alterlab-pymc

alterlab-pymc is a skill for Claude Code from AlterLab-IEU/AlterLab-Academic-Skills. It costs 86 tokens per session (2,001 once invoked), scanned A, original, MIT.

A Python library for Bayesian modeling, a way to combine prior knowledge with observed data to estimate uncertain quantities. It supports models with multiple groups, probability sampling, uncertainty checks, and comparisons between models.

In plain words
What is it for?
Use it to build Bayesian regressions, hierarchical models, time-series models, and models with missing or noisy measurements; estimate credible intervals; check predictions; and compare models.
Why use it?
It helps represent uncertainty directly instead of returning only one estimate. It also provides checks for whether the sampling process and the resulting model are trustworthy.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

Part of the alterlab-data-science plugin — 22 skills shipped together

Good fit Use it to build Bayesian regressions, hierarchical models, time-series models, and models with missing or noisy measurements; estimate credible intervals; check predictions; and compare models.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/alterlab-ieu/alterlab-academic-skills/alterlab-pymc
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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pymc
Clone the repo
git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

Made for: Claude Code.

Or install alterlab-data-science, the plugin that ships this one along with the rest of its 22 skills.

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 alterlab-pymc

README.md
[![agentmods](https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pymc/github.svg)](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pymc)
Your own site
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pymc"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-pymc/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 alterlab-pymc

Your own site · 80×15
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Per session 86 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,001 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. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 1 finding, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium analysis-evasion · line 1
    Suspicious Unicode normalization or mixed-script content
    Fix: Review the flagged content for security risks. Ensure no credentials, secrets, or sensitive data are exposed.
How audits are shown
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 $0.00086 $0.02001
Opus 5 $0.00043 $0.01001
Sonnet 5 $0.00017 $0.00400
Haiku 4.5 $0.00009 $0.00200

Measured 7d ago against content hash 6edfbb9dff97, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

alterlab-pymc 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 7d ago.

The scan reads SKILL.md. This mod also ships 4 executable files (assets/hierarchical_model_template.py, assets/linear_regression_template.py, scripts/model_comparison.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/data-science/alterlab-pymc/SKILL.md · 172 lines

How it starts

The opening of the file, as written. The whole thing — 172 lines — stays where its author put it; the contents beside it link to each section on GitHub.

PyMC Bayesian Modeling

Overview

PyMC is a Python library for Bayesian modeling and probabilistic programming. Build, fit, validate, and compare Bayesian models using PyMC's modern API (version 5.x+), including hierarchical models, MCMC sampling (NUTS), variational inference, and model comparison (LOO, WAIC).

When to Use This Skill

This skill should be used when:

  • Building Bayesian models (linear/logistic regression, hierarchical models, time series, etc.)
  • Performing MCMC sampling or variational inference
  • Conducting prior/posterior predictive checks
  • Diagnosing sampling issues (divergences, convergence, ESS)
  • Comparing multiple models using information criteria (LOO, WAIC)
  • Implementing uncertainty quantification through Bayesian methods
  • Working with hierarchical/multilevel data structures
  • Handling missing data or measurement error in a principled way

Standard Bayesian Workflow

Follow this 8-step workflow for building and validating Bayesian models:

  1. Data preparation — standardize predictors, handle missing data, set up coords
  2. Model building — weakly informative priors, named dims, pm.Data() for predictables
  3. Prior predictive checkpm.sample_prior_predictive; validate priors before fitting
  4. Fitpm.sample(draws=2000, tune=1000, chains=4, target_accept=0.9); include log_likelihood=True for comparison
  5. Diagnostics — R-hat < 1.01, ESS > 400, no divergences, good trace mixing
  6. Posterior predictive checkpm.sample_posterior_predictive; check fit vs. observed data
  7. Analyzeaz.summary, az.plot_posterior, az.plot_forest
  8. Predictpm.set_data then pm.sample_posterior_predictive; extract HDI intervals

Full step-by-step code: references/workflow_examples.md.

Common Model Patterns

PyMC supports linear/logistic/Poisson regression, hierarchical (multilevel) models, and time-series (AR). Ready-to-adapt code for each lives in references/model_patterns.md.

Critical: Always use non-centered parameterization for hierarchical models to avoid divergences. Templates: assets/linear_regression_template.py, assets/hierarchical_model_template.py.

Read the full file on GitHub · 172 lines

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. 7d ago First seen · 172 lines · 86 tokens per session scan A 6edfbb9dff97

Subscribe to this mod's changes

alterlab-pymc is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 6d ago), licensed MIT. It adds 86 tokens to every session and 2,001 once invoked, about $0.0004 per session on Opus 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 2026-09-03.

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