domains entry can now be a named list instead of a
plain variable vector, to express sub-sections within a domain (e.g.
repeated timepoints within a "Mental health" domain). Flat and nested
entries can be mixed freely in the same domains list. For output = "html", this renders as genuine expandable/collapsible nested row
groups via reactable; gt/latex have no native two-level row-group
support, so there it renders as one row group per sub-domain with a
compound "Domain β Subdomain" label instead.clerk_render()/render_gt()/render_latex() gain a footnotes
argument for notes attached to specific rows or columns, alongside the
existing footnote argument (now vectorised, for more than one blanket
note). See vignette("formatting-options").vignette("formatting-options") gains "Nested domains" and "Custom
footnotes" sections.domain_other parameter added to all five tbl_* functions and to
clerk_options(). Controls the label applied to variables not assigned to
any domain, and to all variables when no domains list is supplied.
Default is "" (blank β no section header shown). Set to e.g. "Other"
to collect unassigned variables under a named section.
render_gt() and render_latex() now automatically add a source note
explaining BH FDR correction whenever a p_fdr column is present. Suppress
with fdr_footnote = FALSE or override with a custom footnote = string.
render_reactable() now renders title, subtitle, and footnote as
HTML elements above and below the widget. Previously the title argument
was accepted but silently ignored.
htmltools added to Imports to support the reactable title/footnote
rendering.
New vignette: Formatting options β covers p_style, decimal places,
significance stars, FDR display, domain_other, and session-wide vs
per-call option overrides.
pkgdown site now has a Customisation navbar section linking to the
formatting options vignette.
tbl_simple,
tbl_correlation, tbl_regression, tbl_heritability), .fmt_p()
vector formatting, clerk_options() get/set/reset, domain_other
storage, and the automatic FDR source note.domain_other replaces the previous hardcoded "Other" label for
unmatched variables and "All variables" for tables without a domain list.
Both now default to "".
pkgdown directory added to .Rbuildignore to suppress the
Non-standard file/directory found at top level NOTE.
Fixed a critical formatting bug in .fmt_p() where using ifelse() with a
scalar p_style condition caused all p-values in a vector to format
identically (the value of the first element was recycled across all rows).
Replaced the inner ifelse() with if/else for the scalar check. This
affected all table archetypes when fdr = TRUE β FDR-corrected p-values
were displaying incorrect numeric values.
fdr_ns now reliably replaces non-surviving FDR cells with "ns".
Previously, option lookup could silently return NULL before .onLoad()
had run, causing isTRUE(NULL) to evaluate to FALSE and the replacement
to be skipped. .get_clerk_options() now falls back to built-in defaults
via getOption(key, default = value).
Fixed .attach_domains() crashing on 0-row tables by replacing
tbl[["domain"]] <- "All variables" with rep("All variables", nrow(tbl)).
Renamed fdr_threshold β fdr_alpha throughout to make clear that the
threshold is applied to the BH-adjusted p-value, not the raw p.
Initial release.
tbl_descriptive() β Table 1-style descriptive summary with optional group
comparisons (t-test, ANOVA, chi-squared), domain grouping, log-transform
footnotes, and BH FDR correction.tbl_simple() β Descriptive summary without inferential tests.tbl_correlation() β Partial correlation results with r, p, and optional
FDR-corrected p column. Supports pivot to wide format.tbl_regression() β Regression coefficients (Ξ², SE, 95% CI, p) from
broom::tidy() output. Supports exponentiation and FDR correction.tbl_heritability() β Narrow-sense heritability estimates (hΒ², 95% CI,
LRT p, ΟΒ²a, ΟΒ²e) compatible directly with R-itable::herit_batch().clerk_render() β unified S3 dispatcher.render_gt() β gt output for Word/PDF with domain row groups, themed
headers, and automatic footnotes for log-transformed variables.render_reactable() β interactive reactable HTML output with domain
grouping and search.render_latex() β LaTeX output via gt::as_latex().clerk_options() β session-level formatting defaults following biomed/APA
conventions. Loaded automatically on package attach via .onLoad().
Controls decimal places (digits, r_digits, p_digits), p-value display
style (p_style: "apa", "plain", "stars", "stars_p"), significance
stars, and FDR non-survival labelling (fdr_ns, fdr_alpha, fdr_ns_label).clerk_theme() β gt theme with navy/teal clerkR visual identity.clerk_palette(), clerk_colour() β named palette accessors.clerk_diverging(), clerk_sequential() β colour ramps for visualisation.clerk_example β 300-participant synthetic dataset with metabolic,
anthropometric, cognitive, and mental health variables.clerk_cor_example β 16 synthetic partial correlation results.clerk_reg_example β 7 synthetic regression terms (broom::tidy format).clerk_h2_example β 12 synthetic heritability estimates (herit_batch format).Lucas FranΓ§a and Mario Leocadio-Miguel (Circadia Lab, Northumbria University).