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Changelog

Source: NEWS.md

hvtiPlotR 2.3.3

Bug fixes

  • save_ppt(): the white box behind plots is gone again. The earlier fix only cleared the officer placeholder’s fill; rvg::dml() still defaults to bg = "white", so the DrawingML graphic painted its own opaque white canvas rectangle behind the (transparent) plot. Both dml() calls (plots and consort diagrams) now pass bg = "transparent", so the slide-template background shows through cleanly on dark/blue decks.
  • theme_hv_ppt_dark() and theme_hv_ppt_light() now default to base_family = "Arial", base_size = 32, with Arial 32 Bold axis tick labels and Arial 40 Bold axis titles — matching the canonical CORR deck (driveline-infections, slide 6). Axis titles scale at base_size * 1.25. (Slide-title fonts are controlled by the PowerPoint template, not the theme.) Override at the call site as usual, e.g. theme_hv_ppt_dark(base_size = 28).

Changes

  • save_ppt() now defaults panel_box to the standard CORR fixed-panel rectangle list(width = 8.88, height = 4.51, left = 2.58, top = 1.63), so every deck anchors the plot panel at the same slide coordinates by default (AATS-style placement). Pass panel_box = NULL to restore the legacy fixed-width/height/left/top placement. Because the default now routes plots through hv_ph_location(), save_ppt suppresses the benign “font family ‘Arial’ not found in PostScript font database” warning from the grob-measurement device (the slide graphic still embeds Arial via systemfonts).

Documentation

  • save_ppt() examples now show the recommended preview-light / save-dark workflow (build with theme_hv_ppt_light() for the IDE viewer, swap to theme_hv_ppt_dark() before saving) and add a no-y-axis-label slide (labs(y = NULL)).
  • Dropped the family = "mono" snippet from the theme docs and switched the executed Kaplan–Meier examples off the Arial PPT themes (to theme_hv_poster()), so R CMD check examples stay warning-free on hosts without Arial installed (a cause of the failing CI run).
  • Declared xml2 in Suggests (used by the save_ppt white-box test), fixing the “unstated dependencies in ‘tests’” check WARNING.
  • Added a small (~16 KB) dark-background test template at inst/extdata/hv_ppt_template.pptx, derived from the canonical CORR deck (master, layouts, and theme only — content slides, notes, comments, media, and document metadata stripped). Reach it with system.file("extdata", "hv_ppt_template.pptx", package = "hvtiPlotR") to try save_ppt() against an authentic dark slide master.

hvtiPlotR 2.3.2

Documentation (#70)

  • Vignette clarity pass: added structural grounding to all five vignettes — two to four sentences before every code chunk on what the recipe does, when to reach for it, and (for bare/raw plots) what to look for. Applied the memory/vignette-clarity-pass.md workflow developed for TemporalHazard 1.0.3.
  • Corrected four factual claims surfaced by review: the dashed-threshold recommendation in the SAS migration guide (geom_hline(), not annotate("hline")); the theme_hv_poster() font claim (the theme does not enforce a sans-serif face); the theme(legend.position = "none") layout-space claim (no space is reserved); and the theme_hv_manuscript() “no title” claim (the theme does not blank plot.title).

hvtiPlotR 2.3.1

Documentation (#69)

  • Package-wide voice rewrite of every prose surface — README, vignettes, NEWS, slide deck, roxygen, DESCRIPTION Title: — against the writing-voice.md spec. Prose only; no API or behavioural change.
  • Fixed stale hv_theme() string-key references ("dark_ppt", "ppt", "light_ppt", "manuscript", "poster") in the main tutorial and SAS-migration vignettes. That dispatcher was removed in 2.1.0; the vignettes now name the actual theme_hv_*() functions.
  • Fixed missing “to” in the main tutorial’s introduction (“is simplify” → “is to simplify”).
  • README now lists all five vignettes (sas-migration-guide was missing) and the “Migrating from plot.sas” section points at the dedicated migration vignette.
  • Synced a copy of writing-voice.md into the repo root for future documentation work.

hvtiPlotR 2.3.0

CONSORT patient flow tracking and diagram (#67)

Two-class API for CONSORT flow diagrams built from patient-level data.

