如何使用R包“ gtsummary”在摘要表中生成效果大小[90％CI]？

Question

我正在使用R包“ gtsummary”创建汇总表。这实际上非常好。 add_stat函数使您可以自由地包含附加组件。例如，在我所在的地区，我们希望以置信区间（ES [90％CI]）告知效果大小。因此，我希望将CI范围包括在内。我实现的代码有效，但是没有数字控制并且没有CI范围。

# Packages ----------------------------------------------------------------
library(gtsummary)
library(gt)
library(dplyr)
library(purrr)

# Example 1 ---------------------------------------------------------------
# fn returns ES value
my_EStest <- function(data, variable, by, ...) {
  effsize::cohen.d(data[[variable]] ~ as.factor(data[[by]]), 
                   conf.level=.90, pooled=TRUE, paired=FALSE, 
                   hedges.correction=TRUE)$estimate
}

add_ES <-
  trial %>%
  select(trt, age) %>%
  tbl_summary(by = trt, missing = "no",
              statistic = list(all_continuous() ~ "{mean} ({sd})"),
              digits = list(all_continuous() ~ c(1,1))) %>%
  add_p(test = everything() ~ t.test) %>%
  add_stat(
    fns = everything() ~ my_EStest,
    fmt_fun = style_pvalue,
    header = "**ES**"
  )
add_ES

# counterproof
effsize::cohen.d(age ~ trt, data = trial, conf.level=.90, return.dm=TRUE, pooled=TRUE, paired=FALSE, hedges.correction=TRUE)

Answer 1

我认为最简单的方法是将置信区间与已经格式化的估计值相加。

您更新my_EStest函数以返回已经格式化的统计信息，包括估计值和置信区间。此输出对您有用吗？

library(tidyverse)
library(gtsummary)

my_EStest <- function(data, variable, by, ...) {
  # Cohen's D
  d <- effsize::cohen.d(data[[variable]] ~ as.factor(data[[by]]), 
                   conf.level=.90, pooled=TRUE, paired=FALSE, 
                   hedges.correction=TRUE)

  # Formatting statistic with CI
  est <- style_sigfig(d$estimate)
  ci <- style_sigfig(d$conf.int) %>% paste(collapse = ", ")

  # returning estimate with CI together
  str_glue("{est} ({ci})")
}

add_ES <-
  trial %>%
  select(trt, age) %>%
  tbl_summary(by = trt, missing = "no",
              statistic = list(all_continuous() ~ "{mean} ({sd})"),
              digits = list(all_continuous() ~ c(1,1))) %>%
  add_p(test = everything() ~ t.test) %>%
  add_stat(
    fns = everything() ~ my_EStest,
    fmt_fun = NULL,
    header = "**ES (90% CI)**"
  ) %>%
  modify_footnote(add_stat_1 ~ "Cohen's D (90% CI)")