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 the 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: trueBoth are correct APA output. Nothing else about your document changes.
“One of my tables is on a sideways page by itself.”
This is expected behavior 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. The code
block for a table needs a settings line that starts with
tbl-:
#| label: tbl-correlationsWithout 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 come from that patched copy. Run this once in the project folder:
It installs or repairs the extension, and does nothing at all if the project is already correct.
“A table I typed in markdown is at the end with no number or title.”
With tables collected at the end of the manuscript (the apaquarto default), every table moves to the end pages, including one typed in markdown. A markdown table with no caption has no number and no title, so on the end pages nothing ties it back to the text that introduced it.
Give every table a caption. For a markdown table, put the caption on a separate line after the table, starting with a colon and ending with a label:
| Group | M | SD |
|---------|------|------|
| Control | 4.20 | 1.10 |
| Treated | 5.30 | 0.90 |
: Mean Scores by Group {#tbl-means}The table is then numbered and titled like any other, and
@tbl-means in a sentence prints the number.
“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 the patched
copy of the extension that apaTables installed with the standard one –
while printing [No Change], which is why it is easy to
miss. Put the tested copy back:
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 only the file and they need to run
apa.quarto.setup() once before rendering.
Does your document cache the chunks
(cache: true)? Quarto then reuses the earlier output of a
chunk instead of running it again. After you update apaTables, a table
from a cached chunk in a Word document can come out in larger type with
wider spacing than apaTables gives it. Render once with the cache
refreshed, by typing this in a terminal (not the R console):
quarto render mydocument.qmd --cache-refreshDeleting the mydocument_cache folder beside the document
does the same.
“The numbers in my two-way ANOVA look wrong.”
If apa.aov.table() disagrees with output you
produced yourself, check the contrasts. A Type III two-way
ANOVA needs contrasts that sum to zero. Under the R default contrasts,
the row for each factor is the effect at one level of the other factor,
not the main effect, and nothing in the output says so.
apa.aov.table() takes care of this itself: for a Type
III table it uses sum-to-zero contrasts whether or not you set them, so
the F values in the table match programs such as SPSS. Your own
analysis, for example with car::Anova(), does not. Set the
contrasts before fitting the model so both use the same coding:
The examples on the apa.aov.table() help page set this
line before every model.
“A correlation with p = .010 has two stars.”
The stars come from the exact p-value; the printed p-value is rounded to three decimals. When the exact value is just below .01, rounding prints it as .010, beside two stars. In the same way, a value just below .05 prints as .050, beside one star. The stars are correct: the exact p-value is below the cutoff that the note gives.
For example, in this table the correlation between hp
and drat prints as -.45** with
p = .010 under it:
apa.cor.table(data = mtcars[, c("mpg", "hp", "drat")])The exact p-value is .009989, which cor.test()
shows:
cor.test(x = mtcars$hp, y = mtcars$drat)This happens only for a p-value from .0095 up to .01, or from .0495
up to .05. If a reader or reviewer asks about it, report the exact
p-value from cor.test() in the text.
“My table is missing rows, the note has vanished, or the PDF will not render.”
Are you rendering with documentmode: jou, the two-column
journal layout of apaquarto? Tables are not supported there. A
two-column page cannot break a table across pages, so rows, columns and
whole notes can go missing. Or the render can stop with a LaTeX error
and write no PDF at all; the error reads
longtable not in 1-column mode or
Not in outer par mode. When the PDF does render, apaTables
puts a warning in it, 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().
In the other modes (man, stu and
doc) a long table – an apaTables table or one written in
markdown – continues onto the next page with every row, and the note
prints under the last row. If rows are missing there, the copy of
apaquarto in the project has probably been replaced by the standard one
(running quarto add or quarto update extension
does that). Run apa.quarto.setup() in the project to put
the tested copy back, then render again.
“In my PDF, a long word in a markdown table runs into the next column.”
This happens when a row of a markdown table is longer than 72 characters, in any Quarto PDF, with or without apaquarto. pandoc, the program Quarto uses to convert the document, then sets the column widths in proportion to the number of dashes under each heading, and a word longer than the column prints over the next one. Two fixes: add dashes under the heading of the column that is too narrow, so that column gets a larger share of the width, or keep every row of the table under 72 characters, so that each column is as wide as the widest entry.
“In my PDF, a kable() table has two table numbers, or the note sits on top of the last row.”
This happens with a table made with
knitr::kable(format = "latex") – written that way or inside
kableExtra’s kable_styling() – when the title is given with
kable(caption = ...) in a chunk labeled tbl-.
The table gets an extra, empty table number, every later table is
numbered one too high, and a note from an apa-note settings
line prints over the last row. With a #| tbl-cap: line as
well, the extra number prints over the title. A plain
knitr::kable(scores), without format, given
both caption = ... and a #| tbl-cap: line,
prints the table number and title twice.
In every case the fix is to give the title with a
#| tbl-cap: settings line and leave caption
out of the call. The settings lines and the call look like this:
#| label: tbl-scores
#| tbl-cap: "Mean Scores by Group"
knitr::kable(scores, format = "latex", booktabs = TRUE)format = "latex" is for PDF documents only. In a Word
document it leaves the title with no table under it, so in Word or HTML
leave format out.
The kableExtra option
kable_styling(latex_options = "scale_down") also puts the
note over the last row in a PDF manuscript. If the table fits the page
without that option, leave it out.
“In my PDF, a long kable() table repeats the first row at the top of the next page.”
This happens with a table made with
knitr::kable(format = "latex", col.names = NULL) – no
column headings – and without booktabs = TRUE. A table
continued onto a new page repeats the headings, and with no headings to
repeat, the first row is taken for them. Add
booktabs = TRUE, which is also the APA-style layout:
knitr::kable(scores, format = "latex", booktabs = TRUE, col.names = NULL)format = "latex" is for PDF documents only; in Word or
HTML leave it out.
“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.
“On my Mac, apaTables says XQuartz is missing.”
You may see this message:
apaTables could not load the flextable package, which it uses to measure
and save tables, because your Mac is missing XQuartz, ...or, from an older version or another package, an error that ends with
something like
Library not loaded: /opt/X11/lib/libXrender.1.dylib.
Some R packages that apaTables relies on are built, on some Macs, to use XQuartz, a free add-on that gives a Mac the X11 graphics libraries that parts of R have long expected. Whether you need it depends on where your R packages come from: packages installed from CRAN, which is what R, RStudio and Positron use unless they have been set up otherwise, do not need it. Packages from Posit Package Manager, which some universities and some setups use, can.
The fix that lasts: install XQuartz from xquartz.org, then log out of your Mac, log back in, and restart R (or RStudio, or Positron). Nothing else needs to change, and the problem will not come back.
To keep working right now, run this in the R console:
install.packages("gdtools", repos = "https://cloud.r-project.org")Then restart R. This replaces the one package that needs XQuartz with the CRAN version, which does not. It works at once, but if your R is set up to install from Posit Package Manager, a later package update may bring the problem back – installing XQuartz is what stops that.