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FAQ

1. How do I include a citation or figure reference or r object value in a figure or table caption?

    ```{r chunk1}
    x <- 7
    ```

    (ref:my-caption) A figure caption. See Appendix \@ref(app:my-appendix)). x has 
    the value `r x`. See @viridis2018.

    ```{r my-figure, fig.cap="(ref:my-caption)"}
    plot(1)
    ```

2. How do I include extra packages for latex-rendered documents?

In the index.Rmd file, add the following to the YAML part (the section between the --- and ---) for whatever package you want to include. For this example it is the threeparttablex package:

header-includes:
  - \usepackage{threeparttablex}

Note that if you need to include more than one package you will have to have them on the same line like this:

header-includes:
  - \usepackage{threeparttablex} \usepackage{caption}

This will NOT work, only the first one is added:

header-includes:
  - \usepackage{threeparttablex}
  - \usepackage{caption}

3. I have added appendices after the bibliography, but they are appearing in the document before the bibliography. How do I make the bibliography appear before the appendices?

Add the following line where you want the bibliography to be placed:

<div id="refs"></div>

4. When I click on links in the PDF (e.g. figures or citations) they don't take me to the appropriate figure or reference. How do I fix that? Try running tinytex::tlmgr_install("hyperref").

Notes

1. To see the variables declared in _bookdown.yml, you can do the following from any R chunk within the project:

config <- bookdown:::load_config()

2. To access the YAML metadata located at the beginning of index.Rmd, you can look at the following list from any R chunk within the project:

rmarkdown::metadata

For example if creating a CSAS SR document, the following YAML metadata will be in index.Rmd:

output:
 csasdown::sr_pdf:
   french: true

In the setup R chunk, the following line of code would set up the language for R:

french <- rmarkdown::metadata$output$`csasdown::sr_pdf`$french

3. If writing the document in French, you can change the decimal point to a comma for all numeric values in the project using the following in the setup chunk:

if(french){
  options(OutDec =  ",")
}

4. Knitr chunk names can only have numbers, letters, and dashes. Underscores are not permitted and will cause major problems in rendering with bookdown. Here is an example of a bad chunk:

```{r bad_chunkname, results = "asis"}
    d <- data.frame(x = c(1,2,3,4),
                    y = c(5,6,7,8),
                    z = c(9,10,11,12))
    csasdown::csas_table(d,
                         format = "latex",
                         font_size = 8,
                         caption = "XX - This table is broken")
```

The error for this was:

! Misplaced \noalign.
\toprule ->\noalign 
                    {\ifnum 0=`}\fi \@aboverulesep =\abovetopsep \global \@b...
l.125 ...able is broken\}\textbackslash{} \toprule
                                                   x \& y \& z\textbackslash...

Error: Failed to compile resdoc.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See resdoc.log for more info.
Execution halted

And the resulting TeX file had broken code for the table with many \textbackslash{} commands peppered through it:

\textbackslash{}begin\{longtable\}\{rrr\} \textbackslash{}caption\{(\#tab:broken\_table)XX - This table is broken\}\textbackslash{} \toprule x \& y \& z\textbackslash{} \midrule 1 \& 5 \& 9\textbackslash{} 2 \& 6 \& 10\textbackslash{} 3 \& 7 \& 11\textbackslash{} 4 \& 8 \& 12\textbackslash{} \bottomrule \textbackslash{}end\{longtable\}

Do not include spaces or ~ in any folders in the path to your document. LaTeX doesn't play nicely with them.