Troubleshooting

Each heading below is what you would say out loud, not what is technically happening. If your symptom is here, the fix is under it.

“Where did my tables go? They are all at the end.”

That is not a fault, and it is the most common first surprise. An APA manuscript collects its tables at the end, after the reference list, and apaquarto does that by default because that is the format journals ask for.

If you would rather see each table where you wrote it – which is usually easier while you are drafting – add one line to the settings block at the top of your document:

format:
  apaquarto-pdf:
    floatsintext: true

Both are correct APA output. Nothing else about your document changes.

“One of my tables is on a sideways page by itself.”

This is expected behaviour for apaTables. A table too wide to stand upright is placed on a rotated (landscape) page, and a rotated page cannot also carry ordinary paragraphs, so that table gets a page to itself. apaTables measures each table as the document renders and only rotates the ones that need it.

If you want to overrule that decision, every table function takes a landscape argument: landscape = FALSE forbids a rotated page, and landscape = TRUE insists on one.

“My table has no number, no title, and no note.”

The most likely cause is a missing label. A table’s code block needs a settings line that starts with tbl-:

#| label: tbl-correlations

Without it, Quarto does not treat the block as a table at all. There is then nothing to number, nothing to attach a title to, and no note – no matter what else you write in the block. The label is also what lets you write @tbl-correlations in a sentence and have the number filled in.

The other cause is that the document is not using apaquarto, or is using the standard copy of it rather than the one apaTables ships. The automatic title and note are produced by apaTables’ own patched build. Run this once in the project folder:

apa.quarto.setup()

It installs or repairs the extension, and does nothing at all if the project is already correct.

“I set the title myself and nothing happened.”

Three things can supply a title, and they have a fixed order of precedence: a #| tbl-cap: settings line wins over a title = argument, which wins over the title apaTables generates. So if a tbl-cap line is present, a title = argument is ignored – by design.

The same order applies to #| apa-note: and note =.

If you did not mean to override anything, delete the line and the argument and let apaTables write both.

“My tables looked right before and now they do not.”

Did you run quarto add wjschne/apaquarto or quarto update? Either one replaces apaTables’ patched copy of the extension with the standard one – while printing [No Change], which is why it is easy to miss. Put the tested copy back:

apa.quarto.setup()

Did you send someone just the .qmd file? The extension lives in an _extensions folder next to the document. Send the whole folder and there is nothing for the recipient to do; send the file on its own and they need to run apa.quarto.setup() once before rendering.

“The numbers in my two-way ANOVA look wrong.”

This is the one to check first, because nothing about the output looks wrong. A two-way ANOVA needs contrasts that sum to zero, or the sums of squares are not the ones you meant to report and no warning is given. Set them before the analysis:

options(contrasts = c("contr.sum", "contr.poly"))

The examples on the apa.aov.table() help page set this line before every model for exactly this reason.

“My colleague’s table has different columns from mine.”

apa.d.table() shows confidence intervals for its d values only when the MBESS package is installed. Install it and the columns appear:

install.packages("MBESS")

“My table is missing rows, or its note has vanished.”

Are you rendering with documentmode: jou, apaquarto’s two-column journal layout? Tables are not supported there. A two-column page cannot break a table across pages, so rows, columns and whole notes can go missing with nothing reported. apaTables warns during the render, but there is no setting that makes it safe – render with documentmode: man instead, which is the mode a manuscript is submitted in, or save the table as a Word file with apa.save().

“R says it cannot find apa.ezANOVA.table().”

It was removed in version 4.0.0, because the ez package it depended on was archived by CRAN. Use apa.afex.table() with output from afex::aov_ez() instead, which covers the same repeated-measures and mixed designs.

“R says it cannot find apa.cor.table() when I render.”

Every code block in a Quarto document runs in a fresh R session that knows nothing about your console. Add library(apaTables) to a block near the top of the document.