Unexpected behaviours when making tables for copernicus articles

Inizia dal punto di ingresso del template per articoli Copernicus e renderizza l’esempio fornito tramite bookdown::pdf_book, quindi ispeziona il file .tex generato nella zona intorno a \toprule. Controlla la configurazione dei pacchetti LaTeX del template e la gestione dei riferimenti alle tabelle e delle citazioni. Il lavoro è completo quando il PDF viene compilato con booktabs e sia il riferimento alla tabella sia la citazione @Dirac1953888 vengono visualizzati correttamente.

I want to make a simple table (where booktabs=TRUE) in a copernicus article. When I knit the following copernicus article (using the template provided by the package) to pdf_book

---
title: Template for preparing your manuscript submission to Copernicus journals using RMarkdown
journal: "`r rticles::copernicus_journal_abbreviations(journal_name = 'communication')`"
author:
    # authors can have multiple affiliations, which can also be used to mark deceased coauthors
  - given_name: Daniel
    surname: Nüst
    affiliation: "1, *"
    email: [email protected]
    corresponding: true
  - given_name: Josiah
    surname: Carberry
    affiliation: 2
    email: [email protected]
  - given_name: Markus
    surname: Konkol
    affiliation: "1, *"
  - given_name: Nikolaus
    surname: Copernicus
    affiliation: "3, †"
# If you have more than one corresponding author, add them manually using the following structure (note the commas):
# Two authors: Daniel Nüst ([email protected]) and Josiah Carberry ([email protected])
# Three authors or more: Daniel Nüst ([email protected]), Josiah Carberry ([email protected]), and Markus Konkol ([email protected])
# If the following line is uncommented, the "corresponding: true" above are ignored
#correspongdingauthors: Daniel Nüst ([email protected]) and Josiah Carberry ([email protected])
# If authors contributed equally, please mark the respective author names with an asterisk '*' and add a further affiliation: 'These authors contributed equally to this work.'", see template.
affiliation:
  - code: 1
    address: Institute for Geoinformatics, University of Münster, 48149 Münster, Germany
  - code: 2
    address: Psychoceramics, Wesleyan University, Middletown, CT, United States
  - code: 3
    address: University of Ferrara, Ferrara, Italy
  - code: "†"
    address: deceased, 24 May 1543
  - code: "*"
    address: These authors contributed equally to this work.
abstract: |
  The abstract goes here.
  It can also be on _multiple lines_.
bibliography: sample.bib
running:
  title: R Markdown Template for Copernicus
  author: Nüst et al.
competinginterests: |
  The authors declare no competing interests.
# See https://publications.copernicus.org/for_authors/licence_and_copyright.html, normally used for transferring the copyright, if needed. 
# Note: additional copyright statements for affiliated software or data need to be placed in the data availability section. 
copyrightstatement: |
  The author's copyright for this publication is transferred to institution/company. 
### Note: unless stated otherwise, software and data affiliated with the manuscript are assumed to be published under the same licence as the article (currently Creative Commons 4.0)
availability:
  #  use this to add a statement when having only software code available
  #  use this to add a statement when having only data sets available
  #code: |
  #data: |
  codedata: |
    use this to add a statement when having data sets and software code available
  sample: |
    use this section when having geoscientific samples available
videosupplement: |
  use this section when having video supplements available
authorcontribution: |
  Daniel wrote the package. Josiah thought about poterry. Markus filled in for a second author.
disclaimer: |
  We like Copernicus.
acknowledgements: |
  Thanks to the rticles contributors!
appendix: |
  \section{Figures and tables in appendices}
  \subsection{Option 1}
  If you sorted all figures and tables into the sections of the text, please also sort the appendix figures and appendix tables into the respective appendix sections.
  They will be correctly named automatically.
  \subsection{Option 2}
  If you put all figures after the reference list, please insert appendix tables and figures after the normal tables and figures.
  
  `\appendixfigures` needs to be added in front of appendix figures
  `\appendixtables` needs to be added in front of appendix tables
  
  Please add `\clearpage` between each table and/or figure. Further guidelines on figures and tables can be found below.
  Regarding figures and tables in appendices, the following two options are possible depending on your general handling of figures and tables in the manuscript environment:
  To rename them correctly to A1, A2, etc., please add the following commands in front of them:
output:
  bookdown::pdf_book:
    base_format: rticles::copernicus_article # for using bookdown features like \@ref()
  rticles::copernicus_article: 
    highlight: NULL
    keep_tex: true
---

\introduction[Introduction]

See Table \@ref(tab:t)

```{r t, echo=FALSE}
df = mtcars[1:3, 1:3]
df$ref = "@Dirac1953888"
knitr::kable(df, booktabs = TRUE)
```

I get the following error:

tlmgr update --all --self
tlmgr: package repository https://mirror.easyname.at/ctan/systems/texlive/tlnet (verified)
tlmgr install: package already present: hyperref
! Undefined control sequence.
l.142 \toprule

Error: LaTeX failed to compile t.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See t.log for more info.
Execution halted

Interestingly, when I do not use booktabs (which I need to):

```{r t, echo=FALSE}
df = mtcars[1:3, 1:3]
df$ref = "@Dirac1953888"
knitr::kable(df, booktabs = FALSE)
```

I get:

So, rendering of the document seems to work, but there are 2 problems:

• Table referencing does not work
• Citation (@Dirac1953888) which is included in the sample.bib file (provided by the copernicus template) does not properly show up in the "ref" column of the table

> xfun::session_info('rticles')
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin23.0.0 (64-bit)
Running under: macOS Sonoma 14.2.1, RStudio 2023.12.0.369

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  base64enc_0.1.3   bslib_0.6.1       cachem_1.0.8      cli_3.6.2         digest_0.6.34     ellipsis_0.3.2   
  evaluate_0.23     fastmap_1.1.1     fontawesome_0.5.2 fs_1.6.3          glue_1.7.0        graphics_4.3.2   
  grDevices_4.3.2   highr_0.10        htmltools_0.5.7   jquerylib_0.1.4   jsonlite_1.8.8    knitr_1.45.10    
  lifecycle_1.0.4   magrittr_2.0.3    memoise_2.0.1     methods_4.3.2     mime_0.12         R6_2.5.1         
  rappdirs_0.3.3    rlang_1.1.3       rmarkdown_2.25    rticles_0.26.1    sass_0.4.8        stats_4.3.2      
  stringi_1.8.3     stringr_1.5.1     tinytex_0.49      tools_4.3.2       utils_4.3.2       vctrs_0.6.5      
  xfun_0.41         yaml_2.3.8  

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