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    "text": "Implement missing .pdf features\n\nTables in .pdf jou mode should fit automatically.\nFigure out why text disappears whenever there are too many tables and figures too close together.\n\nImplement missing .docx features\n\nFull control of font, paper size\nRight-align equation numbers\n\nImplement missing Typst features\n\nJournal format\nLine numbering\nFull language option support"
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    "text": "Breaking changes\n\nThe apafg- and apatb- prefixes are no longer used for figures and tables. Use the standard Quarto prefixes (fig- and tbl-), as well as the standard quarto referencing syntax (e.g., @fig-myplot will reference the fig-myplot chunk.).\nThe include statement below the metadata is no longer used and must be deleted. An informative error will provide instruction if the include statement remains."
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    "title": "Changelog",
    "section": "Improvements",
    "text": "Improvements\n\n.docx\n\nThe title page and abstract page are now processed using lua filters instead of R.\nThe officer package is no longer required to create a new reference document every time the document is rendered #5 #29. Now, a lua filter looks for the shorttitle field in your yaml. If that is not found, the title and subtitle fields are used instead. The running header is assigned to the description field in the quarto metadata. This value will show up in the Comments field in the rendered .docx file, which is then inserted into the field box in the header.\nThe .docx running header is set with a lua filter and a docx field that draws from the .docx metadata.\n\n\n\n.pdf\n\nCan number lines #25\nFixed tightlist error #31\nThe jou (journal) mode in .pdf is better supported. There are a few hacky solutions that need a bit of work. #2 #27"
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    "text": "A good place to start learning about writing Quarto documents is here. I will cover material needed to use apaquarto to write an APA Style document in Markdown text.\nMarkdown makes writing in a consistent style straightforward and easy. Its plain-text format was designed to be easy to read and easy to write, yet also flexible and specific enough that it could be converted automatically into fully formatted documents.\nIf you are used to writing with a word processor (e.g., MS Word, Google Docs), it might feel disconcerting to not see what the document will look like as you type. This feeling will pass, and the benefits of typing in a plain-text format will become evident. While writing in APA style, the plain-text Markdown approach prevents the introduction of many inconsistencies and makes it much easier to spot and fix any inconsistencies that are already present."
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    "section": "Level 1 Headings",
    "text": "Level 1 Headings\nAPA Style reserves a small number of level-1 headings with standard names:\n\nMethod\nResults\nDiscussion\nReferences\nAppendices\n\nThere should be no level-1 heading for the introduction. The title acts as the heading for the introduction, and apaquarto places it there automatically."
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    "section": "Levels 2–5",
    "text": "Levels 2–5\nReaders are better able to follow your ideas if you differentiate long sections in your document with headings. I try limit my writing to just levels 1 and 2, but sometimes level 3 headings are needed. I am sparing to the point of stinginess with levels 4 and 5."
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    "section": "What Can Follow a Heading",
    "text": "What Can Follow a Heading\n\nAnything can follow immediately after headings at levels 1–3, including other headings.\nHeadings at levels 4 and 5 must have text paragraphs below them. Why? When rendered, level-4 and level-5 headings appear on the same line as the paragraphs they summarize.\n\n\n# Level 1 Heading\n\nThis paragraph follows the level-1 heading.\n\n## Level 2 Heading \n\n### This Level-3 Heading Directly Follows the Level-2 Heading.\n\nThis paragraph follows the level-3 heading.\n\n#### Level 4 Heading\n\nThis paragraph will appear on the same line as the level-4 heading.\n\nSubsequent paragraphs go on their own lines.\n\n##### Level 5 Heading\n\nThis paragraph will appear on the same line as the level-5 heading.\n\nSubsequent paragraphs go on their own lines."
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    "section": "Level 2 Heading",
    "text": "Level 2 Heading\n\nThis Level-3 Heading Directly Follows the Level-2 Heading.\nThis paragraph follows the level-3 heading.\n\nLevel 4 Heading.\nThis paragraph will appear on the same line as the level-4 heading.\nSubsequent paragraphs go on their own lines.\n\nLevel 5 Heading.\nThis paragraph will appear on the same line as the level-5 heading.\nSubsequent paragraphs go on their own lines."
