Error when trying to render with multiple subfigures with APA-style figure note

[isaactpetersen]

I'm trying to render a Quarto manuscript that has multiple subfigures with an APA-style figure note. However, I am running into some issues. I believe I am using the latest version of apaquarto.

Here are my findings when trying to render to various formats (when including a figure that has multiple subfigures, each of which has an APA-style figure note):

• apaquarto-docx: works fine
• apaquarto-html: works fine
• html (i.e., commenting out apaquarto-html in _quarto.yml): doesn't work; i.e., doesn't show APA-style figure notes
• apaquarto-pdf: error (see below)

Error running filter C:/PROGRA~1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:
Block, list of Blocks, or compatible element expected, got table
	while retrieving function argument content
	while retrieving arguments for function Div
stack traceback:
	...toReprex\_extensions\wjschne\apaquarto\apafloatlatex.lua:254: in local 'filter_fn'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:655: in function <...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:645>
	(...tail calls...)
	[C]: in ?
	[C]: in method 'walk'
	...\RESOUR~1\app\bin\quarto\share\pandoc\datadir\_utils.lua:607: in function '_utils.walk'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:574: in function <...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:552>
	(...tail calls...)
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1317: in local 'callback'
	[string "if pandoc.system.os == "mingw32" then..."]:778: in field 'withScriptFile'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1333: in upvalue 'run_emulated_filter_chain'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1371: in function <...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1368>
stack traceback:
	...\RESOUR~1\app\bin\quarto\share\pandoc\datadir\_utils.lua:607: in function '_utils.walk'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:574: in function <...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:552>
	(...tail calls...)
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1317: in local 'callback'
	[string "if pandoc.system.os == "mingw32" then..."]:778: in field 'withScriptFile'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1333: in upvalue 'run_emulated_filter_chain'
	...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1371: in function <...1/RStudio/RESOUR~1/app/bin/quarto/share/filters/main.lua:1368>
WARN: Error encountered when rendering files

In case it's helpful, here is a minimal reproducible example:

This works and gives no error (@fig-exampleA):

![Sample Image 1.](Figures/sampleImage1.png){
  #fig-exampleA
  fig-alt="Insert description here."
  apa-note="Variable A indirectly causes Variable C."
  }

This results in an error and/or no figure note (@fig-exampleB):

::: {#fig-exampleB layout-ncol=2}
![Sample Image 1.](Figures/sampleImage1.png){
  #fig-sampleImage1
  fig-alt="Insert description here."
  apa-note="Variable A indirectly causes Variable C."
  }

![Sample Image 2.](Figures/sampleImage2.png){
  #fig-sampleImage2
  fig-alt="Insert description here."
  apa-note="The distribution of a variable."
  }

:::

This results in no error but doesn't show the APA-style figure note (@fig-exampleC):

::: {#fig-exampleC layout-ncol=2}
![Sample Image 1.](Figures/sampleImage1.png){
  #fig-sampleImage1
  fig-alt="Insert description here."
  }

![Sample Image 2.](Figures/sampleImage2.png){
  #fig-sampleImage2
  fig-alt="Insert description here."
  }

**Panel A**: Insert description here.
**Panel B**: Insert description here.
:::

[isaactpetersen]

Thanks very much, @dhagmann, for the pull request to address this issue! I appreciate your looking into that. It appears to address the error when rendering to PDF. However, I am also experiencing an issue when rendering to html specifically (not apaquarto-html). When I render to html (i.e., commenting out apaquarto-html in _quarto.yml), it doesn't error out, but it doesn't show the APA-style figure notes. Do you know if the pull request addresses the issue when rendering to html format, or would that need to be a separate fix?

[dhagmann]

Unfortunately the PR doesn't resolve it for plain html -- it only fixes the PDF path. The notes don't show there because apaquarto's note formatting runs only under its own formats (apaquarto-html, etc.), not base html and so the note stays an inert attribute. Rendering to apaquarto-html will give you the styled notes. Making plain html work would be an apaquarto feature request rather than a bug fix.

