scikit-survival Time-to-Event Modeling
davila7/claude-code-templates
Fits and evaluates survival models with scikit-survival: Cox models, Random Survival Forests, boosting, survival SVMs, concordance index, Brier score and competing risks.
Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output.
Install Analyze
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyze --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .claude/skills/analyze && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .claude/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyzeType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyze --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .agents/skills/analyze && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .agents/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyze --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .cursor/skills/analyze && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .cursor/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/61-phdemotions-research-methods/skills/analyze--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyze --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .gemini/skills/analyze && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .gemini/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyzeInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .github/skills/analyze && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .github/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills analyze --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/analyze .opencode/skills/analyze && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "analyze" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/analyze into .opencode/skills/analyze/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "analyze", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
analyze- GitHub stars
- 4.5k
- Token cost
- ~1.6k tokens
- SKILL.md length
- 674 words
- Files
- 8 (incl. references)
- Skills in repo
- 383
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output.
- Works in 8 steps: Read context → Load principles and rubric → Map hypotheses to analyses → …
- The user says test hypotheses
- SKILL.md covers How to run analysis, PROCESS models, Voice and Argument handling
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Analyze is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output. Supports OLS/GLM regression, panel regression (fixest), mixed models (lme4), SEM/CFA (lavaan), meta-analysis (metafor), and delegates PROCESS models to /process-model. Reads pre-registration to align planned analyses, flags deviations, and generates decision log entries for post-hoc choices. Use when the user says "test hypotheses," "run analysis,"…
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including reference files (for example `references/criteria.md`, `references/method-templates/meta-analysis.md` and `references/method-templates/mixed-models.md`).
It sits in Data & Analytics, covering Architecture decision records, Statistics and Machine learning. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…
When your agent uses it
- The user says test hypotheses
- Tasks that involve Architecture decision records
- Tasks that involve Statistics
Example prompts
- “test hypotheses,”
- “run analysis,”
- “confirmatory,”
- “/analyze”
Requirements
- Python 3
Workflow steps
8 steps, taken from the step headings in SKILL.md.
- Read context
- Load principles and rubric
- Map hypotheses to analyses
- Test assumptions (per method)
- Fit models
- Report results
- Flag pre-registration deviations
- Summary and next steps
What it can do on your machine
Read from SKILL.md and the folder at commit 9fa87d8. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Analyze loads about 1.6k tokens when it runs, and up to ~6.9k if it reads all its reference files. Until then it costs about 172 tokens; SKILL.md has 674 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 674 words (~1,643 tokens).
“You are the methodological backbone of this research project. Your job is to execute the analyses that were planned — not to explore, not to fish, not to find "something significant." You test what was hypothesized, report what you find…”
- name
- analyze
- argument-hint
- <hypothesis number, method type, or 'all' — defaults to all pre-registered analyses>
Files
SKILL.md and 7 other files (references) in skills/61-phdemotions-research-methods/skills/analyze of brycewang-stanford/Auto-Empirical-Research-Skills.
- SKILL.md
- references/criteria.md
- references/method-templates/meta-analysis.md
- references/method-templates/mixed-models.md
- references/method-templates/ols-glm.md
- references/method-templates/panel-fixest.md
- references/method-templates/sem-cfa.md
- references/principles.md
Open the folder on GitHubat commit 9fa87d8
Compare with similar skills
Analyze next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Analyze this skillbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~1.6k | Automated safety check: Pass | Custom licence | |
| scikit-survival Time-to-Event Modelingdavila7/claude-code-templates | 32k | 11 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Scenario Experiment AnalysisDrchronx/ai-agent-research-starter-kit | 137 | — | ~1.1k | Automated safety check: Pass | Custom licence | |
| Data Scientistdavila7/claude-code-templates | 32k | 8 repos | ~2.6k | Automated safety check: Pass | MIT | |
| Scientific Toolkit SkillzLanqing/codex-claude-academic-skills | 4.7k | — | ~1.2k | Automated safety check: Pass | MIT | |
| Data Sciencetravisjneuman/.claude | 101 | — | ~2.3k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Analyze
What does Analyze do?
Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output. Analyze is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Confirmatory hypothesis testing matched to pre-registration, with full assumption testing, effect sizes, confidence intervals, and APA 7th formatted output.
When should I use Analyze?
Analyze fits situations like: the user says test hypotheses; tasks that involve Architecture decision records; tasks that involve Statistics.
How do I install Analyze in Claude Code?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a claude-code`. Or copy the skill folder (skills/61-phdemotions-research-methods/skills/analyze in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/analyze in your project. Claude Code loads it when a task matches its description.
How do I install Analyze in Codex?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a codex`. Or copy the skill folder (skills/61-phdemotions-research-methods/skills/analyze in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/analyze in your project. Codex loads it when a task matches its description.
Can I use Analyze in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill analyze -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/analyze, .gemini/skills/analyze, .github/skills/analyze and .opencode/skills/analyze in your project.
What does Analyze need to run?
SKILL.md names no scripts, command-line tools or credentials: Analyze is instructions for the agent only. Our summary lists: Python 3.
Does Analyze access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Analyze safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Analyze use?
Analyze has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Analyze use?
About 1.6k tokens (SKILL.md is roughly 6.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 5.2k tokens, read only when the agent opens those files.
What are the alternatives to Analyze?
Skills that share tags, products or a category with Analyze: scikit-survival Time-to-Event Modeling (davila7/claude-code-templates, 32k stars), Scenario Experiment Analysis (Drchronx/ai-agent-research-starter-kit, 137 stars), Data Scientist (davila7/claude-code-templates, 32k stars) and Scientific Toolkit Skill (zLanqing/codex-claude-academic-skills, 4.7k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Analyze?
brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,542 GitHub stars. The repository holds 383 skills in this directory. The repository was last updated on October 5, 2026.
Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.