Motto

1. Reproduciblity: Thou shalt not copy and paste.
2. Single source of truth in a Git repository (not FINAL.doc; FINAL_rev2.doc; FINAL_rev2_commented.doc; FINAL_correct_reallyfinal.doc)
3. If this is your first night, you have to type.

Setup

prerequisites

1. R installed (preferably on Linux / Mac OS X)
2. Google account (Optional, for Trackdown and RStudio Cloud instance)

```r

setup Latex

install.packages(c("tinytex", "remotes", "trackdown", "here", "broom")) tinytex::install_tinytex()

restart your environment, e.g. BASH

remotes::install_github("crsh/papaja") ```

You may also use the shared RStudio Cloud instance.

https://rstudio.cloud/project/4059380

Create a new article

• RStudio

File -> New File -> R Markdown -> From Template -> APA Article (6th)

Editor-agnostic method

r rmarkdown::draft("article.Rmd", template = "apa6", create_dir = FALSE, package = "papaja", edit = FALSE)

Immediate rendering

A good way to install missing LaTeX components.

r rmarkdown::render("article.Rmd")

here

Announcing this is the base directory (Please don't setwd)

r here::i_am("article.Rmd")

From here: FAQ

Q: I need Microsoft Word.

A: Change output to papaja::apa6_word

Q: This is for anonymous peer review

A: Change mask to yes

Q: I need to insert a table

A: Change your table to a data frame and use apa_table

For example:

```r media <- read.csv(here::here("data", "media.csv"))

model <- lm(radio~gender+age+education, data = media) broom::tidy(model, conf.int = TRUE)

papaja::apa_table(broom::tidy(model, conf.int = TRUE)) ```

Or add this into your rmarkdown as a code chunk

markdown {r, echo = FALSE} media <- read.csv(here::here("data", "media.csv")) model <- lm(radio~gender+age+education, data = media) papaja::apa_table(broom::tidy(model, conf.int = TRUE), caption = "Very important regression table", note = "You need to read this") ```

Q: I need to insert a figure

A: You have the figure file.

r knitr::include_graphics(here::here("fig", "survivorship.png"))

You want to generate the figure on the fly.

r require(ggplot2) ggplot(media, aes(x = radio, y = age)) + geom_point()

Q: I want the figures and tables not at the back.

A: Change floatsintext to yes

Q: I want to insert equations.

A: Use LaTeX.

latex \begin{align} e &= mc^2 \end{align}

Q: I want to insert source code.

A: Use non-executing code block.

Q: I want to do calculation in the text.

A: Use backtick r.

Q: I want to cite something.

A: You need to have your own Bibtex file (You can manage your bib file using Zotero, but that's beyond the scope of this short tutorial.)

1. Create a empty text file, e.g. "bib.bib"

2. Add entries

• Paste from downloaded bibtex files
• Generate from Crossref
• Google Scholar

1. Add to yaml bibliography

markdown @Van_der_Pas_2020 has said something great. This article [@Nanz_2022] says what I want to say. These articles [@Van_der_Pas_2020; @Nanz_2022] are nice.

Q: I want to create a reproducible workflow.

A: My suggestion is actually using make.

Q: I want to ...

A: You probably can find out how to do that either in

• The official papaja manual
• The RMarkdown book

Or zillion of RMarkdown tutorials (e.g. this one by my colleague Paul Bauer) out there.