Appendix C — The rgtlab Software
Several chapters use tools written in the author’s lab, and a reader is entitled to know what those tools are, what they depend on, and how much of the book’s argument rests on them. This appendix is the inventory.
It exists partly as a disclosure. A textbook that teaches its author’s own software has an obvious conflict, and the honest response is to make the extent of it visible rather than to distribute the mentions thinly enough that nobody notices.
C.1 What the book depends on, and what it does not
The chapters were written so that a reader with none of this software installed can still do the work. Every technique the book teaches has a portable expression: renv, Docker, Quarto, Git, and the tidyverse are the substance, and the tools below are conveniences layered on them.
Two exceptions are worth naming plainly. Chapter 13 is about zzcollab and cannot be separated from it, though its Five Pillars framing applies to any compendium. And the two case studies (Chapter 30, Chapter 31) use zztable1 and zzlongplot for table and figure production, which a reader without them should substitute with gtsummary and plain ggplot2; nothing in the analyses depends on the substitution.
Everything else is optional. Where a chapter mentions one of these tools, it names the portable alternative in the same breath, and a reader who ignores the tool loses convenience rather than capability.
C.2 Research infrastructure
zzcollab (github.com/rgt47/zzcollab). A Docker-based research collaboration framework. Composes rrtools-style compendium layout, renv, and containers into one command-line workflow with profile-based project scaffolding. Treated at length in Chapter 13.
zzrenvcheck (github.com/rgt47/zzrenvcheck). Validates that every package used in source code is declared in DESCRIPTION and locked in renv.lock. It complements renv rather than replacing it: renv confirms the lockfile matches the installed library, while this confirms that the code, the manifest, and the lockfile agree. Declaration-only, so it runs without a container or an installed environment. Used in Chapter 11.
zzgit (github.com/rgt47/zzgit). A zsh plugin replacing the git add . && git commit -am reflex with an interactive stage-and-commit: secret scanning of the staged diff via gitleaks, a protected-branch guard, and a Conventional Commits wizard. Discussed in Chapter 7.
zzvim-R (github.com/rgt47/zzvim-R). A Vim and Neovim plugin linking the editor to an embedded R terminal: send a line, a visual selection, or a Quarto chunk, and render the document without leaving the editor. Mentioned in Chapter 5.
C.3 Reporting and presentation
zztable1 (github.com/rgt47/zztable1). Publication-quality summary tables with automatic format detection for LaTeX and HTML. The portable alternative is gtsummary. Used in both case studies.
zzlongplot (github.com/rgt47/zzlongplot). Longitudinal plots with grouping, change scores, and faceting, including CDISC-oriented regulatory themes. The portable alternative is ggplot2 with stat_summary, which Chapter 22 shows explicitly. Used in Chapter 31.
zzobj2fig (github.com/rgt47/zzobj2fig). Generates LaTeX tables from data frames and statistical objects, and crops them to standalone PDF figures. Carries journal themes (APA, Nature, NEJM) and S3 methods for lm and glm. Its main entry point is o2f().
C.4 Statistical methods
zzpower (github.com/rgt47/zzpower). An interactive Shiny power and sample-size calculator across two-group, paired, one-sample, two-proportion, and correlation designs, with power curves and downloadable reports. Used in Chapter 24.
nof1power (github.com/rgt47/nof1power). Power analysis and Monte Carlo simulation for N-of-1 crossover trials, a design Chapter 24 does not otherwise treat. Itself built as a zzcollab compendium.
zzmesoimpute (github.com/rgt47/zzmesoimpute). Imputation for left-censored, below-detection-limit concentrations from multiplexed immunoassays, with a common interface across substitution, uniform draw, regression-on-order-statistics, censored maximum likelihood, and multiple imputation. Discussed in Chapter 23, where the point is that left censoring is not missingness.
zzfisher. Fisher’s exact test for \(r \times 2\) contingency tables, with tree-based and network-based algorithms implemented in R, C, and C++. Relevant to the sparse-table case Chapter 28 uses as its example of a plausibly-wrong statistic.
C.5 Domain and data collection
zzedc (github.com/rgt47/zzedc). A Shiny electronic data capture system for clinical trials: authentication, entry forms, quality-control reports, and export. The setting Chapter 17 describes when it says clinical data usually arrive from a capture system rather than as a file.
zzworld (github.com/rgt47/zzworld). Scoring for the WORLD item in cognitive assessment, computing edit distance between a response and the target word and integrating with MMSE totals. Narrow by design, and included here for completeness rather than because any chapter uses it.
C.6 A caution about depending on any of it
None of these packages is on CRAN. They are installed from GitHub, they carry version numbers that reflect active development rather than stability, and several are below version 1.0. The reproducibility argument of Chapter 11 applies to them with more force than it does to CRAN packages, not less: pin them by commit in renv.lock, and expect that an analysis depending on an unpinned in-house package will not reproduce in two years.
The same caution should temper how much of your own workflow you build on any lab’s internal tooling, including this one. The portable core is what survives a change of institution.