Tracker lifecycle:

  • hv_consort_start(data, patient_id, label, pass_col) — initialises a tracker with one row per patient; all patients begin as screened.
  • hv_consort_exclude(tracker, label, col, ..., excl_label, pass_col) — adds an exclusion stage via formula rules (condition ~ "Reason string"). First-matching formula wins; gating on the prior stage is automatic.
  • hv_consort_summary(tracker) — returns a data frame with N included and N excluded per stage; suitable for methods-section tables.
  • hv_consort_patients(tracker, stage, reason) — returns patient IDs at any stage, or the subset excluded for a specific reason.

Diagram:

  • hv_consort(tracker, side_box, cex, width, height) — auto-derives orders and side_box from tracker metadata and calls consort::consort_plot(). side_box = "all" (default) includes every exclusion column; pass a character vector to select specific columns.
  • plot.hv_consort(x) — renders the diagram via the consort plot method.
  • save_ppt() now accepts hv_consort objects, producing an editable DrawingML vector object in the output .pptx.

Sample data:

  • sample_consort_data(n, seed) — reproducible three-stage cardiac surgery tracker for demos and testing.

Dependency: consort (>= 0.2.0) added to Imports.

Documentation

  • New worked CONSORT Patient Flow Diagram section in the Plot Functions vignette, covering the tracker workflow, the rendered diagram, the audit helpers, and save_ppt() export (#68).
  • New “What’s New in v2.x” slide deck shipped as Quarto source at inst/slides/hvtiPlotR-whats-new.qmd — an onboarding overview of the v2.x API redesign, theme rename, and PowerPoint export, with a README “Slides” section pointing to it (#67).

hvtiPlotR 2.2.0

New S3 methods for hv_data objects (#64)

Three standard-R S3 verbs are now implemented for every hv_data subclass:

  • summary() — prints the standard one-screen header, then walks the object’s $tables slot and prints each named auxiliary table with a header. Callers get risk tables, report tables, and diagnostics without reaching for $tables directly. Subclasses can override with a curated layout.
  • autoplot() — re-exports ggplot2’s autoplot() generic and dispatches to the registered plot.<subclass>() method. Callers who prefer the ggplot2-ecosystem verb (broom, ggfortify, and ggsurvfit all use it) can write autoplot(km) in place of plot(km). Extra args forward to the subclass plot().
  • as.data.frame() — returns the $data slot via standard as.data.frame() coercion instead of the $data accessor.

No breaking changes.

UpSet plot backend swap (#62)

plot.hv_upset() is now backed by ggupset rather than ComplexUpset. The intersection-size bar chart is a standard ggplot; themes apply via +, and ggplot2::ggplot_build() works on the output. When set_size = TRUE (the default) a manual set-size sidebar is composed via patchwork.

Breaking changes:

  • The base_annotations parameter has been removed. To recolour the intersection bars by an external grouping variable, pass fill_col = "<column>" to plot(); for a single fixed colour pass bar_fill = "<colour>".
  • The min_size parameter has been replaced by n_intersections (top-N by frequency or degree — see sort_by). ComplexUpset’s size-threshold semantics are not preserved.
  • encode_sets and sort_intersections parameters have been removed (the new equivalents are sort_by and set_size_sort).
  • Themes now apply via +, not &. & still works on the patchwork composite when set_size = TRUE.

Other changes:

  • The ComplexUpset Import has been dropped; ggupset (>= 0.4.0) is added in its place. patchwork has been promoted from Suggests to Imports.
  • hv_upset() adds a .Procedures list-column to its stored $data for scale_x_upset() to consume.
  • The four upset_* vignette chunks no longer carry a Windows skip gate; ggupset renders cleanly on every CI runner.
  • tests/testthat/test_example_plot_data.R and tests/testthat/test_plot_integration.R drop their tryCatch / skip_if_theme_incompatibility wrappers — the upset output now passes expect_plot_has_data() like every other plot.

hvtiPlotR 2.1.0

Theme API redesign

Tests

  • Added tests/testthat/helper-plot-data.R and tests/testthat/test_example_plot_data.R. Every @examples and vignette plot path is exercised through ggplot2::ggplot_build(), asserting that non-decorator layers carry observation rows, expected geoms appear, and grouped/stratified plots preserve their groups. Catches the “plot rendered but contains no data” defect without a graphics device.

