| name | lint-prereg-skeleton |
| description | Lint and format prereg skeleton.Rmd files. Use when applying consistent Markdown formatting to R Markdown preregistration templates in inst/rmarkdown/templates/*/skeleton/skeleton.Rmd. Fixes spacing between headings, HTML comments, and prompts; normalises list styles; removes trailing whitespace. |
| argument-hint | path to skeleton.Rmd (or omit to format all templates) |
Lint Prereg Skeleton
Applies consistent Markdown formatting to skeleton.Rmd preregistration templates.
The canonical references are vantveer_prereg and secondary_data_analysis_prereg.
See detailed rules with examples.
When to Use
- Adding a new template to
inst/rmarkdown/templates/
- Editing an existing skeleton and wanting to restore consistent style
- Auditing all templates for formatting consistency
Procedure
1. Identify the target file(s)
If an argument is given, format that file. Otherwise format every file matching:
inst/rmarkdown/templates/*/skeleton/skeleton.Rmd
2. Apply the lint script
Run .github/skills/lint-prereg-skeleton/lint_skeleton.R on the target file(s):
Rscript .github/skills/lint-prereg-skeleton/lint_skeleton.R <path/to/skeleton.Rmd>
The script automates Rules 1–11 and 13–15 (see formatting-rules.md):
trailing whitespace, comment delimiter spacing, blank-line removal between headings and comments,
prompt-text normalisation, section spacing, \newpage padding, bullet style, sentence-case headings,
and comment block internal formatting (paragraph joining, blank-line separation, leading whitespace removal).
3. Verify script output
Review the diff produced by the script. Check that every automated rule has been applied correctly and consistently — the script may mis-classify edge cases (e.g. bold sub-labels inside ## sections, slash-compound headings). If a rule was applied incorrectly:
- Evaluate whether the script can be improved to handle the case.
- If so, update
lint_skeleton.R and re-run before continuing.
- Otherwise, revert the incorrect change manually.
4. Apply remaining rules manually
Work through the rules the script does not cover, and fix any edge cases the script missed:
- Rule 12 — Spelling and grammar: fix clear spelling errors and obvious grammar errors in headings and comment text. Preserve original wording and intent; do not paraphrase. Leave examples, R code, LaTeX, and YAML untouched.
- Rule 16 — Unlabeled bullet lists: Rules 13–15 join unlabeled items into paragraphs. After the script runs, inspect joined paragraphs to identify hidden lists and add
- markers manually.
- Missing prompts: add
Enter your response here. to any Type A section that lacks one.
- Encoding issues: correct any garbled characters (e.g.
Í → ').
5. Verify the YAML front matter and References section
Do not alter:
- The YAML front matter block (
--- ... ---)
- The
# References section and the LaTeX spacing commands that follow it
- R inline code (
`r ...`)
- The prose content of comment blocks — only list markers, indentation, whitespace, question-number prefixes, and clear spelling/grammar errors within them may change
- Blank lines within a comment block that separate paragraphs — those are intentional
- Markdown tables and fenced code blocks
6. Final check
After writing, verify:
- No line has trailing whitespace.
- Every
<!-- adjacent to text has a space after it; every --> adjacent to text has a space before it.
- Every heading is immediately followed by a comment or content with no blank line between them.
- Type A sections:
--> → 1 blank → prompt → 2 blank → next heading.
- Type B sections: choices → 2 blank → next heading (no prompt).
- Type C sections:
--> → 2 blank → next heading (no prompt).
- Every
\newpage has 2 blank lines before and after.
- All lists use
N. or - markers with correct indentation, everywhere.
- All heading text (except
# References) is in sentence case.
