10 Manuscript Assembly

The sa-manuscript-quarto module generates publication-ready manuscripts from analysis outputs. It builds Table 1 (baseline characteristics), drafts the results section with extracted statistics, and renders the final document via Quarto in both PDF and DOCX formats.

10.1 IMRAD Structure

The generated manuscript follows the standard Introduction-Methods-Results-And-Discussion (IMRAD) format:

05_manuscript/
├── _quarto.yml          # Render settings
├── manuscript.qmd       # Main Quarto source
├── references.bib       # BibTeX bibliography
├── american-medical-association.csl
└── output/
    ├── manuscript.pdf
    └── manuscript.docx

10.2 Table 1 with gtsummary

Script build_table1.R generates a formatted baseline characteristics table:

library(gtsummary)

df |>
  select(age, sex, stage, comorbidity, group) |>
  tbl_summary(
    by = group,
    statistic = list(
      all_continuous() ~ "{mean} ({sd})",
      all_categorical() ~ "{n} ({p}%)"
    ),
    missing = "ifany"
  ) |>
  add_p() |>
  add_overall() |>
  bold_labels()

Standardised Differences

For observational studies, consider reporting standardised mean differences (SMD) instead of p-values in Table 1, as balance metrics are more informative than hypothesis tests for baseline comparisons.

10.3 Auto-Generated Results Draft

Script build_results_section.R extracts key statistics from the analysis outputs and generates a prose draft:

Sample size and follow-up duration
Event counts and rates
Hazard ratios with 95% CI
Model diagnostics summary
Key figure references

This draft is embedded as a child document in the main manuscript.qmd.

10.4 AMA Citation Style

The pipeline uses the American Medical Association citation style. References are stored in references.bib and formatted via american-medical-association.csl:

# In _quarto.yml
bibliography: references.bib
csl: american-medical-association.csl

Inline citations use the standard Quarto syntax: [@cox1972] renders as a superscript number.

10.5 Rendering

# Build Table 1 and results section
make manuscript PROJECT=my-study

# Render to PDF + DOCX
make render PROJECT=my-study

LaTeX Requirement

PDF rendering requires a LaTeX distribution. Install TinyTeX with quarto install tinytex if PDF output fails.

10.6 Output

The rendered manuscript appears in projects/<name>/05_manuscript/output/ as both manuscript.pdf and manuscript.docx.