Project template

Made by Ryan Straight with APCV 302 in mind, specifically, as the focus is on using R for data analysis, this template is simple enough to fit most needs at the undergraduate level.

The actual report document being produced is an APA 6th edition document using the papaja package, and uses rfordatascience/tidytuesday code. You should also install tinytex, of course, as per the papaja instructions. Some demo code had been added to the script files and dummy text to the draft.Rmd to produce an example PDF. The Bee Colony losses dataset is loaded as an example. You’ll notice heavy use of the here package, as well.

Important: each time you knit draft.Rmd, you will query GitHub. There is a limit on how often you can do this. Manually downloading the data into the /data/raw folder and loading from there will get around this.

An example of how to do this is to remove the tidytuesdayR data loading line from munge.R. Instead, simply run this in the console:

download.file('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2022/2022-01-11/colony.csv', here("data", "raw", "colony.csv"))

Then, your data load in munge.R would be as such and you needn’t worry about loading from GitHub:

colony <- readr::read_csv(here("data", "raw", "colony.csv'))

Authors

1. Make your copy of the contributor’s template and complete as needed. Ensure your spreadsheet’s permissions are set to Anyone with the link can view.
2. Place that URL in step 2 of the tenzing Shiny app. (You can use this spreadsheet as a demonstration if you like.)
3. Choose Show papaja YAML in Step 3.
4. Replace the author and affiliation frontmatter in the draft.Rmd file with this new YAML.

Report

The resultant report from this project is /docs/draft.pdf by default. The papaja document, /docs/draft.Rmd, has a variety of comments and instructions within as comments. These are general suggestions that follow a generic research paper structure.

Folder and file structure

This is the default structure for a project. It’s very basic and you should feel welcome to alter it to your liking.

project-template/
├─ data/
│  ├─ raw/            # Store raw data here, if needed
│  ├─ tidy/           # Cleaned or altered data files go here
├─ docs/
│  ├─ draft.pdf       # Knitted papaja PDF 
│  ├─ draft.Rmd       # papaja draft document
│  ├─ refs.bib        # Put your references here in BibTeX format
│  ├─ r-references.bib# Packages used in document. Generated by papaja.
├─ media/             # Non-generated figures, images, media go here
├─ src/
│  ├─ eda.R           # exploratory data analysis scripts
│  ├─ plots.R         # Plots, figures, graphs, et cetera
│  ├─ munge.R         # Any scripts used on raw data
├─ .gitignore         # Keeps certain files from being seen by GitHub
├─ .Rbuildignore      # List of files to be ignored by R building
├─ project.Rproj      # R project file
├─ LICENSE.md         # Identifies CC-BY license for project template
├─ README.Rmd         # README RMarkdown file. Edit this file.
├─ README.md          # ...not this one.