Requirements

• packages:
  • papaja
  • tinytex
• software (optional)
  • Zotero + a Zotero account
• download from the Moodle or GitHub:
  • references.bib

tinytex

• includes helper functions for installing LaTeX distribution
  • i.e., helps create PDF outputs

# to install tinytex run these two lines
install.packages("tinytex")
tinytex::install_tinytex()

papaja

I want to add a citation

• for APA-formatted scientific manuscripts
  • currently uses APA 6, but we can update it to APA 7

# to install tinytex run these two lines
install.packages("papaja")

Writing

• writing an article or thesis
  • not a report
• should be kept separate from the actual analyses
  • e.g., in its own folder or even own project
  • if in its own project: make sure you transfer over files needed (e.g., figures, data, saved models)

Rmarkdown

• we can also write PDFs in Quarto
  • but its relatively new, and there’s more support for scientific articles in R markdown
• most everything in R markdown is identical to Quarto
  • some important differences: code chunk options (we’ll see these later)

APA-formatting with papaja

• a package specifically for writing APA-formatted manuscripts

• File > New File > R markdown > From template > APA-formatted article (papaja)

  • will open a file with a long YAML
  • render it and see how it looks

Cross-referencing

• e.g., referring to another section
  • in which case, we need number_sections: TRUE in our YAML
• simply provide a label in the same line as a heading, either with {#section_label} or \label{section_label}
  • then provide the label within \ref{}, and the section number will be produced in the output
• the example text below would then be written as Here is some text in Section 1 (assuming the Introduction is numbered as 1)

# Introduction {#section_label}

Here is some text in Section \ref{section_label}.

Figures

• or figure, table, example sentence or equation

```{r fig-iris, eval = TRUE}
library(ggplot2)
iris |> ggplot() + aes(x = Sepal.Length, y = Sepal.Width) + geom_point()
```

Figure 1

• now if we were to write As seen in Figure \ref{fig-iris}, we would get: As seen in Figure 1

• be careful not to use underscores (_) in your figure labels, this causes problems

Images

• You might also include a figure of the trial procedure, or some other visual description of your data
• For example, in Figure Figure 2 we see an overview of the types of iris (flowers) that make up the data from the built-in iris dataset (figure from Mijwil & Abttan, 2021)
• you can then cross-reference to images the same was, by putting the label inside \ref{}

```{r fig-summary, out.width="100%", fig.pos="t", fig.cap="\\label{fig-summary}Visual depiction of dependent variables from the `iris` dataset"}
knitr::include_graphics(here::here("figures", "iris_photo.png"))
```

Figure 2: Visual depiction of dependent variables from the iris dataset

Tables

• e.g., you can give an overview of your stimuli (you could also do this with example sentences)
  • if producing your table with R code, remember to feed it into a function that formats tables
  • e.g., knitr::kable() or papaja::apa_table()

```{r apa-table, eval=F, echo = "fenced"}
library(tidyverse)
tribble(
  ~"Item", ~"Condition", ~"Sentence",
  "1", "a", "Example sentence of condition A",
  "1", "b", "Example sentence of condition B",
  "1", "c", "Example sentence of condition C",
  "1", "d", "Example sentence of condition D",
) |> 
  papaja::apa_table(caption = "Example stimuli")
```

Table labels

• writing “See Table apa-table for example stimuli” will print:
  • See Table 1 for example stimuli.
• For this to work, you need to provide a label in the code chunk settings: {r apa-table, echo=F, eval=T}. + remember to use \ref{tab:label} and replace label with yours (i.e., don’t forget the tab: prefix).

Data tables

• You can of course also present tables of your data or models

• cross-referencing works the same:
  • you write: Mean values are given in Table \ref{tab:iris-table}.
  • R markdown prints: Mean values are given in Table 2.

Placing tables and figures

• To allow figures and tables to appear in-text (i.e., not at the end of the document), change floatsintext: in the YAML to yes (it will be no by default)
  • otherwise papaja pushes all tables and figures to the very end of the document

floatsintext      : yes # CHANGE TO YES to allow figures and tables to float in text

Citations

• the most straightforward way to include citations is by manually adding BibTex citations into your .bib file
  • you can define which .bib file to use in your YAML (we currently have bibliography: r-references.bib)
• you can easily get the BibTex formatted citation via Google Scholar
  • although I suggest using Zotero with the Better BibTex plug in, which stores them locally

BibTex format

• below is an example of a BibTex formatted citation
  • the first info after the opening curly bracked is the reference key (knuth1984literate)
• add this reference to your .bib file

@article{knuth1984literate,
  title={Literate programming},
  author={Knuth, Donald Ervin},
  journal={The computer journal},
  volume={27},
  number={2},
  pages={97--111},
  year={1984},
  publisher={Oxford University Press}
}

In-text citations

• to then include a reference in-text, include the BibTeX reference key preceded @
• so if we write @knuth1984literate we should get a formatted citation: Knuth (1984)
  • and the full citation should be added to our references section
• if we were to write [@knuth1984literate] we would get the reference in brackets (Knuth, 1984)
  • to learn more about how to control the formatting of in-text references check out Section 3.2 (Citations) in the papaja manual

Zotero

• this process can be streamlined by using Zotero + Better BibTex (BBT)
  • there are several walk-throughs of how to do this online, e.g.,
• the benefit: using Zotero keeps a record of your PDFs/readings
  • Zotero Desktop is a nice way to annotate readings and take notes
  • direct integration of BBT with RStudio is possible
• check out this blogpost to learn more

Collaboration

• unfortunately, there’s no elegant method for collaborative writing in R markdown/Rstudio
  • the only real option is to use a remote git repository (e.g., GitHub or GitLab)
  • but this has a steep learning curve and is prone to problems when collaborators aren’t familiar with git
  • track changes are also not as elegant as in Overleaf, Google Docs, Word documents, etc. (e.g., with accept/reject buttons or pop-up comments)
• if you have co-authors, consider they may or may not be R (markdown) or LaTeX or R-savvy

Possible workflows

• you could send collaborators a PDF that they annotate and then you make the changes back in your R markdown script(s)
  • but this is quite labour intensive on your side
• alternatively, you can also output your first draft as a Word document and then use that as a starting point for collaborative writing
  • keep in mind that any changes to the analyses will then need to be done in Rmarkdown and imported to the edited Word document
• there is also the trackdown package which integrates R markdown scripts with Google Docs
  • but there are obvious data protection/ethical concerns with doing so
• currently, I prefer to move the first draft to Overleaf
  • I can always re-run my analyses, re-write up my results section, and just replace the LaTeX code for that section