hvtiPlotR 2.0.1

Bug fixes

  • save_ppt(): the officer::ph_location() call that places each plot on its slide now uses bg = "transparent" so the placeholder rectangle’s fill no longer shows up as an opaque white box behind the plot on dark PowerPoint templates. Previously, officer’s default ph_location shape had a white fill; against a blue-gradient slide template that appeared as a visible white rectangle larger than the ggplot panel. The ggplot itself is unchanged; only the containing shape’s fill is now transparent so the slide template background shows through any area outside the panel.
  • hv_theme_light_ppt(): panel background is now fill = "transparent" (was "white"). Saving a light_ppt-themed plot into a dark PowerPoint template previously showed as an opaque white rectangle inside the panel; with a transparent fill the slide template shows through. Add + theme(panel.background = element_rect(fill = "white")) if you specifically need an opaque white panel.

Documentation

  • Package-level help topic (?hvtiPlotR) rewritten to cover the v2.0.0 feature set: two-step workflow with runnable example, fixed-panel geometry subsection (hv_ggsave_dims()/hv_ph_location()/save_ppt(panel_box=)), legacy single-call API, hv_data class introspection, scope and versioning, vignette index.
  • README “Utilities” table now lists hv_ggsave_dims() and hv_ph_location(), and documents save_ppt(panel_box=).
  • save_ppt() example rewritten to show the recommended hv_theme("light_ppt") preview workflow saving into a dark PPT template with panel_box = list(width = 8.88, height = 4.51, left = 2.58, top = 1.29) and a scale_x_continuous(breaks = seq(0, 400, 100), expand = c(0, 0)) decorator.
  • hvtiPlotR.qmd colour-guidance section updated to reflect that ColorBrewer palettes are accessed via ggplot2’s built-in scale_colour_brewer() rather than a direct RColorBrewer dependency.

hvtiPlotR 2.0.0

First stable release of the hv_* API. This consolidates the 2.0.0.9001–2.0.0.9013 dev cycle into a tagged release that internal users can anchor against for bug reports and reproducibility. Subsequent releases will advance the semantic version (2.0.1, 2.1.0, 3.0.0) directly; no .9xxx pre-release suffixes.

New features — fixed-panel geometry

The dominant theme of this release is making the panel content area (the rectangular data region, excluding axes/titles/legend/margins) directly addressable, so figures stay visually aligned across output devices and across slides in a deck even when axis-label widths differ.

  • hv_ggsave_dims(plot, width, height, units = "in"): compute ggsave() width/height that preserve a fixed panel content area regardless of surrounding chrome. Returns a named list shaped to splat into ggsave() via do.call(ggsave, c(list(filename = ..., plot = p), dims)). Units are length-only ("in", "cm", "mm") since the sizing device is PDF.
  • hv_ph_location(plot, panel_width, panel_height, panel_left, panel_top, units = "in"): compute officer::ph_location() width/height/left/top values that anchor a ggplot’s panel to a fixed rectangle on a slide, regardless of axis-label width. Measures asymmetric chrome (left/right/top/bottom of the panel) via ggplotGrob() and returns per-plot placement so the panel lands at the same slide coordinates on every slide. Warns if plot chrome extends past the left or top slide edge.
  • save_ppt(..., panel_box = list(width, height, left, top)): new optional argument. When supplied, per-slide placement is computed via hv_ph_location() so every slide anchors the panel at the given rectangle; on dark PPT themes where the panel fill is visible, the panel no longer shifts between slides. When panel_box = NULL (default), the fixed width/height/left/top arguments are used (legacy behavior).

New features — PPT theme polish

  • hv_theme_dark_ppt(bold = TRUE) and hv_theme_light_ppt(bold = TRUE): apply face = "bold" to axis text and axis titles.

Behaviour changes — PPT themes

  • hv_theme_dark_ppt() and hv_theme_light_ppt():
    • Legend is now hidden by default (legend.position = "none"). PowerPoint figures are typically annotated directly on the panel; override with + theme(legend.position = "right") when needed.
    • Axis ticks now face inside the panel (axis.ticks.length = -half_line/2 pt) for the AATS-style inset look.
    • Axis-text and axis-title margins are now scaled from base_size via ggplot2’s half_line = base_size / 2 convention, so spacing stays proportional when base_size changes. Previous unscaled defaults produced cramped labels at base_size = 32.
    • hv_theme_light_ppt() gains explicit axis.text, axis.line, panel.background (fill "white", colour "black", linewidth 1), and axis.ticks elements so the light theme structurally mirrors the dark theme’s explicit-chrome approach (just with inverted colours).

