References \ref{fig:chunk_label} in markdown with pdf_document output are only resolved when specifying chunk options in addition to fig.cap

[jranke]

Consider the following example markdown:

---
title: MWE for figure labels
output:
  pdf_document:
    keep_md: true
    fig_height: 2
---

I think his reference should be resolved to the following Figure \ref{fig:plot_1}.

```{r plot_1, fig.cap = "Plot 1"}
plot(0)
```

Generation of the reference is triggered e.g. by requesting centering in the chunk
options (Figure \ref{fig:plot_2}).

```{r plot_2, fig.cap = "Plot 2", fig.align = "center"}
plot(0)
```

Rendering with rmarkdown::render() shows that only the second reference is resolved:

The markdown generated for the plots is the following:

```r
plot(0)
```

![Plot 1](mwe_files/figure-latex/plot_1-1.pdf)

and

```r
plot(0)
```

\begin{figure}

{\centering \includegraphics{mwe_files/figure-latex/plot_2-1} 

}

\caption{Plot 2}\label{fig:plot_2}
\end{figure}

Reading the documentation of the plot specific chunk options, especially of fig.lp, I would expect that the label would also be generated for the first chunk.

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Locale:
  LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
  LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
  LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
  LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
  LC_ADDRESS=C               LC_TELEPHONE=C            
  LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

Package version:
  base64enc_0.1.3  bslib_0.4.0      cachem_1.0.6     digest_0.6.29   
  evaluate_0.15    fastmap_1.1.0    fs_1.5.2         glue_1.6.2      
  graphics_4.2.1   grDevices_4.2.1  highr_0.9        htmltools_0.5.3 
  jquerylib_0.1.4  jsonlite_1.8.0   knitr_1.39       magrittr_2.0.3  
  memoise_2.0.1    methods_4.2.1    R6_2.5.1         rappdirs_0.3.3  
  rlang_1.0.4      rmarkdown_2.14.3 sass_0.4.2       stats_4.2.1     
  stringi_1.7.8    stringr_1.4.0    tinytex_0.40     tools_4.2.1     
  utils_4.2.1      xfun_0.31        yaml_2.3.5      

Pandoc version: 2.9.2.1

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[cderv]

Referencing mechanism for all figure with caption is available through bookdown::pdf_document2 which brings bookdown feature https://bookdown.org/yihui/bookdown/figures.html

Without pdf_document, you get it working in the second case because adding fig.align is among the special option that make knitr write the plot code directly in LaTeX (option that triggers that are c('out.width', 'out.height', 'out.extra', 'fig.align', 'fig.subcap', 'fig.env', 'fig.scap', 'fig.alt'))

In the first case, knitr will generate markdown code ![caption](img/path) that won't have the label feature. That is why it is not working.

Using bookdown feature would get use labelling and numbering for both PDF and HTML.

@yihui is this explain better somewhere ?

[yihui]

That's a clear enough explanation. I don't remember if this is documented anywhere, although I have explained it a few times before in various places.

[jranke]

Thank you both for your time! I did not know about bookdown::pdf_document2, I just tried it and it works nicely for my purposes. And I do not know what would be the best place to document this. I was looking at the knitr chunk options to find out how it works, but I was actually using rmarkdown::pdf_documenta and rmarkdown::render.

[cderv]

I think the fact you ask the question here is part of the documentation for those having the same question. Using bookdown is the really the good way in that case.

Thank for asking !

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