Cross-referencing gt tables does not work when knitting to PDF

[camillebelmin]

Hi,
Thanks a lot for making progress on the gt package to allow cross referencing within bookdown documents. However, I have the impression that it still does not work for PDFs. In the reproducible example below, cross-reference did not work when knitting to bookdown::pdf_document2 (resulting in "Table ??"). It only worked when knitting to bookdown::html_document2 (resulting in "Table 1"). Could you please let me know if there is a trick to make it work with PDF, or whether cross-ref for PDF is planned to be developed in the near future?

I am now referencing Table \@ref(tab:label)

```{r label }
df = data.frame(A = c(1,2,3), B = c(4,5,6))

gt(df, caption = "this is the caption")
```

Originally posted by @camillebelmin in #115 (comment)

[earcanal]

I don't get a caption or table number in this MWE:

---
blind: true
title: |
  MWE
always_allow_html: true
output:
  bookdown::pdf_document2:
    toc: false
    number_sections: false
    latex_engine: lualatex
    template: null
    keep_tex: true
header-includes:
      \usepackage{amsmath}
      
      \usepackage{booktabs}
      
      \usepackage{caption}
      
      \usepackage{longtable}
documentclass: article
link-citations: true
---

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

library(tidyverse)
library(gt)
```

If Table \@ref(tab:mwe) has a caption, then `gt` can probably be used in `bookdown`.

```{r mwe, results='asis'}
df = data.frame(A = c(1,2,3), B = c(4,5,6))
gt(df, caption = "this is the caption") %>% as_latex() %>% as.character() %>% cat()
```

... and the LaTeX generated:

% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
]{article}
\usepackage{amsmath,amssymb}
\usepackage{lmodern}
\usepackage{ifxetex,ifluatex}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
  \usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
  \usepackage{unicode-math}
  \defaultfontfeatures{Scale=MatchLowercase}
  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
  \usepackage[]{microtype}
  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
  \IfFileExists{parskip.sty}{%
    \usepackage{parskip}
  }{% else
    \setlength{\parindent}{0pt}
    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
  \KOMAoptions{parskip=half}}
\makeatother
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\hypersetup{
  pdftitle={MWE},
  hidelinks,
  pdfcreator={LaTeX via pandoc}}
\urlstyle{same} % disable monospaced font for URLs
\usepackage{longtable,booktabs,array}
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\usepackage{amsmath}
\usepackage{booktabs}
\usepackage{caption}
\usepackage{longtable}
\ifluatex
  \usepackage{selnolig}  % disable illegal ligatures
\fi

\title{MWE}
\author{}
\date{\vspace{-2.5em}}

\begin{document}
\maketitle

If Table \ref{tab:mwe} has a caption, then \texttt{gt} can probably be used in \texttt{bookdown}.

\captionsetup[table]{labelformat=empty,skip=1pt}
\begin{longtable}{rr}
\toprule
A & B \\ 
\midrule
1 & 4 \\ 
2 & 5 \\ 
3 & 6 \\ 
\bottomrule
\end{longtable}

\end{document}

> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.04

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gt_0.4.0.9000          forcats_0.5.1          stringr_1.4.0          dplyr_1.0.8            purrr_0.3.4            readr_2.0.0           
 [7] tidyr_1.1.4            tibble_3.1.6           ggplot2_3.3.5          tidyverse_1.3.1        BayesFactor_0.9.12-4.2 Matrix_1.3-2          
[13] coda_0.19-4           

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7         lubridate_1.7.10   mvtnorm_1.1-2      lattice_0.20-41    gtools_3.9.2       assertthat_0.2.1   digest_0.6.29     
 [8] utf8_1.2.2         R6_2.5.1           cellranger_1.1.0   backports_1.4.1    MatrixModels_0.5-0 reprex_2.0.0       evaluate_0.14     
[15] httr_1.4.2         pillar_1.7.0       rlang_1.0.1        readxl_1.3.1       rstudioapi_0.13    rmarkdown_2.9      munsell_0.5.0     
[22] broom_0.7.8.9000   compiler_4.0.4     modelr_0.1.8       xfun_0.27          pkgconfig_2.0.3    htmltools_0.5.2    tidyselect_1.1.2  
[29] bookdown_0.22      fansi_1.0.2        crayon_1.5.0       tzdb_0.1.2         dbplyr_2.1.1       withr_2.4.3        grid_4.0.4        
[36] jsonlite_1.7.2     gtable_0.3.0       lifecycle_1.0.1    DBI_1.1.1          magrittr_2.0.2     scales_1.1.1       cli_3.2.0         
[43] stringi_1.7.6      pbapply_1.4-3      fs_1.5.2           xml2_1.3.2         ellipsis_0.3.2     generics_0.1.2     vctrs_0.3.8       
[50] tools_4.0.4        glue_1.6.1         hms_1.1.0          yaml_2.2.1         parallel_4.0.4     fastmap_1.1.0      colorspace_2.0-3  
[57] rvest_1.0.0        knitr_1.36         haven_2.4.1   

[hansvancalster]

Here is a workaround - specifically for bookdown in combination with gt- that did the trick for me:

---
title: "Untitled"
author: ""
date: "`r Sys.Date()`"
output:
  bookdown::html_document2:
    toc: true
  bookdown::pdf_document2:
    toc: true
---

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


## Table caption with `gt` for pdf or html output


Table \@ref(tab:cars-table)

(ref:cars-table) The cars data set


```{r custom-function}
as_latex_with_caption <- function(gt, chunk_label) {
  gt <- gt::as_latex(gt)
  caption <- paste0(
    "\\caption{\\label{tab:", chunk_label, "}(ref:", chunk_label, ")}\\\\")
  latex <- strsplit(gt[1], split = "\n")[[1]]
  latex <- c(latex[1], caption, latex[-1])
  latex <- paste(latex, collapse = "\n")
  gt[1] <- latex
  return(gt)
}
```

```{r cars-table}
if (knitr::is_latex_output()) {
  gt(cars) %>%
    as_latex_with_caption("cars-table")
}
if (knitr::is_html_output()) {
  gt(cars, caption = "(ref:cars-table)")
}
```

[olivroy]

You are likely to be better off using Quarto LaTeX output. The support for cross-references is done natively.

[olivroy]

the development version of gt now includes a fix for this, thanks to @nielsbock, in case people want to try it out!

pak::pak("rstudio/gt")

We'd love to receive your feedback so please open a new issue if something is not working as expected.