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_tablesthenhelp(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)thenas_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: