如何使用 R 包“gtsummary”在摘要 table 中生成效果大小 [90%CI]？

Question

我正在使用 R 包 "gtsummary" 创建摘要 table。这其实很好。 add_stat 功能让您可以自由地包含附加组件。例如，在我所在的地区，我们希望通过置信区间 (ES [90% CI]) 告知效果大小。所以，我想帮助包括 CI 范围。我实现的代码有效，但没有数字控制，也没有 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添加置信区间以及已经格式化的估计值。

您将 my_EStest 函数更新为 return 已经格式化的统计数据，包括估计值和置信区间。这个输出对你有用吗？

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)")

如何使用 R 包“gtsummary”在摘要 table 中生成效果大小 [90%CI]？

How to generate effect size [90%CI] in the summary table using R package “gtsummary”?

size

r

effect

gtsummary