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    "section": "Block Quotes and Suppressing Indentation",
    "text": "Block Quotes and Suppressing Indentation\nSometimes you want to give a longer quote that needs to go in its own paragraph. Block quotes are on their own line starting with the &gt; character. For example, Jane Austen’s (1814/1990) Mansfield Park has some memorable insights about the mind:\n\n&gt; If any one faculty of our nature may be called more wonderful than the rest, I do think it is memory. There seems something more speakingly incomprehensible in the powers, the failures, the inequalities of memory, than in any other of our intelligences. The memory is sometimes so retentive, so serviceable, so obedient; at others, so bewildered and so weak; and at others again, so tyrannic, so beyond control! We are, to be sure, a miracle every way; but our powers of recollecting and of forgetting do seem peculiarly past finding out. (p. 163)\n\nIf your quote has multiple paragraphs, like this passage from Brown (2012), separate them with a lone &gt; character between the lines:\n\n\n&gt; In the entire field of astronomy, there is no word other than planet that has a precise, lawyerly definition, in which certain criteria are specifically enumerated. Why does planet have such a definition but star, galaxy, and giant molecular cloud do not? Because in astronomy, as in most sciences, scientists work by concepts rather than by definitions. The concept of a star is clear; a star is a collection of gas with fusion reactions in the interior giving off energy. A galaxy is a large, bound collection of stars. A giant molecular cloud is a giant cloud of molecules. The concept of a planet—in the eight-planet solar system—is equally simple to state. A planet is a one of a small number of bodies that dominate a planetary system. That is a concept, not a definition. How would you write that down in a precise definition?\n&gt;\n&gt; I wouldn’t. Once you write down a definition with lawyerly precision, you get the lawyers involved in deciding whether or not your objects are planets. Astronomers work in concepts. We rarely call in the attorneys for adjudication. (p. 242)\nIf the text after a quote is a new paragraph, you can create it in the usual fashion (i.e., plain text with an empty line between the block text and the new paragraph). However, if the text after a quote is part of the same paragraph, you can suppress the indentation by creating a div with the .NoIndent class. As an example:\nInitial paragraph\n\n&gt; Block quote paragraph\n\n:::{.NoIndent}\nBecause this sentence continues the initial paragraph, \nthe indentation is suppresed.\n:::"
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    "section": "Figures in Code Chunks",
    "text": "Figures in Code Chunks\nCode chunk (also known as code blocks) are special sections of a Quarto document that run code. Quarto supports many programming languages, but I will focus on R.\nAn empty code chunk looks like this:\n\n```{r}```\n\n\n\nThose are not single quotes (') that fence in the code chunk. Those are backticks (`), which are usually above the Tab key on most keyboards in the US.\n\n\n\n\nFigure 2\n\n\nKeyboard with backtick hightlighted\n\n\n\n\n\n\n\nDirectly typing the three backticks and the curly braces needed for a code chunk can be tedious. In RStudio, use the keyboard shortcut  to create chunks. If keyboard shortcuts are hard to remember, there is a green button with a white “C” in RStudio’s toolbar that creates code chunks. \nAt a minimum, an APA-Style figure needs a unique label with the fig- prefix, a caption in title case specified with fig-cap, and code for the plot.\n\n```{r}\n#| label: fig-myplot\n#| fig-cap: This Is the Figure Caption.\nlibrary(tidyverse)\ntibble(x = seq(0, 8, .01),\n       y = dlnorm(x)) %&gt;% \n  ggplot(aes(x,y)) + \n  geom_area(fill = \"royalblue\", alpha = .5)\n```\n\n\n\n\n\nFigure 3\n\n\nThis Is the Figure Caption.\n\n\n\n\n\n\n\n\n\nCode chunk options like label and and fig-cap options are preceded by #|. They tell Quarto about how to run the code and present it the document."
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    "text": "Notes below Figures and Tables\nAPA style distinguishes between three types of table notes, each of which need to be in separate paragraphs:\n\nGeneral Note. Contains definitions, abbreviations, and other information needed to understand the table, as well as copyright information.\nSpecific Note. These are notes about specific cells in the table, often in form of footnotes with lowercase letters as markers. Each footnote is in the same paragraph. The APA Manual recommends making the the footnote marker in superscript. The space that separates the marker from the the explanatory text should also be in superscript, hence the ^&nbsp;^ at the beginning of th footnote text.\nProbability Note. This note explains the meanings of probability markers (e.g., * p &lt; .05; ** p &lt; .001; *** p &lt; .001).\n\nYou can add a general note below a figure or table with the chunk option apa-note. The note can have markdown formatting (e.g, bolding and italics).\n\n```{r}\n#| label: fig-myplot2\n#| fig-cap: This Is the Figure Caption.\n#| apa-note: This is the note below the figure.