analysis-methods

Development

Teaches the analyst agent how to write correct, robust Python analysis code for FHIR clinical data using pandas, matplotlib, and scipy.

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How to use this skill

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Prompt to paste

I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/NVIDIA/dgx-spark-playbooks/blob/HEAD/nvidia/station-healthcare-agent/assets/skills/analysis-methods/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/analysis-methods/. Do not write files or run scripts until I approve.

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Analysis Code Guidelines

FHIR Helpers Library

Always import the helpers library at the top of every analysis script:

import sys
sys.path.insert(0, '/sandbox/clinical-intelligence/skills/analysis-methods/scripts')
from fhir_helpers import *

Available functions

Function	Use for	HTTP calls
`get_patients_with_condition(snomed_code)`	Find patients with a condition → list of IDs	1-2
`get_latest_labs_batch(loinc_code, patient_ids)`	Labs for a cohort → dict: pid → (value, unit, date)	1-2
`get_all_medications_batch(patient_ids)`	Meds for a cohort → dict: pid → [med names]	1-2
`build_cohort_df(patient_ids, loinc, lab_name, drug_check_fn)`	Full DataFrame with labs + meds	2-3
`get_latest_lab(patient_id, loinc_code)`	Lab for ONE patient → (value, unit, date)	1
`get_medications(patient_id)`	Meds for ONE patient → [names]	1
`get_latest_bp(patient_id)`	BP for ONE patient → (sys, dia, date)	1-2
`check_drug_class(med_list, drug_names)`	Check if any med matches drug list → bool	0
`fhir_get(path, params)`	Raw FHIR GET → parsed JSON	1
`get_all_pages(path, params)`	Paginated FHIR GET → all entries	1+
`save_chart_to_canvas(fig, filename)`	Save matplotlib figure to canvas directory	0

Performance rules

Cohort queries (2+ patients): Use get_latest_labs_batch() and get_all_medications_batch(). These make 1-2 HTTP calls total regardless of patient count.
Single patient: Use get_latest_lab(), get_medications(), get_latest_bp().
NEVER loop over patients calling get_latest_lab() per patient. Each HTTP call through the sandbox proxy adds 1-3s. For 48 patients = 48 calls = 2+ minutes. The batch function does it in one call.

Execution Rules

Run scripts with python (NOT python3)
Write a SINGLE Python script for the entire task
Write the script to /tmp/<name>.py, then execute it
All HTTP inside the sandbox must use subprocess.run(["curl", ...]) — the requests library does NOT work

Mandatory Workflow

STEP 1 - WRITE SCRIPT (import fhir_helpers, write analysis)
STEP 2 - VALIDATE: python /sandbox/clinical-intelligence/scripts/validate_and_run.py --validate-only /tmp/<name>.py
STEP 3 - EXECUTE: python /tmp/<name>.py
STEP 4 - INTERPRET: explain results using clinical-knowledge skill

Code Structure

Imports (always start with fhir_helpers import)
Data collection (use batch functions)
DataFrame construction
Analysis (filters, aggregations)
Visualization -- use save_chart_to_canvas(fig, filename) (NOT plt.savefig)
Summary (print findings)
Disclaimer

Care Gap Analysis Pattern

# Example: diabetes care gap
patients = get_patients_with_condition("44054006")  # SNOMED for diabetes
df = build_cohort_df(patients, "4548-4", "HbA1c",
                     lambda meds: check_drug_class(meds, ["metformin", "insulin", "glipizide"]))

gap = df[(df['HbA1c'] > 9) & (~df['on_target_med'])]
denom = len(df[df['HbA1c'].notna()])
pct = f"{len(gap)/denom*100:.1f}%" if denom > 0 else "N/A (no HbA1c data)"
print(f"Care gap: {len(gap)}/{denom} ({pct})")

Visualization

Always use dark theme. Use save_chart_to_canvas() instead of plt.savefig() directly.

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

plt.style.use('dark_background')
fig, ax = plt.subplots(figsize=(10, 6))
fig.patch.set_facecolor('#1a1a1a')
ax.set_facecolor('#1a1a1a')

# Histogram with NVIDIA green
ax.hist(values, bins=15, color='#76B900', edgecolor='#1a1a1a', alpha=0.85)
ax.axvline(x=threshold, color='#ff4444', linestyle='--', linewidth=2, label=f'Threshold ({threshold})')
ax.set_title("Title", fontsize=14, fontweight='bold', color='white')
ax.legend()
ax.grid(axis='y', alpha=0.2, color='#444444')
ax.text(0.98, 0.95, f"N = {len(values)}", transform=ax.transAxes, fontsize=11, color='#888888', ha='right', va='top')

# MANDATORY: use save_chart_to_canvas (NOT plt.savefig)
save_chart_to_canvas(fig, "chart.png")
plt.close()

Guardrails

Never compute statistics on fewer than 5 data points
Always report sample size: "45.0% (27 out of 60)"
Flag data quality issues if >30% missing
Do not fabricate data — report what exists, flag what's missing
All charts must include N annotation

Output Format

End every script with:

print(f"\nDisclaimer: This analysis is for research and operational purposes.")
print("Clinical decisions should be made by qualified clinicians.")