Changelog • vernissage

vernissage 0.1.0

First version, gathering the preprocessing and visualisation helpers of the analysis scripts (00_common.R, 01_preprocessing.R, 02_distribution.R, 03_descriptive.R, 04_longitudinal.R, 07_transform_outliers.R and 09_radar_plot.R). The limit-of-detection and cut-off functions are in the companion package lodestar; the modelling functions are kept for a separate package; the clustering functions are not included.

New features

describe_cohort(): overview table of a cohort (type, N, missing values, summaries overall and by group, group test, text histogram), replacing table1(), which depended on functions absent from the scripts (bilille_gt_theme(), .is_typst()).
Column arguments accept character vectors, bare names and tidyselect helpers.
New helpers from repeated code: visit_root(), visit_swap(), gt_sig_colors() (replaces the constant GT_SIG_COLORS), pal_okabe_ito() (replaces the object okabe_ito).
pal_levels() also accepts a palette name ("okabe", hcl.pals(), palette.pals(), RColorBrewer) or a function.
outlier_flag_mad() and outlier_flag_iqr() are exported; outlier_flag_iqr(method = "hinges") reproduces the former outliers_table() (Tukey’s hinges of boxplot.stats()).

Renamed functions

Former name	New name
`make_palette()`	`pal_levels()`
`get_label()`, `expand_labels()`	`label_get()`, `label_expand()`
`p_to_stars()`	`fmt_stars()`
`rotate_x()`	`theme_rotate_x()`
`forest_plot()`	`plot_forest()`
`export_table()`	`dt_export()`
`render_tabset()`, `raw_output_callout()`	`qmd_tabset()`, `qmd_callout_raw()`
`resolve_path()`	`path_resolve_nfc()`
`var_catalog()`	`catalog_vars()`
`visit_suffix_map()`, `to_long()`, `add_deltas()`	`visit_map_suffix()`, `visit_to_long()`, `visit_add_deltas()`
`.flag_mad()`, `.flag_iqr()`, `detect_outliers()`, `outliers_table()`, `mask_outliers()`	`outlier_flag_mad()`, `outlier_flag_iqr()`, `outlier_detect()`, `outlier_mask()`
`choose_transformation()`, `propagate_choice()`, `apply_transformation()`	`transform_choose()`, `transform_propagate()`, `transform_apply()`
`transform_boxcox_car()`, `transform_outcomes_car()`, `apply_outcome_transformation()`	`transform_boxcox()`, `transform_boxcox_resid()`, `transform_apply_resid()`
`na_map()`, `ggNA()`, `complete_case_count()`	`plot_na_map()`, `na_complete_cases()`
`composite_scores()`	`score_composite()`
`normality_table()`	`describe_normality()`
`partial_rank_cor()`, `cor_test_matrix()`	`cor_partial_spearman()`, `cor_matrix_test()`
`paired_visits_plot()`, `radar_plot()`	`plot_paired_visits()`, `plot_radar()`

The former names still work (soft deprecation, see ?vernissage-deprecated).

Bug fixes and behaviour changes

transform_choose() (former choose_transformation()): failed when none of the preferred methods had been computed (e.g. log impossible with values <= 0); the best W is then used. A variable without any Shapiro W keeps its first method with an explicit reason instead of disappearing.
plot_radar(): its local fmt_p() and %||% masked the package ones; the label format (p=0.012) is kept in a private helper. Colours come from pal_levels(): with more groups than colours, the palette is now interpolated instead of recycled. With seed, the random state of the session is restored after the call.
plot_distribution(): the identifier of the metadata join no longer defaults to the cohort-specific "SampleName": id_col is required with metadata.
visit_map_suffix(): select is now required (former default "^MRI_", kept by the deprecated visit_suffix_map()).
label_expand(): the format of categorised variables is an argument (bin_format, bin_format_root) instead of the global options fairpark.bin_label / fairpark.bin_label_root (still read by the deprecated expand_labels()).
The seed of jitters and subsamples is an argument (seed = 1) instead of the global option analysis.seed.
read_cohort_csv() and path_resolve_nfc(): their documentation was merged in the scripts; each function now has its own.
Skewness and kurtosis are computed internally (same moment estimators as e1071::skewness(type = 1) / kurtosis(type = 1)), which removes the dependency on e1071.
Every non-ASCII character of the code is written with \u escapes, as required by R CMD check.