Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
See ## Features above for related details.
scripts/main.py.See ## Prerequisites above for related details.
Python: 3.10+. Repository baseline for current packaged skills.numpy: unspecified. Declared in requirements.txt.pandas: unspecified. Declared in requirements.txt.scipy: unspecified. Declared in requirements.txt.See ## Usage above for related details.
cd "20260318/scientific-skills/Data Analytics/table-1-generator-advanced"
python -m py_compile scripts/main.py
python scripts/main.py --help
Example run plan:
CONFIG block or documented parameters if the script uses fixed settings.python scripts/main.py with the validated inputs.See ## Workflow above for related details.
scripts/main.py.Use this command to verify that the packaged script entry point can be parsed before deeper execution.
python -m py_compile scripts/main.py
Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.
python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py --data patients.csv --group treatment --output table1.csv
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
--data | str | Yes | - | Patient data CSV file path |
--group | str | No | - | Grouping variable (e.g., treatment/control) |
--vars | list[str] | No | - | Variables to include in the table |
--output | str | Yes | - | Output file path for Table 1 |
| Risk Indicator | Assessment | Level |
|---|---|---|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
# Python dependencies
pip install -r requirements.txt
Every final response should make these items explicit when they are relevant:
scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.This skill accepts requests that match the documented purpose of table-1-generator and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
table-1-generatoronly handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Use the following fixed structure for non-trivial requests:
If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.