\n\nlibrary(tidyverse)\ntibble(x = seq(0, 1, .001),\n       y = dbeta(x,8,2)) %&gt;% \n  ggplot(aes(x,y)) + \n  geom_area(fill = \"royalblue\", alpha = .5)\n```\n\n\n\n\n\nFigure 4\n\n\nThis Is the Figure Caption.\n\n\n\n\n\n\n\n\n\n\n\nNote. This is the note below the figure.\n\n\n\nOmit “Note” Prefix in apa-note\nBy default, the first paragraph of the apa-note has a prefix added (Note. ). If you wish to omit this prefix (i.e., for a specific note or a probability note), start the note with “NoNote” like so:\n\n```{r}\n#| label: fig-myplot4\n#| fig-cap: This Is the Figure Caption.\n#| apa-note: NoNote \\\\* *p* &lt; .05; \\\\*\\\\* *p* &lt; .01\n\nlibrary(tidyverse)\ntibble(x = seq(0, 1, .001),\n       y = dbeta(x,8,2)) %&gt;% \n  ggplot(aes(x,y)) + \n  geom_area(fill = \"royalblue\", alpha = .5)\n```\n\n\n\n\n\nFigure 5\n\n\nThis Is the Figure Caption.\n\n\n\n\n\n\n\n\n\n\n\n* p &lt; .05; ** p &lt; .01\n\n\n\n\nMulti-Paragraph Notes\nIf you need multiple paragraphs in the note, separate them with a yaml sequence.\n\n```{r}\n#| label: tbl-penguins\n#| tbl-cap: Some Descriptives\n#| apa-note: \n#|   - First paragraph.\n#|   - Second paragraph.\n\nlibrary(flextable)\n\npenguins %&gt;% \n  select(-year, -island, -sex) %&gt;% \n    rename_with(\n    \\(x) str_replace_all(x, c(len = \"length\", dep = \"depth\")) %&gt;%\n      snakecase::to_title_case()) %&gt;% \n  na.omit() %&gt;%\n  summarizor(by = \"Species\") %&gt;% \n  as_flextable()  %&gt;% \n  theme_apa() %&gt;% \n  valign(valign = \"top\") %&gt;% \n  surround(i = ~ stat == \"mean_sd\",\n           border.top = flextable::fp_border_default()) %&gt;% \n  set_header_labels(variable = \"Variable\", stat = \"Descriptive\")\n```\n\n\n\n\nTable 1\n\n\nSome Descriptives\n\n\n\n\nVariableDescriptiveAdelie(N=151)Chinstrap(N=68)Gentoo(N=123)Bill LengthMean (SD)38.8 (2.7)48.8 (3.3)47.5 (3.1)Median (IQR)38.8 (4.0)49.5 (4.7)47.3 (4.2)Range32.1 - 46.040.9 - 58.040.9 - 59.6Bill DepthMean (SD)18.3 (1.2)18.4 (1.1)15.0 (1.0)Median (IQR)18.4 (1.5)18.4 (1.9)15.0 (1.5)Range15.5 - 21.516.4 - 20.813.1 - 17.3Flipper LengthMean (SD)190.0 (6.5)195.8 (7.1)217.2 (6.5)Median (IQR)190.0 (9.0)196.0 (10.0)216.0 (9.0)Range172.0 - 210.0178.0 - 212.0203.0 - 231.0Body MassMean (SD)3,700.7 (458.6)3,733.1 (384.3)5,076.0 (504.1)Median (IQR)3,700.0 (650.0)3,700.0 (462.5)5,000.0 (800.0)Range2,850.0 - 4,775.02,700.0 - 4,800.03,950.0 - 6,300.0\n\n\n\n\n\n\nNote. First paragraph.\n\n\nSecond paragraph."
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    "section": "Importing Figures with Markdown",
    "text": "Importing Figures with Markdown\nComprehensive details on importing and formatting figures with Markdown is here.\nThe Markdown syntax for creating a figure is\n![caption](file){#fig-label}\nFor example,\n![My Caption](myimage.png){#fig-myimage}\nNote that in this context the figure label must start with #fig-. Additional information can be inserted into the curly braces. Some common options:\n\nfig-alt An accessible description of the image. It is usually not immediately visible, but it is available to a screen reader.\nwidth Image width\napa-note A note below the figure\n\nFor example, in the same same folder as my Quarto document, there is an image file sampleimage.png. We can display this image like so:\n![A Simple Mediation Model](sampleimage.png){\n  #fig-myimportedimage \n  width=\"5in\" \n  fig-alt=\"A mediation model in which A causes B, and B causes C.\" \n  apa-note=\"Variable A indirectly causes Variable C.\"\n  }\n\n\n\n\nFigure 6\n\n\nA Simple Mediation Model\n\n\n\n\n\n\n\n\n\nNote. Variable A indirectly causes Variable C."
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    "section": "Figure References",
    "text": "Figure References\nIn APA style, we often refer to specific tables and figures by their order in the text (e.g., Figure 2, Table 4). Keeping track of which is which is a pain, especially if you decide to reorder them. In Quarto documents, we instead refer to their labels, which are converted to the right numbers later. To refer to the figure created by the code above, we would type @fig-myplot, which will be converted to Figure 3."
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    "text": "Tables in Code Chunks\nThe chunk label must begin with tbl- instead of fig-. The caption is set with tbl-cap. I like making tables with flextable because it ports to to the .docx format without hassle.\n\n```{r}\n#| label: tbl-mytable\n#| tbl-cap: My Table\n#| ft.align: left\n#| apa-note: A note below table\nlibrary(tidyverse)\nlibrary(flextable)\n\ntibble(Letters = c(\"A\", \"B\", \"C\"), \n       Numbers = 1:3) %&gt;% \n  flextable() %&gt;% \n  theme_apa() \n```\n\n\n\n\nTable 2\n\n\nMy Table\n\n\n\n\nLettersNumbersA1B2C3\n\n\n\n\n\n\nNote. A note below table"
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    "section": "Tables Made Directly with Markdown",
    "text": "Tables Made Directly with Markdown\nYou can create tables with Markdown in several ways. See here for details. If you need to make a more complex table in Markdown, I suggest using RStudio’s visual editor. Here is an example of a simple table:\n\n| Letters | Numbers |\n|:-------:|:-------:|\n| A       | 1       |\n| B       | 2       |\n| C       | 3       |\n\n: My Caption {#tbl-mytable2 apa-note=\"Note below table\" data-quarto-disable-processing=\"true\"}\n\n\n\n\nTable 2\n\n\nMy Caption\n\n\n\n\n\n\nLetters\nNumbers\n\n\n\n\nA\n1\n\n\nB\n2\n\n\nC\n3\n\n\n\n\n\n\n\n\nNote. Note below table"
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    "section": "Tables and Figures Spanning Two Columns in Journal Mode (.pdf)",
    "text": "Tables and Figures Spanning Two Columns in Journal Mode (.pdf)\nWhen creating tables and figures in journal mode, care must be taken not to make figures and tables wider than the columns, otherwise sometimes makes them disappear (and sometimes takes large swaths of text with it).\nYou can make figures and tables span the two columns by setting the apa-twocolumn chunk option to true. This will only affect .pdf documents when in journal mode (i.e., documentmode: jou).\n\n```{r}\n#| label: fig-myplot3\n#| fig-cap: A Figure that Will Span Two Columns in Journal Mode\n#| apa-twocolumn: true\n\nlibrary(tidyverse)\ntibble(x = seq(0, 1, .001),\n       y = dbeta(x,2,8)) %&gt;% \n  ggplot(aes(x,y)) + \n  geom_area(fill = \"royalblue\", alpha = .5)\n```\n\n\n\n\n\nFigure 7\n\n\nA Figure that Will Span Two Columns in Journal Mode"
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    "section": "Disable apaquarto processing (.pdf only)",
    "text": "Disable apaquarto processing (.pdf only)\nIf you want a long table to span multiple pages in .pdf format, the table might get cut off after the first page. Quarto makes .pdf tables using the longtable package, which allows for multi-page tables. Unfortunately, longtable does not always play nicely with the apa7 LaTeX package that aqaquarto uses to make .pdf documents. I have not yet found a fully satisfactory way get all of the features of apaquarto to be compatible with longtable’s multi-page tables. If you set disable-apaquarto-processing to true in the chunk or in markdown, you can get a multi-page table. The apa-note function, however, will not place a note below the table.\nTo disable apaquarto processing directly in markdown:\n| Letters | Numbers |\n|:-------:|:-------:|\n|    A    |    1    |\n|    B    |    2    |\n|    C    |    3    |\n\n: My Caption {#tbl-disabledprocessing1 disable-apaquarto-processing=true}\nTo disable processing within a code chunk:\n\n```{r}\n#| label: tbl-disabledprocessing2\n#| tbl-cap: Table with apaquarto processing disabled (note does not appear below)\n#| ft.align: left\n#| disable-apaquarto-processing: true\ntibble(Letters = c(\"A\", \"B\", \"C\"), \n       Numbers = 1:3) %&gt;% \n  flextable() %&gt;% \n  theme_apa() \n```\n\n\n\n\nTable 3\n\n\nTable with apaquarto processing disabled (note does not appear below)\n\n\n\n\nLettersNumbersA1B2C3"
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    "text": "Parenthetical Citations\nA parenthetical citation uses the reference label in square brackets and starts with @ like so:\nA sentence that needs a citation [@CameronTrivedi2013].\nA sentence that needs a citation (Cameron & Trivedi, 2013).\n\nWith Multiple Citations\n2 or more citations are separated by a semicolon: [@CameronTrivedi2013; @cohen2003applied] becomes (Cameron & Trivedi, 2013; Cohen et al., 2003).\n\n\nWith Page Numbers\nPage references (or any other suffixes) are placed after the reference. If you want a comma, you’ll need to insert it yourself: [@CameronTrivedi2013, pp. 35--41] becomes (Cameron & Trivedi, 2013, pp. 35–41).\n\n\nWith Prefixes\n\nPrefixes (with or without a comma) are placed before the reference: [e.g., @CameronTrivedi2013] becomes (e.g., Cameron & Trivedi, 2013).\nIf you need a prefix at the beginning of 2 or more citations, you will have rearrange the citations so that the prefix accompanies the citation that is first alphabetically (e.g., Cameron & Trivedi, 2013; Cohen et al., 2003). That is, [e.g., @CameronTrivedi2013; @cohen2003applied], not [e.g., @cohen2003applied; @CameronTrivedi2013].\nAny prefixes or suffixes needing a literal semicolon will confuse Quarto (actually Pandoc). To make it clear that you need to print a semicolon, put a backslash before the semicolon: First Outer Inner Last [FOIL\\;@CameronTrivedi2013] becomes First Outer Inner Last (FOIL; Cameron & Trivedi, 2013).\n\n\n\n\n\n\n\nWarning\n\n\n\nThis “escaped backslash in front of the semicolon trick” is a hack. When you switch to Visual Mode in RStudio or Positron, it thinks you made a mistake, and it removes the backslash. If the citation above looks wrong, it is because I forgot to fix it after switching to visual mode and back. I reported this bug to the RStudio/Positron developers at Posit. I hope the bug will be fixed soon.\n\n\n\n\nSuppressing Parenthetical Ampersands\nStrict APA style uses ampersands in parenthetical citations with multiple authors. If you want the word “and” instead, add this field to your YAML header:\nno-ampersand-parenthetical: true\nIf you are not writing in English, you can set “and” to whatever is appropriate. For example, “and” in Spanish is “y”, which can be set like so:\nlanguage:\n  citation-last-author-separator: \"y\""