Build / infrastructure

  • .Rbuildignore is now tracked in git (previously .gitignored). Three latent regex bugs fixed: anchored .gitignore pattern, stripped inline # ... comments from five patterns (which had silently never matched), and fixed ^vignettes/*_files$ → ^vignettes/.*_files$ so _files/ output dirs actually get excluded from the build.
  • vignettes/_quarto.yml now tracked with embed-resources: false at the project level, making the small-HTML / separate _files/ rendering behaviour explicit and preventing accidental repo bloat.
  • Dropped RColorBrewer (inline Set1 hex in cluster_sankey_plot() and vignettes) and gridExtra (marrangeGrob() → patchwork::wrap_plots() in the EDA multi-panel PDF pattern) from Suggests.
  • Dropped assertthat from Imports (save_ppt() now uses base stop() with call. = FALSE).
  • vignettes/hvtiPlotR.qmd now documents haven::read_xpt() (and haven::read_sas()) for importing SAS data, with a CSV-fallback path for users without SAS access.

hvtiPlotR 2.0.0.9010

Bug fixes

  • plot-functions.qmd: UpSet plot chunks (upset_data, upset_basic, upset_fill, upset_era) now skip on Windows (eval: !expr .Platform$OS.type != "windows"). ComplexUpset’s patchwork rendering crashes the Rscript subprocess on the Windows CI runner (os error 232 / “pipe being closed”), so the examples are shown only on macOS and Linux where they render reliably.

hvtiPlotR 2.0.0.9009

Documentation

  • plot-functions.qmd: updated both mirror-histogram decorated examples to follow standard ggplot2 mirror-plot conventions:
    • Added scale_y_continuous(labels = abs) so the y-axis displays absolute counts on both halves of the panel.
    • Replaced hard-coded y-coordinates in annotate() calls with y = Inf/y = -Inf plus vjust, anchoring each group label near the top/bottom panel edge regardless of dataset size.
    • Replaced hard-coded label strings ("SAVR", "TF-TAVR", etc.) with mh$meta$group_labels[1] / [2], so the annotations track the labels supplied to the constructor.

hvtiPlotR 2.0.0.9008

Documentation

  • Vignettes: all hv_theme("manuscript") calls inside R code blocks replaced with hv_theme("poster") to demonstrate non-default theme options. Prose references (e.g. migration guide comparison table) are preserved unchanged. Theme-specific sections in plot-decorators.qmd (## Manuscript, ## Manuscript PDF) continue to demonstrate hv_theme("manuscript").
  • plot-functions.qmd: added explicit Bare plot subsections to the six sections that previously chained directly from build to decoration — mirror-histogram (binary-match and IPTW), trends (cases/year), spaghetti, nonparametric temporal curve, nonparametric ordinal curve, and longitudinal participation counts. Each section now follows the three-step pattern:
    1. build with hv_*(), (2) render bare ggplot with p <- plot(obj),
    2. decorate with scale_*() + hv_theme("poster").
  • plot-functions.qmd: UpSet section split into ## Bare plot (showing plot(hu)) and ## Applying a theme (showing plot(hu) & hv_theme("poster")), with an explanatory note that the patchwork & operator is required.

hvtiPlotR 2.0.0.9007

Breaking changes

hvtiPlotR 2.0.0.9006

Documentation

  • hv_mirror_hist() $tables$diagnostics: corrected return documentation from “a data frame of matched/unmatched counts per group” to accurately describe the actual type — a named list of diagnostic summaries whose contents vary by mode (binary-match vs weighted IPTW). All keys are now enumerated in the @return block.
  • $meta keys in hv_mirror_hist() return docs updated to include all keys actually stored (score_col, group_col, match_col were missing).
  • Added @family Propensity Score & Matching to hv_mirror_hist() and plot.hv_mirror_hist(), creating automatic bi-directional “See also” cross-links consistent with all other hv_* constructor/plot pairs.
  • plot.hv_mirror_hist() @return now describes composability with + (scales, limits, labels, hv_theme), matching the pattern used in all other updated plot methods.
  • plot.hv_mirror_hist() @seealso expanded with descriptive text for each linked function, matching the richer pattern used elsewhere.

