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power-optimization-patterns
Direct and tradeoff-based optimization strategies for clinical trial design. Use when optimizing sample size, selecting design parameters, or performing sensitivity analysis.
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GitHub
stan-fundamentals
Foundational knowledge for writing Stan 2.37 models including program structure, type system, distributions, and best practices. Use when creating or reviewing Stan models.
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GitHub
time-to-event-methods
Survival analysis methods including weighted logrank, MaxCombo, RMST, and milestone tests. Use when analyzing TTE data or choosing analysis methods for non-proportional hazards.
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GitHub
nma-methodology
Deep methodology knowledge for network meta-analysis including transitivity, consistency assessment, treatment rankings, and model selection. Use when conducting or reviewing NMA.
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GitHub
hierarchical-models
Patterns for hierarchical/multilevel Bayesian models including random effects, partial pooling, and centered vs non-centered parameterizations.
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GitHub
model-diagnostics
MCMC diagnostics for Bayesian models including convergence assessment, effective sample size, divergences, and posterior predictive checks.
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GitHub
tidy-itc-workflow
Master tidy modelling patterns for ITC analyses following TMwR principles. Covers workflow structure, consistent interfaces, reproducibility best practices, and data validation. Use when setting up ITC analysis...
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GitHub
meta-analysis
Bayesian meta-analysis models including fixed effects, random effects, and network meta-analysis with Stan and JAGS implementations.
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GitHub
survival-models
Bayesian survival analysis models including exponential, Weibull, log-normal, and piecewise exponential hazard models with censoring support.
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GitHub
ml-nmr-methodology
Deep methodology knowledge for ML-NMR including IPD/AgD integration, population adjustment, numerical integration, and prediction to target populations. Use when conducting or reviewing ML-NMR analyses.
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GitHub
regression-models
Bayesian regression models including linear, logistic, Poisson, negative binomial, and robust regression with Stan and JAGS implementations.
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GitHub
mediana-fundamentals
Core Mediana package functions for Clinical Scenario Evaluation (CSE). Use when designing data models, analysis models, evaluation models, and running comprehensive trial simulations.
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GitHub
pymc-fundamentals
Foundational knowledge for writing PyMC 5 models including syntax, distributions, sampling, and ArviZ diagnostics. Use when creating or reviewing PyMC models.
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GitHub
pairwise-ma-methodology
Deep methodology knowledge for pairwise meta-analysis including fixed vs random effects, heterogeneity assessment, publication bias, and sensitivity analysis. Use when conducting or reviewing pairwise MA.
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GitHub
group-sequential-methods
Group sequential design methods for interim analyses, alpha spending, and futility stopping. Use when designing trials with interim looks or implementing spending functions.
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GitHub
stc-methodology
Deep methodology knowledge for STC including outcome regression approach, effect modifier selection, covariate centering, and comparison with MAIC. Use when conducting or reviewing STC analyses.
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GitHub
pr-response
Respond directly to individual PR review comments using the GitHub API. Use when asked to reply to PR comments, address reviewer feedback, or communicate with reviewers on a PR.
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GitHub
today
Get today's date for web searches and date-sensitive tasks. Auto-invoke before any WebSearch that includes a year (e.g., "React 2024", "Python 2025"), when searching for current documentation, latest releases,...
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GitHub
agentviewer
Display rich content (markdown, code, diffs, mermaid diagrams) to users in a browser viewer. Use when you need to show complex content that benefits from rich rendering - reports, documentation, code with synta...
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GitHub
consolidate-branches
Consolidate multiple PR branches onto a target branch using jj multi-parent rebase with intelligent AI-powered conflict resolution
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GitHub
script-banner
Automatically add standardized info banners to all new scripts and tools. Use when creating new PowerShell scripts, Bash scripts, or any executable tools in this repository.
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GitHub
changelog-manager
Automatically create and update CHANGELOG.md files for scripts and tools following Keep a Changelog format. Use when creating new scripts, updating existing scripts, fixing bugs, or adding features to any tool...
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GitHub
git-commit
Suggest commit messages based on staged changes and assist with committing using an editor.
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GitHub
gemini-image
Generate images using Google Gemini/Imagen API. Use when the user asks to create, generate, or make an image, picture, photo, illustration, artwork, or visual content.
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