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    "text": "Narrative (In-Text) Citations\nTypically, a plain citation without any brackets works without any fuss:\n@CameronTrivedi2013 said some interesting things.\nCameron and Trivedi (2013) said some interesting things.\n\n\n\n\n\n\nWarning\n\n\n\nOutside of apaquarto, a limitation of the .csl format requires a special filter to change the separator for multiple authors from & toand. If you render your document in a different format, @CameronTrivedi2013 will be “Cameron & Trivedi (2013).”\n\n\n\nWith Page Numbers\nIf you need to include page references, use square brackets afterwards:\n@CameronTrivedi2013 [101-103] said some interesting things. So did @cohen2003applied [21].\nCameron and Trivedi (2013, pp. 101–103) said some interesting things. So did Cohen et al. (2003, p. 21).\nYou do not not need to add “p.” or “pp.” Quarto will get it right automatically. A hyphen (-) between two page numbers will automatically be converted to an en dash (–).\n\n\nPossessive Citations\nA useful feature specific to apaquarto is automatic “possessive citations.”\n@CameronTrivedi2013 ['s] position becomes Cameron and Trivedi’s (2013) position.\nYou can add page numbers with possessive citations. @CameronTrivedi2013 ['s, 35] idea was great. @CameronTrivedi2013 ['s, 124-125] other idea was good, too. becomes Cameron and Trivedi’s (2013, p. 35) idea was great. Cameron and Trivedi’s (2013, pp. 124–125) other idea was good, too.\nIf you render your document in another format, you would need to supply the name in text like this: Cameron and Trivedi's [-@CameronTrivedi2013] position, which becomes Cameron and Trivedi’s (2013) position. This works because putting a hyphen before the reference suppresses the author name. That is, [-@CameronTrivedi2013] becomes (2013).\n\n\nNarritive Citations with Ampersands\nIf you have narrative citation in a table, APA Style encourages the use of ampersands to save space (Parenthetical citations already have ampersands.). To suppress the conversion of ampersands to “and”, place an ampersand in brackets after the citation:\n@CameronTrivedi2013 [&] said something becomes Cameron & Trivedi (2013) said something.\nThis works with possessive citations and/or page numbers:\n@CameronTrivedi2013 [&, 's] idea is interesting becomes Cameron & Trivedi’s (2013) idea is interesting.\nThe order of these tags is unimportant, but they must be separated by a space. The comma is optional.\n@CameronTrivedi2013 ['s &] idea is interesting becomes Cameron & Trivedi’s (2013) idea is interesting.\nPut page numbers in the last position, separated by a space. The comma is optional.\n@CameronTrivedi2013 [&, 35--36] have an interesting idea becomes Cameron & Trivedi (2013, pp. 35–36) have an interesting idea.\n@CameronTrivedi2013 [&, 's, 35--36] idea is interesting becomes Cameron & Trivedi’s (2013, pp. 35–36) idea is interesting."
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    "section": "Citations for Articles Included in a Meta-Analysis",
    "text": "Citations for Articles Included in a Meta-Analysis\nIn a meta-analytic study, all studies included in the meta-analysis should appear in the References section but ordinarily should not be cited in the text. Quarto allows references not cited in the text to appear in the References section when they are listed in the the nocite field in the metadata. All articles listed in the nocite field will be marked with an asterisk in the References section.\nnocite: |\n  @schneider2015intelligence, @schneider2012cattell\nIf marking nocite studies with an asterisk is unwanted, set the meta-analysis field to false,\nmeta-analysis: false\nnocite: |\n  @schneider2015intelligence, @schneider2012cattell"
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    "section": "Masked Citations for Anonymous Peer Review",
    "text": "Masked Citations for Anonymous Peer Review\nSuppose you want to cite a previous reference of yours, but your anonymity is supposed to be protected in the review process. You can “mask” any citation you wish by setting the mask field in the metadata yaml to true. Then list all citations that need to be masked in the masked-citations field like so:\nmask: true\nmasked-citations:\n  - schneider2015intelligence\n  - schneider2012cattell\nIf the mask field is set to false, the masked citations will print as usual. When mast is true, depending if they are narrative or parenthetical citations, they will be listed as “Masked Citations (n.d)” or “(Masked Citations, n.d)”. In parenthetical citations, it is possible to mix masked and unmasked citations.\nSetting mask to true will also remove the authors, affiliations, and author notes from the title page.\nThe text for masked citations have these defaults:\nlanguage:\n  citation-masked-author: \"Masked Citation\"\n  citation-masked-date: \"n.d.\"\n  citation-masked-title: \"Masked Title\"\nThey can be changed to another language or alternate text in English in your YAML header. For example:\nlanguage:\n  citation-masked-author: \"Author masked for review\"\n  citation-masked-date: \"Date masked\"\n  citation-masked-title: \"Title masked for review\""
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    "text": "Keeping track of apquarto’s many options can be difficult, and with each new feature, the list of options grows. I have make a small app that makes it easier to create the initial apaquarto document.\nThe app can be accessed here. Be patient as it loads.\n\n\n\n\n\n\nFigure 1: Screenshot of apaquarto web app\n\n\n\nThe app is mostly self-explanatory. You fill in necessary information or select options that suit your purpose. When ready, click Make Document in the side menu and then click Update. Copy the resulting text into an existing Quarto file."
