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sdtm-oak

sdtm-oak is a skill for Claude Code, Codex from RConsortium/pharma-skills. It costs 113 tokens per session (4,390 once invoked), scanned A, original, no licence file.

A skill for turning raw clinical study data from electronic data capture forms or electronic health records into CDISC SDTM datasets using the sdtm.oak R package. SDTM is a standard format for submitting clinical-trial data to regulators.

In plain words
What is it for?
Creating SDTM Events, Findings, and Interventions domains, including adverse events, medications, medical history, vital signs, laboratory results, ECGs, and exposure, as executable R code.
Why use it?
It removes much of the manual work involved in mapping study data into the required SDTM structure.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 137repo +8 14d ago A scan 113 tokens no licence

Good fit Creating SDTM Events, Findings, and Interventions domains, including adverse events, medications, medical history, vital signs, laboratory results, ECGs, and exposure, as executable R code.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/rconsortium/pharma-skills/sdtm-oak
View source ↗ RConsortium/pharma-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add RConsortium/pharma-skills --skill sdtm-oak
Clone the repo
git clone --depth 1 https://github.com/RConsortium/pharma-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for sdtm-oak

README.md
[![agentmods](https://agentmods.dev/badge/skills/rconsortium/pharma-skills/sdtm-oak/github.svg)](https://agentmods.dev/skills/rconsortium/pharma-skills/sdtm-oak)
Your own site
<a href="https://agentmods.dev/skills/rconsortium/pharma-skills/sdtm-oak"><img src="https://agentmods.dev/badge/skills/rconsortium/pharma-skills/sdtm-oak/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for sdtm-oak

Your own site · 80×15
<a href="https://agentmods.dev/skills/rconsortium/pharma-skills/sdtm-oak"><img src="https://agentmods.dev/badge/skills/rconsortium/pharma-skills/sdtm-oak.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 113 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,390 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00113 $0.04390
Opus 5.5 $0.00045 $0.01756
Sonnet 5.5 $0.00023 $0.00878
Haiku 4.5 $0.00011 $0.00439

Measured 2mo ago against content hash 0eff740690a7, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

sdtm-oak scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

sdtm-oak/SKILL.md · 461 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 461 lines · 113 tokens per session scan A 0eff740690a7

Subscribe to this mod's changes

sdtm-oak is a skill published in the GitHub repository RConsortium/pharma-skills (137 stars, last pushed 14d ago), with no licence file. It adds 113 tokens to every session and 4,390 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific
Related

sdtm-oak compared with skills from other repositories

sdtm-oak next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
sdtm-oakRConsortium/pharma-skillsSkill13714d agononeA113Claude Code, Codex
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k2d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code