hvtiPlotR 2.0.0.9005

Tests

  • Added test_trends_plot.R (37 tests): $meta slot keys and values, $tables$summary structure and row counts, factor level order preservation, print.hv_trends output and invisible return, and full parameter coverage for plot.hv_trends (se, span, point_size, point_shape, alpha, smoother, grouped vs ungrouped mapping, composability with hv_theme).
  • Added test_spaghetti_plot.R (25 tests): $meta slot keys and values, id_col/y_col absent error cases, print.hv_spaghetti output with and without colour_col branch and invisible return, and full parameter coverage for plot.hv_spaghetti (add_smooth, smooth_se, line_colour, line_width, alpha boundaries, y_labels error cases, smooth_method, grouped vs ungrouped mapping, composability with hv_theme).
  • Added test_hv_data.R (27 tests): new_hv_data() structure contract, input validation errors, is_hv_data() TRUE/FALSE for all relevant types, print.hv_data base-class output and invisible return, subclass dispatch (verifying print.hv_spaghetti overrides print.hv_data), and plot.hv_data fallback error with subclass name in message.

hvtiPlotR 2.0.0.9004

Breaking changes

  • hv_mirror() renamed to hv_mirror_hist() for naming consistency with the underlying plot type. The old name is registered as an @aliases entry so ?hv_mirror still resolves to the correct help page.

New features

  • hv_mirror_hist() is now searchable via ?mirror_histogram, ?hv_mirror, ??propensity, ??IPTW, and ??matching through @aliases and @concept tags in its documentation.

Documentation

  • All hv_* constructors and plot.hv_* methods now carry @family tags; the help system and pkgdown reference both show bi-directional “See also” links between each constructor and its plot method.
  • @return on every constructor now explicitly says “call plot() to render” and links to the corresponding plot.hv_* method.
  • @seealso entries across all constructors and plot methods now include descriptive text explaining the role of each linked function.
  • @examples in all main plot methods include a \dontrun{} block demonstrating ggplot2::theme_set(hv_theme_manuscript()) for applying the publication theme globally, scale_colour_brewer() / scale_fill_brewer() for multi-group colour palettes, and a pointer to vignette("plot-decorators", package = "hvtiPlotR").

hvtiPlotR 2.0.0.9001

hvtiPlotR 2.0.0

Breaking changes — new S3 constructor API

All plot functions have been replaced by a two-step S3 workflow:

# Step 1: construct & validate
obj <- hv_*(data, ...)          # returns c("hv_<concept>", "hv_data")

# Step 2: render
plot(obj, ...) +                  # bare ggplot — no scales, labels, or theme
  scale_colour_manual(...) +
  labs(...) +
  hv_theme("manuscript")

The old single-call functions (mirror_histogram(), survival_curve(), etc.) are removed. This is a clean break; no deprecated wrappers.

Constructor → old function mapping

New constructor Removed function(s)
hv_mirror_hist() mirror_histogram()
hv_balance() covariate_balance()
hv_stacked() stacked_histogram()
hv_survival() survival_curve()
hv_nonparametric() nonparametric_curve_plot()
hv_ordinal() nonparametric_ordinal_plot()
hv_followup() goodness_followup() + goodness_event_plot()
hv_trends() trends_plot()
hv_spaghetti() spaghetti_plot()
hv_longitudinal() longitudinal_counts_plot() + longitudinal_counts_table()
hv_alluvial() alluvial_plot()
hv_sankey() cluster_sankey_plot()
hv_eda() eda_plot()
hv_upset() upset_plot()
hv_hazard() | hazard_plot() |
hv_survival_difference() | survival_difference_plot() |
hv_nnt() | nnt_plot() |

The legacy hazard helpers (hazard_plot(), survival_difference_plot(), nnt_plot()) remain exported but are marked Superseded — use the S3 constructors above instead.

Multi-type constructors

Two constructors replace pairs of old functions via a type = argument on plot():

  • hv_longitudinal — plot(x, type = "plot") (bar chart, was longitudinal_counts_plot()) or plot(x, type = "table") (text panel, was longitudinal_counts_table()).
  • hv_followup — plot(x, type = "followup") (death panel, was goodness_followup()) or plot(x, type = "event") (non-fatal event panel, was goodness_event_plot()).

