilirubin

**If yes, please specify:**

| Relative | Condition | Age at Diagnosis | Notes |
|----------|-----------|------------------|-------|
| | | | |

### 1.2 Anemia / Blood Disorders

Have any blood relatives been diagnosed with:
- [ ] Hereditary spherocytosis
- [ ] Sickle cell disease or trait
- [ ] Thalassemia
- [ ] G6PD deficiency
- [ ] Other hemolytic anemia
- [ ] Iron deficiency requiring treatment
- [ ] Needed their spleen removed

**If yes, please specify relationship and details:**

---

## Section 2: Medication Responses 🟡 HIGH

*Gap detected: Several medications were discontinued without documented reasons.*

### 2.1 Discontinued Medications

Please provide details for each medication you stopped:

**Omeprazole** (appears stopped around 2025-06)
- Why did you stop? [ ] Side effects [ ] Not effective [ ] No longer needed [ ] Cost [ ] Other
- If side effects, what were they?:
- Would you take it again if needed? [ ] Yes [ ] No [ ] Maybe

**Vitamin D 2000 IU** (appears stopped around 2025-09)
- Why did you stop?:
- Current vitamin D status: [ ] Taking different form [ ] Not taking any [ ] Unknown

### 2.2 Current Medication Efficacy

For medications you're currently taking, rate effectiveness:

| Medication | Works Well (1-5) | Any Side Effects? | Would Recommend? |
|------------|------------------|-------------------|------------------|
| Lisinopril 10mg | | | |
| Metformin 500mg | | | |

---

## Section 3: Symptom Deep Dive 🟡 HIGH

*Gap detected: "Fatigue" appears 8 times without characterization.*

### 3.1 Fatigue Pattern Analysis

Your records show fatigue mentioned on: 2025-03-15, 2025-04-02, 2025-05-18,
2025-06-30, 2025-08-12, 2025-09-25, 2025-11-08, 2026-01-05

**Severity by episode** (use scale 1-5):
| Date | Severity | Duration | Possible Trigger |
|------|----------|----------|------------------|
| 2025-03-15 | | | |
| 2025-04-02 | | | |
| [continue...] | | | |

**Pattern Questions**:
- Worse at specific times? [ ] Morning [ ] Afternoon [ ] Evening [ ] Variable
- Related to sleep quality? [ ] Yes [ ] No [ ] Uncertain
- Related to meals? [ ] Yes [ ] No [ ] Uncertain
- Related to stress? [ ] Yes [ ] No [ ] Uncertain
- Relieved by rest? [ ] Yes [ ] No [ ] Partially

**Associated symptoms when fatigued**:
- [ ] Brain fog / difficulty concentrating
- [ ] Muscle weakness
- [ ] Headache
- [ ] Dizziness
- [ ] Other:

---

## Section 4: Lab Correlations 🟢 MEDIUM

*Gap detected: Abnormal values without follow-up context.*

### 4.1 Elevated Bilirubin

Your bilirubin has been elevated on multiple tests. Please document:

- Do you notice yellowing of eyes when bilirubin is high? [ ] Yes [ ] No [ ] Never checked
- Does it correlate with: [ ] Fasting [ ] Stress [ ] Illness [ ] Exercise [ ] Unknown
- Have you ever been told you have Gilbert syndrome? [ ] Yes [ ] No [ ] Suspected

### 4.2 Missing Tests

Based on your conditions, these tests might be informative but aren't in your records:

| Test | Would you be willing to get this? | Notes |
|------|-----------------------------------|-------|
| Reticulocyte count | [ ] Yes [ ] No [ ] Already done | |
| Haptoglobin | [ ] Yes [ ] No [ ] Already done | |
| LDH | [ ] Yes [ ] No [ ] Already done | |
| Direct Coombs | [ ] Yes [ ] No [ ] Already done | |

---

## Section 5: Open-Ended 🟢 MEDIUM

### 5.1 Anything Else?

Is there anything about your health that:
- You've been meaning to document but haven't?
- You think is important but doesn't fit standard categories?
- You've noticed as a pattern but aren't sure is significant?

**Space for notes:**




---

## Next Steps

After completing relevant sections:

1. **Update health log entries** with new details using health-log-parser
2. **Run targeted analyses** with enriched data
3. **Consider investigate-root-cause** for conditions with new family history
4. **Prepare provider visit** using `prepare-provider-visit` with augmented data
5. **Schedule recommended tests** identified in Section 4.2

---

**Questionnaire Version**: 1.0
**Generated**: 2026-01-23
**Priority Gaps Identified**: 12
**Estimated Completion Time**: 20-30 minutes