tbl_summary function

[Jovinjo]

Hello everyone, I am currently working on the package "gtsummary" and use its function tbl_summary to create descriptive statistics table. I want to add a 95% CI of mean to the table and according to this article FAQ + Gallery • gtsummary I should add the function "ll" and "ul"

This is my code:

ll <- function(x) t.test(x)$conf.int[[1]] # Lower 95% CI of mean
ul <- function(x) t.test(x)$conf.int[[2]] # Upper 95% CI of mean
      
# create table 1
table <- df() %>% select(input$indStat,input$depStat) %>% 
        tbl_summary(by=input$indStat,type=all_continuous()~"continuous2",statistic = list(all_continuous()~c("{mean}","{sd}","{ll}","{ul}","{median}", "{p25} , {p75}","{min} , {max}")),missing="no",digits = all_continuous() ~ 3) 

however, it shows an error as follows:

Warning: Error in : Problem with mutate() input df_stats.
x Problem with mutate() input value.
x could not find function "ll"
i Input value is purrr::map2_dbl(...).
i Input df_stats is pmap(...).
129:

I am creating a shiny web app and anyone has idea how to solve this one? I dont understand why it has something to do with mutate() function and why it could not find function "ll". Thank you so much!

[statistishdan]

Can you post an example data set illustrating the problem? When I run your code on the trial data included with gtsummary, I don't see any error.

ll <- function(x) t.test(x)$conf.int[[1]] # Lower 95% CI of mean
ul <- function(x) t.test(x)$conf.int[[2]] # Upper 95% CI of mean

# create table 1
table <-
  trial %>%
  select(trt, age) %>%
  tbl_summary(
    by = trt,
    type = all_continuous() ~ "continuous2",
    statistic = all_continuous() ~ c("{mean}", "{sd}", "{ll}", "{ul}", "{median}", "{p25} , {p75}", "{min} , {max}"),
    missing = "no",
    digits = all_continuous() ~ 3
  )

[Jovinjo]

That works when I run the code in R console, but unfortunately when I try to put it in the R Shiny Script it shows the error. So the problem apparently located on the function "ll" and "ul", somehow if I put it in the R Shiny script within the server, it can not read the function and gives the error that "x could not find function ll". But when I remove the ll and ul from gtsummary table, it works fine. Here is example in shiny code:

library(gtsummary)
library(gt)
library(dplyr)

ui <- fluidPage(
  titlePanel("Hello Shiny!"),
  sidebarLayout(
    sidebarPanel(),
    mainPanel(
      gt_output("tblsummary"),
    ) )
)

# Define server logic required to draw a histogram ----
server <- function(input, output) {
  
  output$tblsummary <- render_gt({
    ll <- function(x) t.test(x)$conf.int[[1]] # Lower 95% CI of mean
    ul <- function(x) t.test(x)$conf.int[[2]] # Upper 95% CI of mean
    
    # create table 1
    table <-
      trial %>%
      select(trt, age) %>%
      tbl_summary(
        by = trt,
        type = all_continuous() ~ "continuous2",
        statistic = all_continuous() ~ c("{mean}", "{sd}", "{ll}", "{ul}", "{median}", "{p25} , {p75}", "{min} , {max}")
      ) %>% as_gt()
    
  })
  
}
shinyApp(ui, server)

[statistishdan]

Hmmm, I am not sure! I don't use Shiny much. I'll ask around and report back!

[Jovinjo]

Thank you so much! that would be great!

[Nate884]

It's a scoping issue. That code belongs outside of the server step. Confirmed following code works.

Nate

library(gtsummary)
library(gt)
library(dplyr)
library(shiny)

ll <- function(x) t.test(x)$conf.int[[1]] # Lower 95% CI of mean
ul <- function(x) t.test(x)$conf.int[[2]] # Upper 95% CI of mean

ui <- fluidPage(
  titlePanel("Hello Shiny!"),
  sidebarLayout(
    sidebarPanel(),
    mainPanel(
      gt_output("tblsummary"),
    ) )
)

# Define server logic required to draw a histogram ----
server <- function(input, output) {

  output$tblsummary <- render_gt({
   
    
    # create table 1
    table <-
      trial %>%
      select(trt, age) %>%
      tbl_summary(
        by = trt,
        type = all_continuous() ~ "continuous2",
        statistic = all_continuous() ~ c("{mean}", "{sd}", "{ll}", "{ul}", "{median}", "{p25} , {p75}", "{min} , {max}")
      ) %>% as_gt()
    
  })
  
}
shinyApp(ui, server)

[Jovinjo]

I have tried that one as well and it does not work, still the same error above appears. Does it work when you run it?

[Nate884]

Ok, well let's use the global assignment and see if that works.

library(gtsummary)
library(gt)
library(dplyr)
library(shiny)


ll <<- function(x) t.test(x)$conf.int[[1]] # Lower 95% CI of mean
ul <<- function(x) t.test(x)$conf.int[[2]] # Upper 95% CI of mean
ui <- fluidPage(
    titlePanel("Hello Shiny!"),
    sidebarLayout(
        sidebarPanel(),
        mainPanel(
            gt_output("tblsummary"),
        ) )
)

# Define server logic required to draw a histogram ----
server <- function(input, output) {
    
    output$tblsummary <- render_gt({
        
        
        # create table 1
        table <-
            trial %>%
            select(trt, age) %>%
            tbl_summary(
                by = trt,
                type = all_continuous() ~ "continuous2",
                statistic = all_continuous() ~ c("{mean}", "{sd}", "{ll}", "{ul}", "{median}", "{p25} , {p75}", "{min} , {max}")
            ) %>% as_gt()
        
    })
    
}

# Run the application 
shinyApp(ui = ui, server = server)

[statistishdan]

That worked for me! Thank you @Nate884 !

[Jovinjo]

That worked for me too! Thank you so much @Nate884 for your help!

[mosotieno]

It works pretty well