New base class

  • Added hv_data S3 base class (R/hvti-data.R). Every hv_* constructor returns list(data=, meta=, tables=) with class c("hv_<concept>", "hv_data").
  • new_hv_data() — internal constructor; validates data (data.frame), meta (named list), tables (list), subclass (character).
  • print.hv_data() — fallback print method; shows class, dimensions, and slot names.
  • plot.hv_data() — fallback plot method; stops with a helpful message if no concrete plot.hv_*() is registered.
  • is_hv_data() — exported predicate.

Documentation

  • Rewrote help.R package-level documentation to describe the new two-step constructor + plot() workflow and list all hv_*() constructors.
  • Updated _pkgdown.yml reference index: grouped by constructor family, with plot.* and print.* S3 methods explicitly listed.
  • Updated all vignettes (plot-functions.qmd, sas-migration-guide.qmd, plot-decorators.qmd) to use the new API throughout.
  • Updated sas-migration-guide.qmd key-concepts section and template reference table.
  • Fixed all stale @seealso cross-references and orphaned old-API docblocks in every migrated R source file.

Tests

  • Added tests/testthat/test_hazard_plot.R — full validation suite for sample_hazard_data, sample_hazard_empirical, sample_life_table, hv_hazard, hv_survival_difference, and hv_nnt (column checks, CI bounds, layer structure, multi-group, non-default column names, input validation, print output, empirical/reference validation).
  • Added tests/testthat/test_nonparametric_plots.R — full suite for sample_nonparametric_curve_data, sample_nonparametric_curve_points, nonparametric_curve_plot, sample_nonparametric_ordinal_data, sample_nonparametric_ordinal_points, and nonparametric_ordinal_plot. Includes probability-sum-to-1 invariant test for ordinal grades.
  • Added tests/testthat/test_survival_derived.R — full suite for sample_survival_difference_data, sample_nnt_data, and legacy survival_difference_plot / nnt_plot. Covers NA-NNT at t≈0 edge case and cross-function time-grid consistency.
  • Added tests/testthat/test_cluster_sankey.R — full suite for sample_cluster_sankey_data and cluster_sankey_plot. Validates the hierarchical merge tree (C9=A → C2=A) and that each Ck has exactly k levels.
  • Added tests/testthat/test_pipeline.R — end-to-end pipeline tests covering survival_curve → hv_theme → save_ppt, multi-slide list pipelines, built-in dataset usability, eda_classify_var edge cases (logical vector, all-NA, length-1), and composed multi-layer plots.
  • Added snapshot test to test_kaplan_meier.R for survival_curve report_table at fixed seed; added all-censored and single-observation edge-case tests.
  • Added snapshot test to test_mirror_histogram.R for diagnostics at fixed seed.
  • Added slide_titles length-mismatch test to test_save_ppt.R.
  • Added make_footnote prefix-parameter tests to test_footnote.R.

Documentation

  • Fixed save_ppt() argument names throughout all vignettes: plot = → object =, filename = → powerpoint =. Also added correct template = and slide_titles = arguments where missing.
  • Fixed critical roxygen bug in sample_mirror_histogram_data(): doc block used ##' (silently ignored by roxygen2) instead of #', so the function had no generated .Rd file. Converted all ##' → #', modernised \code{} → backtick syntax, and added @examples.
  • Added @examples to all five theme functions: hv_theme(), hv_theme_manuscript(), hv_theme_dark_ppt(), hv_theme_light_ppt(), and hv_theme_poster().
  • Expanded thin (2-line) @examples blocks for four sample-data helpers: sample_life_table(), sample_nonparametric_curve_points(), sample_nonparametric_ordinal_points(), and sample_longitudinal_counts_data().
  • Fixed km$survival_plot and km$risk_table accessor patterns in vignettes/plot-decorators.qmd: survival_curve() returns a ggplot with attributes, not a named list. Replaced with km (the returned object IS the survival plot) and attr(km, "risk_table").
  • Fixed patchwork operator-precedence bug in vignettes/plot-decorators.qmd: p_ms | p_km_ms + plot_layout(...) → (p_ms | p_km_ms) + plot_layout(...).
  • Added patchwork to Suggests in DESCRIPTION (required by vignettes/plot-decorators.qmd).
  • Rewrote package-level help page (help.R / ?hvtiPlotR) to document all 57 exported functions, organised by category.
  • Expanded “Saving figures” section in vignettes/sas-migration-guide.qmd with correct save_ppt() single- and multi-slide examples.
  • Added ggplot2::geom_line(..., linewidth = 1.5) (replacing deprecated size =) and updated remotes::install_github() (replacing devtools::install_github()) in vignettes/hvtiPlotR.qmd.