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    "title": "Introduction to apaquarto",
    "section": "",
    "text": "Style guides facilitate scientific communication. Because scholars often write about inherently difficult topics, preventing any avoidable barriers to communication is all the more necessary. Style guides make information easier to absorb because it is presented in a predictable sequence and a familiar format. Still, in removing unnecessary barriers to communication on the reader’s end, style guides themselves often place unnecessary roadblocks before the writer.\nAPA style is fussier than most discipline-specific guides. Because it was introduced in the pre-computer age (Bentley et al. 1929), its quirks and charms resist easy automation. Even after decades of experience, I still need to look things up. Constantly. The basics of APA style are easy enough to learn, but there are a lot of particulars to keep in mind. Not only are there rules and exceptions to rules to remember, there are exceptions to the exceptions that must not be forgotten.\nI wrote apaquarto so that I would never have to worry about APA style ever again. With very little extra effort, your documents are formatted according to APA style. In Figure 1 we see an example of apaquarto’s output to “manuscript mode”. Switching the document to “journal model, produces output formatted like an APA journal (see Figure 2).\n\n\n\nUnable to display PDF file. Download instead.\n\n\nFigure 1: Example document in manuscript mode\n\n\n\n\n\n\nUnable to display PDF file. Download instead.\n\n\nFigure 2: Example document in journal mode\n\n\n\n\nQuarto makes writing scientific documents easier\nThe apaquarto extension is built on Quarto, an open-source publishing system specifically adapted for scientific and technical documents such as journal articles, books, blogs, slides, and dashboards, and websites. Not only does Quarto offer considerable flexibility by itself, it was designed to be extensible. Thus, Quarto can take care of most of the formatting, and an extension can be written to handle whatever specific formatting rules a style guide requires. The apaquarto extension takes care of all the fussy details of APA-style so that you can focus on the content of your writing.\nYou do not need to know any programming languages to use Quarto. You can use it in a completely non-technical way to write well-formatted text, tables, figures, and references. However, if your document communicates the results from data analyses, then Quarto offers you something quite remarkable. You can perform your analyses and communicate your findings in the same file! That is, you write text and code together in a source document and then you “render” the document into its final format (e.g., .html, .pdf, .docx). So instead of performing your analyses elsewhere (e.g., SPSS) and then copying the results into a word processor (e.g., MS Word), you build your document in one step.\nThe advantages of this kind of workflow are profound. If you discover a mistake in your analysis, there is no need to find and replace the primary results and their downstream consequences scattered throughout the document. Instead, you just re-render the document, and everything in it is updated. When the document is published, the Quarto file serves as a fully reproducible record of your analysis. Making the Quarto file available in a public repository increases trust in your work because anyone can inspect it and trace any result you report back to the source code that created it.\n\n\n\n\n\nReferences\n\nBentley, Madison, CA Peerenboom, FW Hodge, Edward B Passano, HC Warren, and MF Washburn. 1929. “Instructions in Regard to Preparation of Manuscript.” Psychological Bulletin 26 (2): 57."
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    "text": "Installing apaquarto is not hard, but it takes a bit more effort than installing a standalone program. There are four main steps:"
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    "section": "Install Quarto",
    "text": "Install Quarto\nThe current stable version of Quarto can be installed here.\nIf you use a recent version of RStudio, Quarto is already installed. If you are not sure if your version of Quarto is recent enough, there is no harm in re-installing it.\n\n\n\n\n\n\nNoteHow to check which version of Quarto is installed\n\n\n\n\n\nIn a terminal, run\n\n\n\nTerminal\n\nquarto --version"
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    "section": "Install a Programming Language",
    "text": "Install a Programming Language\nYour primary options are\n\nR\nPython\nJulia\n\n\n\n\n\n\n\nTipWhat if I do not want to use any programming languages?\n\n\n\n\n\nIf you just want to use apaquarto to make APA-style documents, but do not plan to do any analyses, install R and RStudio. You do not need R for anything, but the Quarto experience will be easier in RStudio with R installed."
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    "text": "Install your programming environment\nAt the same link for installing Quarto, there are links for selecting an environment for using Quarto. Your options include:\n\nRStudio will probably give the smoothest experience to anyone new to data analysis. It is made by Posit, the same company that makes Quarto.\nPositron is made by Posit, the same company that makes Quarto and RStudio. It is inspired by RStudio but is multi-lingual by design. Positron will likely become the default recommendation on this list when it is further along in its development.\nVS Code works for any language. Some R users really like VS Code, but those who do will likely migrate to Positron because Positron is a data-science-specific fork of VS Code.\nJupyter, as its name indicates, works with Julia, Python, and R.\nNeovim, a hyperextensible Vim-based text editor\nAny text editor will do. Everyone has options—Quarto won’t box you in."
