adding arsenal tables to jamovi

[sbalci]

Dear developers,
I am trying to add arsenal tables into jamovi in the ClinicoPath module.

Users are informed that arsenal package is used and citation is given with each analysis. I would like to ask your help regarding pfootnotes.

• Screenshots of output:

• The code I use is:

                tablearsenal <- arsenal::tableby(formula = formula,
                                                 data = mydata,
                                                 total = TRUE,
                                                 digits = 1,
                                                 digits.count = 1
                )

                tablearsenal <- summary(tablearsenal,
                                        text = 'html',
                                        pfootnote = TRUE
                                        )


                tablearsenal <-
                    kableExtra::kable(tablearsenal,
                                      format = "html",
                                      digits = 1,
                                      escape = FALSE
                                      )

• My issue is that: Although I use pfootnote = TRUE I could not get it work with kable. The output does not give test names.

• I assume since the names of tests are outside </table>, the kable function does not return them in the output.
  The summary produces following:

   <td style="text-align:center;"> 122 (49.2%) </td>
   <td style="text-align:right;">  </td>
  </tr>
</tbody>
</table>
1. Linear Model ANOVA
2. Pearson's Chi-squared test

As a note I tried other output options but I could avoid   blank spaces only with kable.

Would you please guide me in adding the test names to the output?

Best wishes and thank you for the package.

[eheinzen]

Try this:

summary(tableby(sex ~ age + arm, data = mockstudy), text = "html", pfootnote = "html")

Does that work?

[sbalci]

Thank you.

Now, the footnote is html tagged. However since it is below </table> it is still not added to table output.

In R markdown the results are also separated. Table is in knit_asis part, the footnote is in R Console part.

Is it possible to combine these two summary outputs, the knit_asis part and console part?

Is there any method to do this with R I can try for my case.

Best wishes

...
  </tr>
</tbody>
</table>
<ol>
<li>Linear Model ANOVA</li>
<li>Pearson's Chi-squared test</li>
</ol>

[sbalci]

Using capture.output()I have managed to make it work.
Thank you for your time.

[eheinzen]

Oh yes--sorry! I should've mentioned that you'd probably need capture.output()