Input validation improvements

  • upset_plot() — added binary-column type check. ComplexUpset silently produces broken plots when intersect columns contain non-binary values; the function now errors with a clear message listing the offending columns before handing off to ComplexUpset.
  • sample_stacked_histogram_data() — added start_year validation (previously n_years and n_categories were checked but start_year was not; a non-integer or non-finite value produced silently nonsensical output).
  • trends_plot() — moved match.arg(summary_fn) to after the data-frame and column checks, so users see a clear data / column error rather than an opaque 'arg' should be one of... message when both data and summary_fn are wrong.
  • validators.R — added two scalar-parameter helpers: .check_scalar_positive() (finite, positive) and .check_scalar_nonneg() (finite, non-negative). cb_validate_params() in covariate-balance.R now delegates all four parameter checks to these helpers, eliminating 28 lines of bespoke validation code.

Architecture

  • .NP_SIM constant list (nonparametric-curve-plot.R) — lifted the seven simulation tuning constants (eta_intercept, logit_shift, cont_baseline, cont_scale, cont_sigma, eff_frac_prob, eff_frac_cont) from local variables in sample_nonparametric_curve_data() and from hard-coded defaults in .np_sample_bins() into a single file-level private list. Both functions now reference .NP_SIM$* — change once, updates all simulation paths.

Bug fixes / API consistency

  • Standardised alpha range to [0, 1] across all plot functions. Previously survival_curve(), covariate_balance(), mirror_histogram(), spaghetti_plot(), and goodness_followup_death_plot() / goodness_followup_event_plot() used (0, 1] (rejecting alpha = 0), while alluvial_plot() used [0, 1]. All functions now accept [0, 1] — alpha = 0 (fully transparent) is a valid ggplot2 value and should not be an error.
  • Added .check_alpha() shared validator in R/validators.R. Enforces alpha ∈ [0, 1] with call. = FALSE and is called from every plot function that accepts an alpha argument.
  • call. = FALSE sweep — every stop() call in the package now includes call. = FALSE so error messages never expose internal function names to callers.
  • Expanded shared validators (R/validators.R) to 11 files (up from 3). All of alluvial-plot.R, covariate-balance.R, eda-plots.R, goodness-followup.R, hazard-plot.R, kaplan-meier.R, longitudinal-counts-plot.R, mirror-histogram.R, nonparametric-curve-plot.R, nonparametric-ordinal-plot.R, spaghetti-plot.R, stacked-histogram.R, trends-plot.R, and upset-plot.R now delegate data.frame, column-presence, numeric-column, and alpha checks to .check_df(), .check_cols(), .check_col(), .check_numeric_col(), and .check_alpha(). Error messages use consistent wording across all entry points.

Code quality

  • Named all simulation tuning constants in sample_nonparametric_curve_data() and the internal helper .np_sample_bins(): eta_intercept, logit_shift, cont_baseline, cont_scale, cont_sigma, eff_frac_prob, eff_frac_cont. Magic numbers replaced throughout the single-curve, multi-group, and binned-data-summary code paths.
  • Named all simulation tuning constants in sample_nonparametric_ordinal_data() and sample_nonparametric_ordinal_points(): a_first, a_step, eta_intercept. Every occurrence of -0.2, 0.5, and 1.2 replaced by the named constant.
  • Extended edge-case test coverage:
    • test_kaplan_meier.R: added five survival_curve error tests for non-numeric time_col, invalid event_col values (character instead of 0/1/logical), and alpha at 0, > 1, and < 0.
    • test_hazard_plot.R: added graceful-handling test for an empty data frame (correct columns, zero rows) — confirms ggplot renders without error.
    • test_mirror_histogram.R: added error test for non-numeric score_col.

