v1.3.1: modern theme refresh, new theme/group.mean.overlay arguments

[xuyiqing]

Summary

Plot-system refresh for v1.3.1. Drop-in upgrade with two opt-in arguments and a soft deprecation.

Visual refresh (all four plot types):

• Plain left-aligned titles at base size 11, white status-heatmap background, subtle major-x gridlines on trajectories, thin gray dashed treatment-onset marker.
• Multi-level discrete-status palette refreshed to a muted, perceptually distinct sequence.
• Outcome control trajectories lightened to grey75; binary blue cascade and continuous gradient unchanged.
• Outcome draw order fixed via three explicit geom_line layers (co → tr → tr.pst). The previous single geom_line(group=id) drew in id order, not type order, so treated trajectories were being covered by the control band.
• by.group / by.group.side suptitle (textGrob path) now routes through the modern title style via a new .pv_modern_top_grob helper.

New arguments:

• theme = c("default", "red") — opt-in "red" theme activates a high-contrast publication-paper recipe (gray control / dark-gray treated-pre / brick-red treated-post + solid-black dashed onset marker).
• group.mean.overlay = FALSE — when TRUE, dims per-unit trajectories and overlays a heavy group-mean line plus a 10–90% quantile ribbon per treatment-status group. Scoped to the main DID continuous-outcome path.

Deprecations:

• theme.bw = FALSE is soft-deprecated. Still functional; emits a one-time warning per call. The tutorial no longer demonstrates it.

Tutorial:

• New "Themes" subsections in 01-treat and 02-outcome.
• New red-theme demo in 03-bivariate.
• Capacity-dataset demo showing all three legend categories (Under Control, Under Treatment, Missing).
• v1.3.1 entry added to the changelog chapter; index version table + argument table updated.

Backwards compatibility:

• Default behavior unchanged for existing users except for the visual refresh (titles, background, palette).
• Pre-1.3.1 visuals can be largely recovered by setting theme.bw = FALSE (with the deprecation warning).

Test plan

• devtools::test() — 116/116 pass
• R CMD check --as-cran on the built tarball — Status: OK (0 errors / 0 warnings / 0 notes, including a clean CRAN-incoming-feasibility check)
• Clean-cache quarto render of all 7 tutorial chapters — succeeds; new figures (treat2-theme-red-*, outcome1-3*, bivar1-6b) render correctly
• Smoke-tested user-reported scenarios: outcome plot draw order, control gray density, theme.bw = FALSE deprecation warning, by.group title alignment

🤖 Generated with Claude Code