AI Coding Tools for CLIF

Multiple AI-assisted coding setups are available for CLIF development. Choose the one that fits your workflow.

Table of contents

1. Overview
2. Comparison
3. Option 1: Official CLIF Skills (Marketplace)
   1. Installation
   2. What’s Included
4. Option 2: Kaveri’s Claude Setup
   1. Installation
   2. What’s Included
   3. Best For
5. Option 3: J.C.’s clif_skills_agents
   1. Installation
   2. Auto-Detection
   3. 8 Rules That Prevent Cross-Site Bugs
   4. Best For
6. Quick Config Files
   1. Python (clif_config.json)
   2. R (config/config_template.yaml)
7. Which Should I Use?
8. Contributing

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Overview

The CLIF community has developed several AI coding assistant configurations. All include CLIF-specific knowledge (schema, mCIDE vocabularies, best practices) to help you write correct code faster.

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Comparison

	Official CLIF Skills	Kaveri’s claude-setup	J.C.’s clif_skills_agents
Repo	Common-Longitudinal-ICU-data-Format/skills	kaveriC/claude-setup	RushAI-jcr/clif_skills_agents
Install	Marketplace (/plugin install)	Copy files + marketplace skill	Copy files (standalone)
Platforms	Claude Code	Claude Code	Claude Code, Kilo Code (VS Code), Codex CLI
Languages	Python	Python	Python and R
Notebooks	—	—	marimo, Jupyter, Quarto, RMarkdown
CLIF Schema	Full mCIDE + schemas	References official skill	Full 2.1 schema embedded
Session Commands	—	/start-clif-session, /end-clif-session	/start-session, /end-session
Best For	Marketplace users	Quick Claude Code setup	Multi-platform teams, R users

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Option 1: Official CLIF Skills (Marketplace)

The canonical, consortium-maintained skill. Install via Claude Code’s plugin marketplace.

Installation

# Inside Claude Code
/plugin marketplace add Common-Longitudinal-ICU-data-Format/skills
/plugin install clif-icu@clif-skills

What’s Included

• Full CLIF 2.1 data dictionary
• mCIDE controlled vocabularies (labs, vitals, meds, etc.)
• YAML schema definitions
• clifpy API reference
• Example scripts

This is the recommended approach for most users. The skill is maintained by the consortium and stays up-to-date with CLIF schema changes.

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Option 2: Kaveri’s Claude Setup

A quick-start configuration that installs the official skill plus adds useful workflow features.

Installation

# Clone the repo
git clone https://github.com/kaveriC/claude-setup

# Copy global config
cp claude-setup/CLAUDE.md ~/.claude/CLAUDE.md
cp claude-setup/settings.json ~/.claude/settings.json
cp claude-setup/commands/*.md ~/.claude/commands/

# Install CLIF skills plugin (inside Claude Code)
/plugin marketplace add Common-Longitudinal-ICU-data-Format/skills
/plugin install clif-icu@clif-skills

What’s Included

File	Purpose
CLAUDE.md	Workflow rules: plan mode, verification, task tracking, lessons learned
settings.json	Extended thinking enabled, CLIF plugin, voice notification hook
commands/start-clif-session.md	/start-clif-session — reads progress, presents state
commands/end-clif-session.md	/end-clif-session — documents progress, saves lessons

Best For

Claude Code users who want:

• Structured session management
• Voice notifications when Claude finishes
• Built-in task tracking and lessons learned

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Option 3: J.C.’s clif_skills_agents

A comprehensive, multi-platform setup supporting Python, R, and multiple notebook types.

Installation

Claude Code (recommended):

cd your-clif-project/
cp -r /path/to/clif_skills_agents/.claude .claude
cp /path/to/clif_skills_agents/CLAUDE.md ./CLAUDE.md
cp /path/to/clif_skills_agents/SKILL.md ./SKILL.md

Kilo Code (VS Code):

cp /path/to/clif_skills_agents/AGENTS.md ./AGENTS.md
cp -r /path/to/clif_skills_agents/.kilocode .kilocode

Codex CLI:

cp /path/to/clif_skills_agents/AGENTS.md ./AGENTS.md

Auto-Detection

Just run /start-session — the assistant auto-detects your setup:

Your project files	Language	Notebook	Skills loaded
.py + marimo in pyproject.toml	Python	marimo	clif-data, python-dev, marimo, batch, figures
.ipynb only	Python	Jupyter	clif-data, python-dev, jupyter, figures
.R / .Rmd / renv.lock	R	RMarkdown	clif-data, r-dev, r-data-tooling, rmarkdown, figures
.qmd	R	Quarto	clif-data, r-dev, r-data-tooling, quarto, figures

8 Rules That Prevent Cross-Site Bugs

The assistant enforces critical rules automatically:

1. Filter on _category, never _name — Categories are the CLIF controlled vocabulary

2. Validate before analysis — Python: clif.validate_all()

   R: CLIF-TableOne

3. Use ADT for ICU times, not hospitalization — Filter adt where location_category == 'icu'
4. Log row counts at every filter step — CONSORT-style attrition tracking
5. Use encounter stitching — One ICU stay can span multiple hospitalization records
6. Distinguish continuous vs intermittent meds — Drips vs boluses
7. All timestamps are UTC — Timezone conversion is mandatory
8. JAMA figure style — Arial, 8pt min, no overlap, legends outside plot area

Best For

• R users — Only option with R support
• VS Code users — Works with Kilo Code extension
• Multi-notebook teams — Supports marimo, Jupyter, Quarto, RMarkdown
• Standalone setups — No marketplace dependency

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Quick Config Files

Python (clif_config.json)

{
  "data_directory": "/path/to/clif/parquet/files",
  "timezone": "US/Eastern",
  "site_name": "YOUR_SITE"
}

R (config/config_template.yaml)

site: "YOUR_SITE"
file_type: "parquet"
clif_data_path: "/path/to/clif/parquet/files"
site_time_zone: "US/Eastern"

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Which Should I Use?

Start with the Official CLIF Skills if you:

• Use Claude Code
• Want the consortium-maintained, always-up-to-date skill
• Prefer marketplace installation

Add Kaveri’s setup if you also want:

• Session management commands
• Voice notifications
• Task tracking built-in

Use J.C.’s clif_skills_agents if you:

• Need R support
• Use VS Code with Kilo Code
• Want a self-contained setup without marketplace
• Work with multiple notebook types

These are complementary! Kaveri’s setup actually installs the official skill. J.C.’s is a standalone alternative for broader platform coverage.

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Contributing

Have improvements to share? PRs welcome to any of these repos:

• Official CLIF Skills
• Kaveri’s claude-setup
• J.C.’s clif_skills_agents