Cross-referencing in rticles - r

Question

The bookdown offers great cross-referencing options for equations, figures, tables and sections:
https://bookdown.org/yihui/bookdown/cross-references.html
However, they seems to not work when I set as an output 'rticles::elsevier_article'.
What are the available options for cross-referencing in rticles?

Answer 1

I haven't tried, but there is a possible solution here: https://bookdown.org/yihui/bookdown/a-single-document.html
Particularly, specify in your YAML metadata:
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article

Answer 2

Since I am new using R Markdown I have decided to post this answer as some people may incur in the same mistake. I have tried myself F Rodriguez-Sanchez answer but it did not work. I got the following message:
! LaTeX Error: File `elsarticle.cls' not found.
! Emergency stop.
<read *>
Erro: Failed to compile report.tex. See report.log for more info.
It did not work because I was making a rookie mistake since I was trying to add the suggested answer choosing New Markdownand then choosing Document.
I have then tried to open a New R Markdown choosing From Template and Elsevier Journal Article from rticles package. After that, I have used F Rodriguez-Sanchez suggested answer and it worked!
The final yaml header was:
---
title: Short Paper
author:
- name: Alice Anonymous
email: alice#example.com
affiliation: Some Institute of Technology
footnote: Corresponding Author
- name: Bob Security
email: bob#example.com
affiliation: Another University
address:
- code: Some Institute of Technology
address: Department, Street, City, State, Zip
- code: Another University
address: Department, Street, City, State, Zip
abstract: |
This is the abstract.
It consists of two paragraphs.
journal: "An awesome journal"
date: "`r Sys.Date()`"
bibliography: mybibfile.bib
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article
---

Answer 3

#maycca please make sure to open the RMarkdown by choosing New Files from Template and select the Elsevier Journal version/template. The template(s) will be available after the rticles installation.
This will setup the article "infrastructure" (in particular the respective cls and other files). This also includes a mybibfile.bib example (thus, I would have not needed to comment the biblio out).
If you choose to save this in a sub-folder, make sure that your Rmd file is saved in that sub-folder.
As presented above/below change the output: tag of the YAML to include the bookdown and baseformat rticles::elsevier_article pointer.
Check the use of colons and tabs carefully.
Based on the example above, you can then use the bookdown cross-referencing as shown below. I used
(i) an external (bookdown) figure caption defined before the code chunk using (ref:awesomeplotcaption). This is useful to keep the chunk options short(er).
(ii) a (bookdown) cross-reference to the figure \#ref(fig:awesomeplot). Please note that the \#ref(fig:...) uses the chunk-name to make the pointer work. Thus, make sure your chunk-name comes with standard letters, numbers, and dashes, i.e. no underscore!
Hitting the knit button will do the magic!
---
title: Short Paper
author:
- name: Alice Anonymous
email: alice#example.com
affiliation: Some Institute of Technology
footnote: Corresponding Author
- name: Bob Security
email: bob#example.com
affiliation: Another University
address:
- code: Some Institute of Technology
address: Department, Street, City, State, Zip
- code: Another University
address: Department, Street, City, State, Zip
abstract: |
This is the abstract.
It consists of two paragraphs.
journal: "An awesome journal"
date: "`r Sys.Date()`"
#bibliography: mybibfile.bib
output:
bookdown::pdf_book:
base_format: rticles::elsevier_article
---
# First Heading
Some cool introductory text.
And an even more fascinating plot.
(ref:awesomeplotcaption) A simple demo plot
```{r awesomeplot, fig.cap="(ref:awesomeplotcaption)"}
x <- -5:5
y <- x^2
plot(x,y)
```
More explanatory text.
Using bookdown cross-referencing, have again a closer look at Fig. \#ref(fig:awesomeplot).
This results in the following:
P.S. Focus on the cross-reference and ignore the code-chunk, this could be hidden with echo = FALSE. The figure follows below (in this example, placed via LATEX). I truncated it to keep the figure manageable :)