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    "text": "Options are set in the metadata section at the top of the .qmd file. Quarto metadata uses YAML, a format that allows us to store data in a format that is easy to write and easy to read. In its simplest form, it has a key and a value:\nIf the value is simple, it does not need any quotes. If it has any characters that have special meaning in yaml (e.g., :), you will need to put the value in quotes.\nAny optional key you do not use can be deleted or commented out. If you would prefer to keep the key visible but empty, you can make the value NULL with the tilde symbol ~ like so:\nHere is a minimal example of what the YAML metadata might look like:"
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    "text": "Authors\nThe apaquarto uses the standard Quarto schema for authors. It has a lot of options, some of which are not needed for the apaquarto extension (e.g., fax).\nThe author field contains author names, author affiliations, and author roles. Where possible, specify each author’s orcid for easy, unambiguous identification.\nThe corresponding author is specified by setting the author’s corresponding field to true (i.e., corresponding: true). This author needs to list an email and list a mailing address in the affiliation data. Only one author can be the corresponding author. Other authors do not need to list their addresses.\nauthor:\n  - name: W. Joel Schneider\n    corresponding: true\n    orcid: 0000-0002-8393-5316\n    email: schneider@temple.edu\n    affiliations:\n      - name: Temple University\n        department: College of Education and Human Development\n        address: 1301 Cecil B. Moore Ave.\n        city: Philadelphia\n        region: PA\n        postal-code: 19122-6091\n    role:\n      - writing\n      - conceptualization\n  - name: Fulano Zutano Mengano\n    affiliations: Universidad de Dondequiera\n    orcid: 0000-0000-0000-0001\n    role:\n      - formal anlaysis\n      - visualization\n      - editing\n  - name: Thomas Richard Harris\n    affiliations: \n      - name: Generic State University\n        department: Department of Scholarly Studies\n    orcid: 0000-0000-0000-0002\n    role:\n      - editing\n      - funding acquisition\n  - name: Wut C. Whosis\n    affiliations: Whatchama College\n    orcid: 0000-0000-0000-0003\n    role:\n      - software\n      - methodology\n      - editing"
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    "text": "Affiliations\nThe apaquarto extension uses the standard Quarto schema for affiliations.\n\n\n\n\n\n\n\nField\nExplanation\n\n\n\n\nid\nA unique identifier for the affiliation. The id can be useful for specifying an affiliation shared by multiple authors:\nauthor:\n  - name: William Joel Schneider\n    affiliations:\n      - name: Temple University\n        department: College of Education and Human Development\n        address: 1301 Cecil B. Moore Ave.\n        city: Philadelphia\n        region: PA\n        postal-code: 19122-6091\n        id: temple\n  - name: Renée M. Tobin\n    affiliations:\n      - ref: temple\n\n\nname\nThe name of the organization.\nauthor:\n  - name: Fred Jones\n    affiliation:\n      - name: Generic State University\nIf the author is unaffiliated, list the author’s city and region/state instead:\nauthor:\n  - name: Fred Jones\n    affiliation:\n      - city: San Francisco\n        region: CA\n\n\ndepartment\nA specific division within the organization.\n\n\ngroup\nA subdivision within the department\nauthor:\n  - name: Fred Jones\n    affiliation:\n      - name: Generic State University\n        department: Department of Psychology\n        group: Counseling Psychology\n\n\naddress\nThe street address\n\n\ncity\nCity\n\n\nregion\nThe region, state, or province.\nYou may specify state instead, if you prefer.\n\n\ncountry\nCountry\n\n\npostal-code\nPostal code (zip code in the U.S.)\n\n\n\n\nMultiple Affiliations\nIf an author has more than one affiliation:\nauthor:\n  - name: William Joel Schneider\n    affiliations:\n      - name: Temple University\n        department: College of Education and Human Development\n        address: 1301 Cecil B. Moore Ave.\n        city: Philadelphia\n        region: PA\n        postal-code: 19122-6091\n      - name: My Second Affiliation\n\n\nShared Affiliations\nIf two authors have the same affiliation, you can type the same affiliation twice. If you do this, make sure the affiliations are EXACTLY the same in every detail. Otherwise they will be listed as different. To make sure they are listed as the same affiliation, it is safer to use a reference id to make sure that there are no accidental differences that creep in to the editing process. In this example, the affiliation information was entered once, and the id was specified. For the second author with the same affiliation, the ref field is used to reference the previously specified id.\nauthor:\n  - name: William Joel Schneider\n    affiliations:\n      - name: Temple University\n        department: College of Education and Human Development\n        address: 1301 Cecil B. Moore Ave.\n        city: Philadelphia\n        region: PA\n        postal-code: 19122-6091\n        id: temple\n  - name: Renée M. Tobin\n    affiliations:\n      - ref: temple\n\n\nListing Authors and Affiliations Separately\nIf there are a lot of authors with shared affiliations, it might be easier to list the affiliations separately and specify each affiliation’s id, which can be looked up with the ref field:\nauthor: \n  - name: Fred Jones\n    affiliation: \n      - ref: temple\n      - ref: tamu\n  - name: Wanda James\n    affiliation:\n      - ref: temple\n      - ref: ucb\naffiliations:\n  - id: temple\n    name: Temple University\n  - id: tamu\n    name: \"Texas A&M University\"\n  - id: ucb\n    name: University of California, Berkeley"
