add_significance_stars: Add significance stars

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

Description

\lifecycle

experimental Add significance stars to estimates with small p-values

Usage

add_significance_stars(
  x,
  pattern = "{estimate}{stars}",
  thresholds = c(0.001, 0.01, 0.05),
  hide_ci = TRUE,
  hide_p = TRUE,
  hide_se = FALSE
)

Arguments

x	a 'tbl_regression' or 'tbl_uvregression' object
pattern	glue-syntax string indicating what to display in formatted column. Default is "{estimate}{stars}". Other common patterns are "{estimate}{stars} ({conf.low}, {conf.high})" and "{estimate} ({conf.low} to {conf.high}){stars}"
thresholds	thresholds for significance stars. Default is c(0.001, 0.01, 0.05)
hide_ci	logical whether to hide confidence interval. Default is TRUE
hide_p	logical whether to hide p-value. Default is TRUE
hide_se	logical whether to hide standard error. Default is FALSE

Future Updates

There are planned updates to the implementation of this function with respect to the pattern= argument. Currently, this function replaces the numeric estimate column, with a formatted character column following pattern=. Once gt::cols_merge() gains the rows= argument the implementation will be updated to use it, which will keep numeric columns numeric. For the vast majority of users, the planned change will be go unnoticed.

Example Output

Example 1

Example 2

Example 3

Examples

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

# Example 1 ----------------------------------
add_significance_stars_ex1 <-
  tbl %>%
  add_significance_stars(hide_ci = FALSE, hide_p = FALSE)

# Example 2 ----------------------------------
add_significance_stars_ex2 <-
  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 <br> to put a line break between beta and SE in HTML output
add_significance_stars_ex3 <-
  tbl %>%
  add_significance_stars(
    hide_se = TRUE,
    pattern = "{estimate}{stars}<br>({std.error})"
  ) %>%
  modify_header(estimate ~ "**Beta (SE)**") %>%
  modify_footnote(estimate ~ "SE = Standard Error", abbreviation = TRUE) %>%
  as_gt() %>%
  gt::tab_style(style = "vertical-align:top",
                locations = gt::cells_body(columns = vars(label)))

ddsjoberg/gtsummary documentation built on April 8, 2021, 5:48 a.m.