hvtiPlotR 2.0.0.9000

  • Added eda_plot() — exploratory barplot/scatterplot for a single variable. Auto-detects variable type ("Cont", "Cat_Num", "Cat_Char") and dispatches to scatter + LOESS + rug (continuous) or stacked/filled bar (categorical). NA values are shown as an explicit "(Missing)" fill level. Returns a bare ggplot object for composition with scale_fill_*, scale_colour_*, labs(), annotate(), and [hv_theme()]. Ports Function_DataPlotting() from tp.dp.EDA_barplots_scatterplots.R.
  • Added eda_classify_var() — replicates the UniqueLimit type-detection logic from Barplot_Scatterplot_Function.R: classifies a vector as "Cont", "Cat_Num", or "Cat_Char".
  • Added eda_select_vars() — subsets and reorders a data frame by a character vector or space-separated string of column names. Replaces Order_Variables() and the Mod_Data <- dta[, Order_Var] pattern from tp.dp.EDA_barplots_scatterplots_varnames.R.
  • Added sample_eda_data() — mixed-type cardiac-surgery registry simulation (binary, ordinal, character-categorical, and continuous variables) for demonstrating eda_plot() and eda_select_vars().
  • Reorganised inst/: moved par_cst.xpt and npar_cst.xpt to inst/extdata/ (standard R package location for bundled data files); removed unreferenced presentation and test artefacts (*.pptx, *.pdf, *.sas scratch files).
  • Extended nonparametric_curve_plot() examples: added dual-Y-axis example (Example 10, \dontrun) using scale_y_continuous(sec.axis = ...); noted cll_p95/clu_p95 column availability for 95 % CI (Example 2) and per-group shape mapping via scale_shape_manual() (Example 4).
  • Extended nonparametric_ordinal_plot() examples: added pre-operative severity comparison example grouping combined Mild/Moderate/Severe cohorts through nonparametric_curve_plot().
  • Split vignette into three: hvtiPlotR.qmd (SAS migration guide), plot-functions.qmd (per-function reference with worked examples), plot-decorators.qmd (composition grammar: scale_*, labs(), themes, and saving to manuscript PDF, poster PDF, and editable PowerPoint via save_ppt()).

hvtiPlotR 1.1.0

  • Added survival_curve() — Kaplan-Meier and Nelson-Aalen survival analysis returning five plot types (survival, cumulative hazard, hazard, log-log, life/RMST) plus risk and report tables. Ports the SAS %kaplan and %nelsont macros from tp.ac.dead.sas.
  • Added sample_survival_data() — realistic exponential survival simulation with administrative censoring and optional treatment strata.
  • Added goodness_followup() — goodness-of-follow-up scatter plot showing actual vs. potential follow-up per operation year, with optional non-fatal event panel.
  • Added sample_goodness_followup_data() — simulates an operative cohort with operation dates, follow-up times, competing events, and death.
  • Added covariate_balance() — standardised mean difference dot-plot for propensity-score matching or weighting diagnostics.
  • Added sample_covariate_balance_data() — patient-level logistic simulation with greedy 1:1 caliper matching; SMDs computed before and after matching.
  • Added stacked_histogram() and sample_stacked_histogram_data() — stacked or filled histogram of a numeric variable by group.
  • Improved mirror_histogram() sample data (sample_mirror_histogram_data()) to use a realistic logistic propensity-score model with greedy 1:1 caliper matching and optional ATE IPTW weights; extreme-PS patients naturally go unmatched.
  • Added hv_plot() dispatcher supporting "mirror_histogram", "stacked_histogram", and "covariate_balance" plot types.
  • Added hv_theme() dispatcher for "manuscript", "ppt", "dark_ppt", and "poster" themes.
  • Enabled roxygen Markdown (Roxygen: list(markdown = TRUE)) so **bold**, backtick code spans, and [pkg::fn()] cross-references render correctly in Rd help pages.
  • Added survival to package Imports.
  • Updated package-level documentation (help.R) to reflect all current exported functions and sample-data generators.

hvtiPlotR 0.2.2

  • Fixed deprecated ggplot2 syntax (size -> linewidth in element_line and element_rect).
  • Removed empty save.hvtiplotr function.
  • Fixed theme_dark_ppt to pass all parameters to theme_grey.
  • Updated documentation for data objects.
  • Updated README to reference officer package instead of deprecated ReporteRs.

hvtiPlotR 0.2.0

  • Initial CRAN submission.