How to do repeated measures Anova and Friedman test in gtsummary? - gtsummary

Question

I have repeated measures data for fasting glucose of few patients which are measured in Day 0, 3 and 7 during a clinical trial. I want to do friedman.test (and repeated measures anova for another data). Is it possible in gtsummaryto do Friedman test and repeated measures Anova?
This is my code
library(gtsummary)
library(dplyr)
smpl %>% select(c(Participant.ID, value, Day)) %>%
tbl_summary(by = Day, include = -Participant.ID) %>% add_p()
By default gtsummary does Kruskal-Wallis rank sum test for the three groups in my data (Day 0, 3 and 7). As it is a repeated measures I wanted to do friedman.test on these groups. So I tried the following code
my_friedman <- function(data, variable, by, random, ...) {
data <- data[c(variable, by)] %>% dplyr::filter(complete.cases(.))
friedman.test(variable ~ data[[by]] | random, data = data)
}
smpl %>% select(c(Participant.ID, value, Day)) %>%
tbl_summary(by = Day) %>%
add_p(test = value ~ "my_friedman", random = Participant.ID)
But that gives an error..
this is the dput for my sample data smpl
structure(list(Participant.ID = c(1002, 1007, 1010, 1017, 1018,
1022, 1044, 1050, 1051, 1052, 1002, 1007, 1010, 1017, 1018, 1022,
1044, 1050, 1051, 1052, 1002, 1007, 1010, 1017, 1018, 1022, 1044,
1050, 1051, 1052), Randomization = c("Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone"
), Day = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L), .Label = c("0", "3", "7"), class = "factor"),
value = c(31.92, 53.25, 34.69, 33.32, 25.94, 34.69, 22.65,
33.32, 24.33, 25.94, 31.92, 46.54, 44.74, 145.12, 37.34,
39.89, 22.65, 27.5, 25.94, 25.94, 37.34, 53.25, 29.02, 37.34,
25.94, 34.69, 22.65, 27.5, 29.02, 31.92)), row.names = c(NA,
-30L), class = c("tbl_df", "tbl", "data.frame"))
Can someone kindly help?
Here is the direct call to friedman.test
> friedman.test(value ~ Day | Participant.ID, data = aa)
Friedman rank sum test
data: value and Day and Participant.ID
Friedman chi-squared = 1.2667, df = 2, p-value = 0.5308

Answer 1

Your code was close! I made some small adjustments. See below!
library(gtsummary)
#> #BlackLivesMatter
smpl <-
structure(list(Participant.ID = c(1002, 1007, 1010, 1017, 1018,
1022, 1044, 1050, 1051, 1052, 1002, 1007, 1010, 1017, 1018, 1022,
1044, 1050, 1051, 1052, 1002, 1007, 1010, 1017, 1018, 1022, 1044,
1050, 1051, 1052), Randomization = c("Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone",
"Pioglitazone", "Pioglitazone", "Pioglitazone", "Pioglitazone"
), Day = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L), .Label = c("0", "3", "7"), class = "factor"),
value = c(31.92, 53.25, 34.69, 33.32, 25.94, 34.69, 22.65,
33.32, 24.33, 25.94, 31.92, 46.54, 44.74, 145.12, 37.34,
39.89, 22.65, 27.5, 25.94, 25.94, 37.34, 53.25, 29.02, 37.34,
25.94, 34.69, 22.65, 27.5, 29.02, 31.92)), row.names = c(NA,
-30L), class = c("tbl_df", "tbl", "data.frame"))
my_friedman <- function(data, variable, by, group, ...) {
# construct the formula
formula <- stringr::str_glue("{variable} ~ {by} | {group}") |> as.formula()
# perform Friedman test
friedman.test(
formula = formula,
data = data
) |>
broom::tidy()
}
my_friedman(data = smpl, variable = "value", by = "Day", group = "Participant.ID")
#> # A tibble: 1 × 4
#> statistic p.value parameter method
#> <dbl> <dbl> <dbl> <chr>
#> 1 1.27 0.531 2 Friedman rank sum test
tbl <-
smpl %>%
select(Participant.ID, value, Day) %>%
tbl_summary(
by = Day,
include = -Participant.ID
) %>%
add_p(test = value ~ "my_friedman", group = Participant.ID)
Created on 2023-01-08 with reprex v2.0.2