Statistical tests not displayed in HTML output with pfootnote = TRUE in Shiny

[PietropaoliLab]

Hello,
I’m experiencing an issue with including statistical tests in the HTML output of a Shiny app using the arsenal package. Despite setting pfootnote = TRUE in the summary(tableby(...)) function, the statistical tests do not appear in the generated HTML output.

Here is the code I am using:

library(shiny)
library(arsenal)
data(mockstudy)

shinyApp(
  ui = fluidPage(tableOutput("table")),
  server = function(input, output) {
    output$table <- renderTable({
      as.data.frame(summary(tableby(sex ~ age, data = mockstudy), text = "html", pfootnote = TRUE))
    }, sanitize.text.function = function(x) x)
  }
)

The HTML output generated by this code is as follows:

<table>
 <thead>
  <tr>
   <th style="text-align:left;">  </th>
   <th style="text-align:center;"> Female (N=6) </th>
   <th style="text-align:center;"> Male (N=13) </th>
   <th style="text-align:center;"> Total (N=19) </th>
   <th style="text-align:right;"> p value </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> <strong>DM</strong> </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:right;"> 0.405<sup>1</sup> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> &nbsp;&nbsp;&nbsp;No </td>
   <td style="text-align:center;"> 4 (66.7%) </td>
   <td style="text-align:center;"> 6 (46.2%) </td>
   <td style="text-align:center;"> 10 (52.6%) </td>
   <td style="text-align:right;">  </td>
  </tr>
  <tr>
   <td style="text-align:left;"> &nbsp;&nbsp;&nbsp;Yes </td>
   <td style="text-align:center;"> 2 (33.3%) </td>
   <td style="text-align:center;"> 7 (53.8%) </td>
   <td style="text-align:center;"> 9 (47.4%) </td>
   <td style="text-align:right;">  </td>
  </tr>
  <tr>
   <td style="text-align:left;"> <strong>age</strong> </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:center;">  </td>
   <td style="text-align:right;"> 0.216<sup>2</sup> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> &nbsp;&nbsp;&nbsp;Mean (SD) </td>
   <td style="text-align:center;"> 70.500 (8.503) </td>
   <td style="text-align:center;"> 64.308 (10.250) </td>
   <td style="text-align:center;"> 66.263 (9.943) </td>
   <td style="text-align:right;">  </td>
  </tr>
  <tr>
   <td style="text-align:left;"> &nbsp;&nbsp;&nbsp;Range </td>
   <td style="text-align:center;"> 59.000 - 83.000 </td>
   <td style="text-align:center;"> 45.000 - 86.000 </td>
   <td style="text-align:center;"> 45.000 - 86.000 </td>
   <td style="text-align:right;">  </td>
  </tr>
</tbody>
</table>
1. Pearson's Chi-squared test
2. Linear Model ANOVA

As shown, the statistical tests (footnotes) are included at the bottom, but they do not appear as expected in the rendered HTML output. It seems that the pfootnote argument is not being applied correctly.

Could you please assist in diagnosing this issue or suggest a workaround to ensure the statistical tests are displayed properly in the HTML output?

Thank you!

[PietropaoliLab]

I solved this issue with HTML(capture.output(x)).
Here the code chunk:

library(shiny)
library(arsenal)
data(mockstudy)

shinyApp(
  ui = fluidPage(tableOutput("table")),
  server = function(input, output) {
    output$table <- renderTable({
      
      # Use capture.output and HTML to solve the issue
      HTML(capture.output(summary(tableby(sex ~ age + race + bmi, data = mockstudy), text = "html", pfootnote = TRUE)))
      
    }, sanitize.text.function = function(x) x)
  }
)