How to add the Chi-square effect size Cramer's V in the summary table using R package “gtsummary”?

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I am working with a gtsummary table that includes statistical tests for both means and frequencies. I want to include effect sizes to the table and came across this post which shows how to do it for Wilcox test effect size. The code also works for Cohen's d, but I am struggling to modify it for Cramer's V. It seems the cramer_v() function needs to call a ready-made contingency table, rather than working with raw data. Is there any way to calculate and include Cramer's V for the chi-square in the gtsummary table?

Example

library(tidyverse)
library(rstatix)
library(gtsummary)
theme_gtsummary_mean_sd()

my_ES_test <- function(data, variable, by, ...) {
  rstatix::cohens_d(data, as.formula(glue::glue("{variable} ~ {by}")))$effsize
}

gtTable <- mtcars %>% 
  select(hp, vs, am) %>% 
  tbl_summary(by = vs) %>% 
  add_p() %>% 
  add_stat(fns = all_continuous() ~ my_ES_test) %>% 
  modify_header(add_stat_1 ~ "Effect size")
print(gtTable)

contTable <- table(mtcars$vs, mtcars$am)
chisq.test(contTable, correct = FALSE)
#> 
#>  Pearson's Chi-squared test
#> 
#> data:  contTable
#> X-squared = 0.90688, df = 1, p-value = 0.3409
cramer_v(contTable)
#> [1] 0.1042136

Daniel D. Sjoberg · Accepted Answer · 2021-09-07 14:06:51Z

1

I added an example including Cramer's V in the output table. Happy Programming!

library(gtsummary)

my_ES_test <- function(data, variable, by, ...) {
  rstatix::cohens_d(data, as.formula(glue::glue("{variable} ~ {by}")))$effsize
}
my_cramer_v <- function(data, variable, by, ...) {
  table(data[[variable]], data[[by]]) %>%
    rstatix::cramer_v()
}

gtTable <- 
  mtcars %>% 
  select(hp, vs, am) %>% 
  tbl_summary(by = vs) %>% 
  add_p() %>% 
  add_stat(
    fns = list(all_continuous() ~ my_ES_test,
               all_categorical() ~ my_cramer_v)) %>% 
  modify_header(add_stat_1 ~ "**Effect size**")

^{Created on 2021-09-07 by the reprex package (v2.0.1)}

FYI, there is built-in support for Cohen's D so you don't need to create a custom method. You can see a complete list here https://www.danieldsjoberg.com/gtsummary/reference/tests.html

edited Sep 7, 2021 at 14:06

answered Sep 7, 2021 at 13:31

Daniel D. Sjoberg

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How to add the Chi-square effect size Cramer's V in the summary table using R package “gtsummary”?

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