Conventions

This page summarises the visual and structural conventions used throughout the book.

Code

Two kinds of code appear. R code is shown in syntax-highlighted blocks; its output is prefixed with #> to make the boundary between input and output explicit:

mean(c(1, 2, 3, 4, 5))
#> [1] 3

Shell commands, which recur constantly in this book, are shown with a $ prompt that is not part of the command:

$ zzc status

Inline code is in monospace. File and directory names (renv.lock, analysis/) and command names (make, zzc) are also set in monospace.

Callouts

Four callout types appear:

Tip

A small practical recommendation.

Check your understanding: example

A short question testing comprehension of the just-read material. Click to expand the answer.

Warning

A pitfall the reader may otherwise hit.

The honest level

A reminder that a reproducibility claim must be matched to the level actually reached, never asserted above it.

The reproducibility levels

Throughout the book, an analysis is placed on a four-rung ladder, and the reader is trained to name the rung:

L0, locatable. Under version control; the source can be found, but no computational input is pinned.
L1, pinned packages. The package versions are fixed by a lockfile.
L2, pinned environment. The operating system, the runtime, and the system libraries are fixed as well, usually in a container.
L3, verified. The recorded computational outputs have been regenerated and shown to match.

Cross-references

Sections, figures, and tables are referenced by their Quarto label (@sec-levels, @fig-ladder, @tbl-tools). Literature is cited by @bibkey and collected in the References.