add_significance_stars: Add significance stars

In gtsummary: Presentation-Ready Data Summary and Analytic Result Tables

Add significance stars

Description

Add significance stars to estimates with small p-values

Usage

add_significance_stars(
  x,
  pattern = ifelse(inherits(x, c("tbl_regression", "tbl_uvregression")),
    "{estimate}{stars}", "{p.value}{stars}"),
  thresholds = c(0.001, 0.01, 0.05),
  hide_ci = TRUE,
  hide_p = inherits(x, c("tbl_regression", "tbl_uvregression")),
  hide_se = FALSE
)

Arguments

x	(gtsummary) A 'gtsummary' object with a 'p.value' column
pattern	(string) glue-syntax string indicating what to display in formatted column. Default is "{estimate}{stars}" for regression summaries and "{p.value}{stars}" otherwise. A footnote is placed on the first column listed in the pattern. Other common patterns are "{estimate}{stars} ({conf.low}, {conf.high})" and "{estimate} ({conf.low} to {conf.high}){stars}"
thresholds	(numeric) Thresholds for significance stars. Default is c(0.001, 0.01, 0.05)
hide_ci	(scalar logical) logical whether to hide confidence interval. Default is TRUE
hide_p	(scalar logical) logical whether to hide p-value. Default is TRUE for regression summaries, and FALSE otherwise.
hide_se	(scalar logical) logical whether to hide standard error. Default is FALSE

Value

a 'gtsummary' table

Examples

tbl <-
  lm(time ~ ph.ecog + sex, survival::lung) |>
  tbl_regression(label = list(ph.ecog = "ECOG Score", sex = "Sex"))

# Example 1 ----------------------------------
tbl |>
  add_significance_stars(hide_ci = FALSE, hide_p = FALSE)

# Example 2 ----------------------------------
tbl |>
  add_significance_stars(
    pattern = "{estimate} ({conf.low}, {conf.high}){stars}",
    hide_ci = TRUE, hide_se = TRUE
  ) |>
  modify_header(estimate = "**Beta (95% CI)**") |>
  modify_footnote(estimate = "CI = Confidence Interval", abbreviation = TRUE)

# Example 3 ----------------------------------
# Use '  \n' to put a line break between beta and SE
tbl |>
  add_significance_stars(
    hide_se = TRUE,
    pattern = "{estimate}{stars}  \n({std.error})"
  ) |>
  modify_header(estimate = "**Beta  \n(SE)**") |>
  modify_footnote(estimate = "SE = Standard Error", abbreviation = TRUE) |>
  as_gt() |>
  gt::fmt_markdown(columns = everything()) |>
  gt::tab_style(
    style = "vertical-align:top",
    locations = gt::cells_body(columns = label)
  )

# Example 4 ----------------------------------
lm(marker ~ stage + grade, data = trial) |>
  tbl_regression() |>
  add_global_p() |>
  add_significance_stars(
    hide_p = FALSE,
    pattern = "{p.value}{stars}"
  )

gtsummary documentation built on Oct. 5, 2024, 1:06 a.m.