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CLAUDE.md — Vis-MLM-book Project

Quick-start reference for resuming work on this Quarto book project.

Project

Title: Visualizing Multivariate Data and Models in R: A Romance in Many Dimensions Author: Michael Friendly Publisher: CRC Press / Chapman & Hall Repo: https://github.com/friendly/vis-MLM-book HTML site: https://friendly.github.io/Vis-MLM-book/ (served from docs/)

Book structure

15 chapters in 4 parts + appendix, all .qmd files at the project root:

Part Chapters
Orienting Ideas 01-Prelude, 02-intro, 03-getting_started
Exploratory Methods 04-multivariate_plots, 05-pca-biplot
Univariate Linear Models 06-linear_models, 07-linear_models-plots, 08-lin-mod-topics, 09-collinearity-ridge
Multivariate Linear Models 10-hotelling, 11-mlm-review, 12-mlm-viz, 13-eqcov, 14-infl-robust, 21-discrim (Ch. 15)
End Matter 91-colophon, 95-references
Appendix (online only) 15-case-studies, 30-Rcode, 31-exercises

Front matter: index.qmd, 00-Author.qmd

Note: .qmd file-name prefixes no longer match printed chapter numbers (e.g. 21-discrim.qmd is Chapter 15; 15-case-studies.qmd is the online-only Appendix). Trust chapter order in _quarto.yml (print) / _quarto-online.yml (online extras) over file-name prefixes.

Key directories

Directory Contents
R/ 130+ R scripts for chapter examples, organized by dataset/topic
bib/ Bibliography files (references.bib, pkgs.bib, R-refs.bib, packages.bib, Rpackages-4.5.1.bib)
child/ Child .qmd docs included into chapters
latex/ LaTeX config: preamble.tex, before-body.tex, after-body.tex
figs/ Figure output, organized by chapter (ch01–ch15, discrim, etc.)
images/ Static images (cover, logos, diagrams)
docs/ HTML output (deployed to GitHub Pages)
pdf/ PDF copies (manually maintained)
issues/ Issue tracking and task files — start here
working-text/ Background notes, drafts, RA instructions
test/ Experimental code and test renders
reviews/ Reviewer PDFs (Reviewer 1.pdf, Reviewer 2.pdf)

Build

HTML + PDF together: Use Build -> All Formats (not Render Book). Building only HTML wipes out docs/ and can leave inconsistent filenames between formats; building all formats together avoids this.

Output locations:

  • PDF → ./index.pdf (project root). Named after the entry point index.qmd, not after output-file: Vis-MLM in _quarto.yml (that setting names the .tex intermediate only).
  • HTML → docs/ (served to GitHub Pages)
  • TeX intermediate → ./Vis-MLM.tex (kept because keep-tex: true)
  • Older PDF copies are manually archived to pdf/

PDF: Uses xelatex + documentclass: krantz (CRC house style).

  • Quarto PDF build is unreliable — often fails with LaTeX errors.
  • Workaround: keep-tex: true is set; compile Vis-MLM.tex manually in TeXStudio.
  • Both MikTeX and TinyTeX are installed on this Windows machine; Quarto prefers TinyTeX.
  • Close index.pdf in Acrobat before every build — Quarto cannot overwrite the file while it is open and will fail with "process cannot access the file" (os error 32).
  • See issues/quarto-pdf-help.md and quarto-dev/quarto-cli#11087

R setup: R/common.R is sourced at the start of each chapter. It defines:

  • pkg() — format R package names (bold + optional citation)
  • colorize() / colorize_bg() — colored text for HTML and PDF
  • write_pkgs() — auto-generate bib/packages.bib from library() calls

Current priorities

See issues/Tasks-Issues.md for the full prioritized list. Top items:

  1. PDF build reliability — make Render Book work end-to-end
  2. Author index — authorindex Perl script fails
  3. Cover page — can't include via Quarto; currently added manually in Acrobat
  4. Conditional content — links as footnotes in PDF; GIFs only in HTML
  5. pkg() formatting — needs \index{} for PDF, different style for HTML vs PDF
  6. Reviewer comments — see reviews/MichaelT-*.Rmd and reviews/*.pdf
  7. Content additions — see issues/content-todos.md

Blog posts

Some work done on this book may be worth writing up as posts on Michael's blog at https://friendly.github.io/ (source: C:\R\projects\friendly.github.io).

Candidates so far:

  • Diagrams in Quarto with Mermaid, TikZ, and smartdiagram — the examples in test/test-diagrams.qmd showed all three toolchains working together; the %| vs #| chunk-option gotcha and the extra.preamble nesting bug are both worth documenting for other Quarto/knitr users.

Claude Memory

Session context and persistent notes live in memory/ at the project root (git-tracked). Always read memory/MEMORY.md at the start of each session to load prior context.

Conventions

  • \index{} entries are being added incrementally; systematic pass still needed.
  • Figure paths: figs/chNN/ set via knitr opts_chunk$set(fig.path = "figs/") in each chapter.
  • Conditional format blocks: ::: {.content-visible when-format="html"} / when-format="pdf"
  • Package references: first use → bold + citation e.g. **ggplot2** [@R-ggplot2]
  • Citation style: APA (bib/apa.csl)