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    "text": "Author Roles\nAPA Style encourages but does not require papers with multiple authors to describe author roles using the Contributor Roles Taxonomy (CRediT). There are 14 contributor roles:\n\n\n\n\n\n\n\nRole\nDescription\n\n\n\n\nconceptualization\nIdeas; formulation or evolution of overarching research goals and aims.\n\n\ndata curation\nManagement activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use.\n\n\nformal analysis\nApplication of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data.\n\n\nfunding acquisition\nAcquisition of the financial support for the project leading to this publication.\n\n\ninvestigation\nConducting a research and investigation process, specifically performing the experiments, or data/evidence collection.\n\n\nmethodology\nDevelopment or design of methodology; creation of models.\n\n\nproject administration\nManagement and coordination responsibility for the research activity planning and execution.\n\n\nresources\nProvision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools.\n\n\nsoftware\nProgramming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components.\n\n\nsupervision\nOversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team.\n\n\nvalidation\nVerification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs.\n\n\nvisualization\nPreparation, creation and/or presentation of the published work, specifically visualization/data presentation.\n\n\nwriting\nPreparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation).\n\n\nediting\nPreparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages.\n\n\n\nIt is possible to list the roles for each author:\nauthor: \n  - name: Fred Jones\n    role: \n      - conceptualization\n      - funding acquisition\n      - writing\n  - name: Wanda James\n    role:\n      - conceptualization\n      - formal analysis\n      - visualization\n      - editing\nWhen 2 or more authors have the same role, one may specify the degree of contribution (lead, equal, supporting):\nauthor: \n  - name: Fred Jones\n    role: \n      - conceptualization: lead\n      - visualization: supporting\n      - investigation: equal\n      - funding acquisition\n      - writing\n  - name: Wanda James\n    role:\n      - conceptualization: supporting\n      - visualization: lead\n      - investigation: equal\n      - formal analysis\n      - editing"
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    "text": "Author Notes\nThe first paragraph of the Author Note will be populated with all the ORCID IDs that have been specified.\nThe second paragraph consists of status changes:\n\n\n\n\n\n\n\nField\nExplanation\n\n\n\n\naffiliation-change\nDescribe author affiliation changes.\nExample:\nauthor-note:\n  status-changes:\n    affiliation-change: Fred Jones is now at Generic State University\n\n\ndeceased\nDisclose names of authors who are now deceased.\nExample:\nauthor-note:\n  status-changes:\n    deceased: Fred Jones is deceased.\n\n\n\nThe third paragraph consists of study details and author disclosures:\n\n\n\n\n\n\n\nField\nExplanation\n\n\n\n\nstudy-registration\nDescribe where the study was registered.\nExample:\nauthor-note:\n  disclosures:\n    study-registration: \"This study was registered at ClinicalTrials.gov (Identifier NTC998877).\"\n\n\ndata-sharing\nData/materials that have been shared\nExample:\nauthor-note:\n  disclosures:\n    data-sharing: \"Data from this study can be accessed at https://academicdata.org/jones2024.\"\n\n\nrelated-report\nAcknowledge and cite data/materials that were used previously\nExample:\nauthor-note:\n  disclosures:\n    related-report: \"This article is based on the dissertation completed by Graham (2018)\"\n\n\nconflict-of-interest\nDisclose author conflicts of interest\nExample:\nauthor-note:\n  disclosures:\n    conflict-of-interest: \"Fred Jones has been a paid consultant for Corporation X, which funded this study.\"\n\n\nfinancial-support\nAcknowledge funding sources\nExample:\nauthor-note:\n  disclosures:\n    financial-support: \"This study was supported by Grant 123 from Academic Funders United.\"\n\n\ngratitude\nAuthors can express gratitude.\nExample:\nauthor-note:\n  disclosures:\n    gratitude: \"The authors are grateful to Sidney Fiero for thoughtful comments on an early draft of this paper.\"\n\n\nauthorship-agreements\nAuthors can disclose any agreements they entered into regarding the paper.\nExample:\nauthor-note:\n  disclosures:\n    authorship-agreements: \"Because the authors are equal contributors, order of authorship was determined by a fair coin toss.\"\n\n\n\nThe fourth paragraph of the Author Note consists of the correspondence information. It will created automatically from the contact information from the author marked as the corresponding author. If you wish to override this paragraph with one entirely of your own, you can set it via the correspondence-note subfield in the author-note field.\nauthor-note:\n  correspondence-note: This will override the correspondence note that would otherwise be generated."
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    "text": "APA-Style Books\n\nAmerican Psychological Association (2020). Publication manual of the American Psychological Association (7th ed.). Author. https://doi.org/10.1037/0000173-000\nAmerican Psychological Association (2020). Concise guide to APA Style: The official APA Style guide for students (7th ed.). Author. https://doi.org/10.1037/0000173-000\nAmerican Psychological Association (2021). Mastering APA Style student workbook. Author. https://doi.org/10.1037/0000271-000"
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    "text": "APA-Style Helper Functions in R\nMany packages have helper functions for reporting statistics in and creating tables and figures in APA Style. Here are a few:\n\nrempsyc\npapaja\napa\napaTables"
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    "text": "Alternatives to apaquarto\nTo my knowledge, there is no working quarto extension other than apaquarto that takes a comprehensive approach to APA style with output options in .docx, .html, and .pdf. However, there are other ways to automate the production of APA-style documents.\n\nAPA style with knitr and \\(\\LaTeX\\)\nThe ability to automate APA style via \\(\\LaTeX\\) has been around for some time—first via apa (APA Style, 5th Edition), then via apa6 (APA Style, 6th Edition), and now via apa7 (APA Style, 7th Edition). The apaquarto package uses apa7 to create .pdf documents. To intermingle R code and \\(\\LaTeX\\) code in the same document, R-users could write in an .Rnw file using sweave or knitr. I still do so when I need the full flexibility of \\(\\LaTeX\\).\n\n\nAPA style with Rmarkdown and papaja\nUnfortunately, most psychology journals require submissions in MS Word (and most collaborators do as well). Learning \\(\\LaTeX\\) is fun for some people (e.g., me), but most will not bother. With the arrival of Rmarkdown, it became possible to automate document production with a system that takes just a few minutes to learn.\nThe papaja package by Frederick Aust uses Rmarkdown syntax and does a fantastic job of creating APA-style (6th Edition) documents in .pdf and gets close to perfect .docx output. With a bit of tweaking, papaja can do most of APA Style (7th Edition) for .pdf documents."
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