Conditional independence symbol when rendering to pdf

[jfieberg]

I am trying to compile a quarto document to both HTML and pdf that includes a conditional independence symbol and a "not" version (see below). I've tried several options, but can only seem to get things to work when compiling to HTML. Here is the quarto file:

---
title: "Reproducible Quarto Document"
format: pdf
---


 
...two types of associations between $X$ and $Y$, with and without conditioning on a third variable, $Z$. In the top panels, $X$ and $Y$ are marginally dependent (i.e., $X  \not\!\perp\!\!\!\perp Y$), but become independent when we condition on $Z$ (i.e., $X \perp\!\!\!\perp Y | Z$).  

Here is the output in the terminal window:

==> quarto preview test2.qmd --to pdf --no-watch-inputs --no-browse

pandoc 
  to: latex
  output-file: test2.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  
metadata
  documentclass: scrartcl
  classoption:
    - DIV=11
    - numbers=noendperiod
  papersize: letter
  header-includes:
    - \KOMAoption{captions}{tableheading}
  block-headings: true
  

Rendering PDF
running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999996 (TeX Live 2024) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode
  
updating tlmgr

updating existing packages
ERROR: 
compilation failed- error
Missing { inserted.
<to be read again> 
                   \mskip 
l.164 \(X  \not\!
                 \perp\!\!\!\perp Y\)), but become independent when we 

see test2.log for more information.

I am using quarto version 1.6.33 and Microsoft Windows [Version 10.0.26100.2033]. Here is the output from quarto check:

C:\Users\jfieberg\Documents\Teaching\Sandbox>quarto check
Quarto 1.6.33
[>] Checking environment information...
      Quarto cache location: C:\Users\jfieberg\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.6.33
      Path: C:\Users\jfieberg\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\jfieberg\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2024

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....(None)

      Unable to locate an installed version of Python 3.
      Install Python 3 from https://www.python.org/downloads/

[>] Checking R installation...........OK
      Version: 4.4.1
      Path: C:/Users/jfieberg/AppData/Local/Programs/R/R-4.4.1
      LibPaths:
        - C:/Users/jfieberg/AppData/Local/Programs/R/R-4.4.1/library
      knitr: 1.48
      rmarkdown: 2.27

[>] Checking Knitr engine render......OK

[mcanouil]

Could you properly format your post using code blocks for code and terminal outputs? Thanks.
If your code contains code blocks, you need to enclose it using more backticks, i.e., usually four ````.
See https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us.

[jfieberg]

Thanks. I don't have any code blocks in the file, only text/latex code. I'm not sure I formatted the output correctly. Happy to try again. Thanks!

[mcanouil]

Your entire post is a code block right now.
Separate your comments, etc. from the code to reproduce your issues.
Don't mixe everything together which makes it hard to know what is what.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[jfieberg]

Thanks for your patience! I think I got it this time (sorry for the confusion on my part!).

[cderv]

I think this is LaTeX problem directly. Quarto defaults to xelatex and this is what causes the issue.

If you set pdf-engine: pdflatex it works

---
title: "Reproducible Quarto Document"
format: 
  pdf:
    pdf-engine: pdflatex
---


 
...two types of associations between $X$ and $Y$, with and without conditioning on a third variable, $Z$. In the top panels, $X$ and $Y$ are marginally dependent (i.e., $X  \not\!\perp\!\!\!\perp Y$), but become independent when we condition on $Z$ (i.e., $X \perp\!\!\!\perp Y | Z$).  

So I would look into why this specific latex equation syntax for xelatex or lualatex engine.

Using pandoc -t pdf -f markdown -o test.pdf --pdf-engine=xelatex test.qmd gives me the same error so I don't think this is related to Quarto directly unfortunately.

[jfieberg]

Thanks! I'm happy to switch to pdflatex as that seems to solve the problem!