clerkR session options

clerk_options() gets or sets session-level formatting defaults used by all tbl_* constructors. Defaults are loaded automatically when the package is attached and follow biomed/APA conventions.

Call with no arguments to inspect current settings. Call with named arguments to change one or more. Call with reset = TRUE to restore factory defaults.

Usage

clerk_options(
  digits = NULL,
  r_digits = NULL,
  p_digits = NULL,
  p_threshold = NULL,
  p_style = NULL,
  stars = NULL,
  star_thresholds = NULL,
  fdr_ns = NULL,
  fdr_alpha = NULL,
  fdr_ns_label = NULL,
  domain_other = NULL,
  reset = FALSE
)

Arguments

digits

Integer. Decimal places for continuous summary statistics (default 2).

r_digits

Integer. Decimal places for correlation coefficients and h² estimates (default 3).

p_digits

Integer. Decimal places for p-values (default 3).

p_threshold

Numeric. Raw p-values below this are shown as "< {threshold}" (default 0.001). Display only, not a significance threshold.

p_style

Character string controlling p-value display style:

"apa"

APA format: = 0.032, < 0.001 (default).

"plain"

Plain decimal: 0.032, < 0.001.

"stars"

Significance stars only, no numeric p.

"stars_p"

Stars alongside numeric p.

stars

Logical. Append significance stars (default FALSE).

star_thresholds

Numeric vector of length 3. Cutoffs for *, **, *** (default c(0.05, 0.01, 0.001)).

fdr_ns

Logical. Replace the FDR p-value cell with fdr_ns_label when p(FDR) >= fdr_alpha (default TRUE).

fdr_alpha

Numeric. Alpha applied to the BH-adjusted p-value. Cells where p(FDR) >= fdr_alpha show fdr_ns_label (default 0.05).

fdr_ns_label

Character string for non-surviving FDR cells (default "ns").

domain_other

Character string used as the domain label for variables not assigned to any domain, and for all variables when no domains are specified. Default "" (blank — no section header shown). Set to e.g. "Other" to collect unassigned variables under a named section.

reset

Logical. Restore factory defaults (default FALSE).

Value

A named list of current option values, returned invisibly.

Examples

clerk_options()
clerk_options(p_style = "apa", stars = TRUE)
clerk_options(fdr_alpha = 0.01)
clerk_options(domain_other = "Other")
clerk_options(reset = TRUE)