bio-reporting-publication-tables

Installation
SKILL.md

Version Compatibility

Reference examples tested with: gtsummary 2.0+, gt 0.10+, flextable 0.9+, kableExtra 1.4+, great_tables 0.13+, pandas 2.2+, tableone 0.9+, openpyxl 3.1+

Before using code patterns, verify installed versions match. If versions differ:

  • R: packageVersion('gtsummary') then ?tbl_summary (gtsummary had a major API refresh at v2.0)
  • Python: pip show great_tables then help(great_tables.GT.save)

If code throws an error, introspect the installed package and adapt the example to the actual API rather than retrying.

Publication-Ready Tables

"Make my Table 1" / "export this results table for the paper" -> Generate the table programmatically with the right statistics and export it to the journal's target format.

  • R: gtsummary::tbl_summary(data, by=arm) then as_flex_table() -> Word
  • Python: great_tables.GT(df) -> HTML/PNG; tableone.TableOne(...) for a descriptive table

The Load-Bearing Idea: A Table Is Structure + Precision + the Right Statistics

Three orthogonal concerns, and conflating them is where tables go wrong:

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