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plot-survival

plot-survival is a command for Claude Code from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (293 once invoked), scanned A, original, MIT.

A command for analysing how long patients remain event-free, using Kaplan–Meier charts and Cox statistical models. It covers outcomes such as survival, prognosis, and risk over time.

In plain words
What is it for?
Use it to compare survival between groups, create Kaplan–Meier plots, test model assumptions, and report median survival, confidence intervals, log-rank results, and hazard ratios.
Why use it?
It helps avoid common analysis errors, such as reversed event labels, unsupported hazard ratios, missing risk information, and incorrect handling of competing causes of death.

Command for Claude Code

Written for Claude Code: allowed-tools in frontmatter. Also seen: positional $N argument.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to compare survival between groups, create Kaplan–Meier plots, test model assumptions, and report median survival, confidence intervals, log-rank results, and hazard ratios.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/zamushwani/biomedical-ai-skills/plot-survival
View source ↗ zamushwani/biomedical-ai-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.

Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

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 plot-survival

README.md
[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/plot-survival/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/plot-survival)
Your own site
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/plot-survival"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/plot-survival/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 plot-survival

Your own site · 80×15
<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/plot-survival"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/plot-survival.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 293 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 original 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 $0.00000 $0.00293
Opus 5.5 $0.00000 $0.00117
Sonnet 5.5 $0.00000 $0.00059
Haiku 4.5 $0.00000 $0.00029

Measured 2mo ago against content hash 1adc404368cf, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

plot-survival 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.

.claude/commands/plot-survival.md · 20 lines

What it actually says

Build survival analysis for $0, stratified by $1.

Follow the survival-analysis skill. The parts that are usually got wrong:

  1. Check the event coding. survival expects 1 = event, 0 = censored. A flipped indicator silently inverts every conclusion.
  2. Test the proportional hazards assumption with cox.zph() before reporting any hazard ratio. A violated PH assumption makes a single HR meaningless.
  3. Do not dichotomize a continuous variable at the median by reflex. If you use an optimal cutpoint, correct for the multiple testing it induces.
  4. Report median survival with its CI, the number at risk, and the log-rank p — a KM plot without a risk table is not interpretable.
  5. Use competing risks (Fine-Gray or cumulative incidence) when death from other causes is common; a naive KM overestimates the event probability.

Report: median survival per group with CI, log-rank p, hazard ratio with CI, and the PH test result.

If $0 is empty, ask which clinical table to use.

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 · 20 lines · 0 tokens per session scan A 1adc404368cf

Subscribe to this mod's changes

plot-survival is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 293 tokens. 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 2026-08-31.

Analytics and metricsDESeq2Scientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

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