Referencing custom tables

[mbojan]

Hi!

I wrote some code that generates LaTeX or HTML code for custom-made tables. I would very much like to take advantage of \@referencing syntax of bookdown.

It was fairly simple with LaTeX as I had to simply throw in \label{} somewhere in the output.

I am trying to understand how does it work with HTML output. In the md file generated with bookdown::html_document2 a table produced with knitr::kable inserts something like

Table: (\#tab:knitrtable)This is knitr kable table.

Variable    num  ch   f    logical 
---------  ----  ---  ---  --------
A             1  a    a    FALSE   
B             2  b    b    TRUE    
C             3  c    c    TRUE    
D             4  d    d    TRUE    
E             5  e    e    FALSE   

See table \@ref(tab:knitrtable).

I tried inserting <caption> tags with the similar structure as the corresponding HTML output from bookdown::html_document2 but it does not work. I am not sure at which stage of document processing bookdown resolves the references.

Any suggestions how could I make it work?

[yihui]

It will be nice if you can provide a minimal example of what you tried exactly so I don't have to guess. Anyway, I think if your table caption is of this form <caption>(#tab:label), \\@ref(label) should work.

[mbojan]

Yes, sorry about the lack of example. The original code would be overwhelming with details so I started to distill a simple example. While doing that I was able to get it to work :D

Thanks for the suggestion! I was mislead by the \ in the Markdown code above.

Here is what works for me (essentially):

The code

library(magrittr)

test_table <- function(caption, label) {
  require(magrittr)
  m <- matrix(1:2, 4, 3)
  lab <- paste0("(#tab:", label, ")")
  out <- c(
    "<table style='width: 50%;'>",
    paste0("<caption>", lab, caption, "</caption>"),
    structure( paste0("<td>", m, "</td>"), dim=dim(m) ) %>%
      apply(1, paste, collapse="") %>%
      paste0("<tr>", ., "</tr>"),
    "</table>"
  )
  cat(out, sep="\n")
}

and later in Rmarkdown

   Blah blah
   ```{r tableone, results="asis"}
   test_table("This is a table", label="tableone")
   ```

   See \@ref(tab:tableone).

[yihui]

Okay, great!

[mbojan]

Well, in fact, I'm still fighting with it. I am trying to hack htmlTable. See this:

tab <- withr::with_options(
  list(htmlTableCompat="html"),
  htmlTable::htmlTable(matrix(1:12, 4 ,3), caption="(#tab:tabletwo) A table")
)
cat(unclass(tab))

gives the following HTML:

<table class='gmisc_table' style='border-collapse: collapse; margin-top: 1em; margin-bottom: 1em;' >
<caption style='caption-side: top'>
(#tab:tabletwo) A table</caption>
<thead>
</thead>
<tbody>
<tr>
<td style='text-align: center;'>1</td>
<td style='text-align: center;'>5</td>
<td style='text-align: center;'>9</td>
</tr>
<tr>
<td style='text-align: center;'>2</td>
<td style='text-align: center;'>6</td>
<td style='text-align: center;'>10</td>
</tr>
<tr>
<td style='text-align: center;'>3</td>
<td style='text-align: center;'>7</td>
<td style='text-align: center;'>11</td>
</tr>
<tr>
<td style='border-bottom: 2px solid grey; text-align: center;'>4</td>
<td style='border-bottom: 2px solid grey; text-align: center;'>8</td>
<td style='border-bottom: 2px solid grey; text-align: center;'>12</td>
</tr>
</tbody>
</table>

When run in RMarkdown \@ref(tab:tabletwo) seems to give correct hyperlinked reference with number, but the table caption does not work and in browser looks like (#tab:tabletwo) A table.

Any ideas?

[mbojan]

I did a bit of debugging...

It seems that the caption fails to be updated because the regexp in parse_fig_labels (https://github.com/rstudio/bookdown/blob/4a8a9f5d7955740ab701afd3213ff78eb4f1cbd7/R/html.R#L521) is looking for "^<caption>" so assumes that there are no tag attributes. This fails in my code because the <caption> tag has attributes.

Am I correct that the search is done only to check if the (#tab:label) piece is mentioned within HTML <caption>?

Perhaps the regexp could just catch "^<caption"?

[mbojan]

I forked, tried, and it fixes the problem. I'm not 100% sure if it does not break anything, but so far so good.

Want a PR?

[yihui]

I don't know if it is going to break anything, either, but I have merged it anyway. If I discover problems in the future, I may revert it. Thanks!

[CarolineXGao]

Hi Yihui,

I have a similar issue. Referencing seems to work for html and word but not pdf. Do you know where things might be wrong ?

Thanks

Caroline

---
title: "Test"
output:
    bookdown::pdf_document2 
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE,warning=FALSE,message=FALSE)

This is a reference to Table \@ref(tab:tableone).

cat("<caption> Table (\\#tab:tableone)  A Caption </caption>")

[andreapierucci]

HI, @yihui and @mbojan I have a problem similar to Caroline.

When I use \cite{} in my table in bookdown::pdf_book: like

\begin{tabular}{|l|l|l|l|} \hline reference & Charactersitic 1 & Charactersitic 2 & Charactersitic 3 \ \hline \cite{stefc2009partII} & method xx & method xy & method xz \ \hline \cite{stefc2009partII} & method yx & method yy & method yz \ \hline \end{tabular}

it works only for :word_document2: but not for bookdown::pdf_book:

I also tried with \@cite{stefc2009partII} ; \cite[@stefc2009partII]}; \cite[@stefc2009partII]} ; \@cite(stefc2009partII) no one works...

I'm very new to LaTeX, Rmd ,and bookdown, I'm using those for writing down my PhD Thesis.

Could you help me, please?

.bib @article{stefc2009partII, title={Report of the SGMED-09-03 Working Group on the Mediterranean Part II}, author={Massimiliano Cardinale, Anna Cheilari, Hans-Joachim Rätz}, journal={EUR - Scientific and Technical Research Reports (STEFC) }, year={2009}, publisher={JRC} }

[cderv]

Hi @andreapierucci Can you open a new issue following the issue guide https://yihui.org/issue/ ?

Or ask in one of the QA site before if not already done in case you are not sure this is an issue ? Thanks!

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