[wjschne]

@isaactpetersen and @dhagmann, I believe this is fixed now. Thanks @dhagmann for the suggestions. Let me know if there are still problems. @dhagmann is correct that apa-note is not a feature that works with html, but I can imagine making a standalone filter that would do the job. Interestingly, knitr just asked support for fig.note, which, I may incorporate into apaquarto eventually.

[isaactpetersen]

Thanks for the note and fix. I will go ahead and close this. Would be great to incorporate apa-note or fig.note for html output down-the-line. Would you like me to open an issue for that?

[wjschne]

@isaactpetersen, I think I have it working. Assuming that apaquarto is installed to the project, you add this to your YAML:

filters:
  - apanote

Let me know if this is what you were hoping for.

[isaactpetersen]

Works great--thanks for the fix! I'll go ahead and close this. Much appreciated!

[isaactpetersen]

One thing I noticed when using the apanote filter is that the APA-style figure note displays correctly in html format when the figure is embedded directly, but the figure note does not display in html format when the figure is embedded from another .qmd document.

For instance, this works (the figure notes shows correctly):

```{r}
#| label: fig-mtcars
#| fig-cap: "My Figure Caption"
#| apa-note: "My APA-style figure note."

plot(mtcars)
```

But this doesn't work (the figure notes do not show):

{{< embed notebooks/analyses.qmd#fig-mtcars2 >}}

where notebooks/analyses.qmd contains:

```{r}
#| label: fig-mtcars2
#| fig-cap: "My Figure Caption"
#| apa-note: "My APA-style figure note."

plot(mtcars)
```

Here's a minimal reproducible example and output.

Let me know if it'd be helpful for me to create a new issue.

[wjschne]

@isaactpetersen, how about now? Does the newest version fix it for you?

[isaactpetersen]

Yes, that works--thanks! One quick question: what syntax would you recommend for figure notes in multi-panel figures (i.e., figure notes that you want to include a line break)? For instance, the figure note for the following figure outputs fine to html and pdf format, but it shows up weird in Word format (i.e., it keeps the quote symbols and leading dash as part of the figure note):

```{r}
#| label: fig-mtcars
#| fig-cap: "My Figure Caption"
#| apa-note:
#|   - "**Panel A**: Insert figure note here."
#|   - "**Panel B**: Insert figure note here."

plot(mtcars)
```

The minimal reproducible example is here, and here is the output of html, Word, and PDF. (In my case, the "multi-panel" figure is in a single image.) Thanks in advance!

[wjschne]

Looking at examples from the APA manual, multiple figures with notes look like this:

That is, there are letter labels and the single-paragraph note at the bottom describes each panel. The easiest way of achieving this would be via the patchwork package. For example:

#| label: fig-patchwork
#| fig-cap: A multipanel plot using patchwork
#| fig-height: 4
#| apa-note: "Not only do statistical distributions have distinct shapes, they are used for diverse purposes. Panel A: Because a Cauchy distribution has a location but no mean and no variance, it has thick tails, making it useful when modeling variables with extreme events. Panel B: A Weibull distribution (shown here with shape = 2) is used to model time between events."
library(patchwork)
library(ggplot2)
p1 <- ggplot(data.frame(x = c(-20, 20)), aes(x)) +
  stat_function(fun = dt, 
                args = list(df = 1),
                geom = "area",
                n = 1000,
                color = NA,
                fill = "#41448780") +
  theme_void(base_size = 14)

p2 <- ggplot(data.frame(x = c(0, 3)), aes(x)) +
  stat_function(fun = dweibull, 
                args = list(shape = 2),
                geom = "area",
                n = 1000,
                color = NA,
                fill = "#21511760") +
  theme_void(base_size = 14)

p1 + p2 + 
  plot_annotation(tag_levels = 'A') 

That said, I do not always want what the manual suggests. I think that apaquarto can give better options for subpanels. Let me see what I can do.