install.packages(
c("quarto","tidyverse","BayesFactor","patchwork","renv","usethis"))Monash Data Fluency: Reproducible Research in R (with Quarto)
Workshop material
We will be working through material from the Carpentries incubator. The Data Fluency program at Monash University is almost entirely based on the Carpentries teaching philosophy. This new material caught our attention by perfectly capturing current thinking about some good scientific practices and practical means to achieve them.
We will use this example GitHub repository:
Some slides to put things in context:
Setup
You can use RStudio on your own laptop (preferred) or use Posit Cloud. If using RStudio on your own laptop, follow the software installation instructions below. If using Posit Cloud, please still do steps 3 and 4 below.
If you have a Monash University supplied laptop, you may need to submit a service request to eSolutions to be allowed to install software. For now, use Posit Cloud.
1. Install R
2. Install RStudio
3. In RStudio, run this R code to install some packages:
4. Create an account on GitHub if you don’t already have one.
5. Install git:
Windows users should install Git for Windows (includes Git Credential Manager*).
Mac users should install Apple’s Xcode command line tools, which includes git. This is also worthwhile because it will let you install R packages that need compilation. Open the Terminal app, type the command below, and press return:
xcode-select --install(Mac users can also the binary installer here: https://git-scm.com/download/mac. It is slightly out of date but should be fine. This method will be faster.)
Mac users should also install Git Credential Manager*: download page, installation instructions. Download and open the appropriate “.pkg” file for your machine, gcm-osx-arm64-…pkg if you have an M1 or M2 mac, gcm-osx-x64-…pkg otherwise.
* Git Credential Manager should let us push (upload) changes to repositories on GitHub using the https method. Otherwise we would need to set up an ssh key to push changes, which is beyond the scope of this workshop.
If you run into problems installing any of these, you can use Posit Cloud for the workshop.
Authentication without Git Credential Manager
There is an alternative method to push changes to GitHub using tokens.
This method will also work from Posit Cloud.
Log in to github.com
→ Click the top right corner to open your account menu
→ Settings
→ Developer settings
→ Personal access tokens
→ Fine-grained personal access tokens (beta)
→ Generate new token
Select:
- Repository access:
- only select repositories → the repository we are working on
- Repository permissions:
- commit statuses → access level: read & write
- contents → access level: read & write
In the Terminal pane in RStudio you need to configure who you are for git with the following (filling in your details):
git config --global user.email "your.email@monash.edu"
git config --global user.name "your_github_username"When pushing from RStudio, enter your GitHub username and then paste the token when prompted for a password.
Optional further software
RStudio comes bundled with Quarto and LaTeX, but you can install them separately if you want to use them from the command line. LaTeX is used to create PDFs. We won’t use this in the workshop.
Bits and pieces
Quarto user guides ← topics give a good idea of what is possible!
Quarto cross-references ← a useful but hard to discover feature
More information on the BibTex format
More information about writing equations
Monash themed Quarto templates by Rob Hyndman
Example of a peer-reviewed “knitted” publication
Example of a GitHub repository associated with a publication
Example of workshop material (in bookdown)
(Jointly developed by University of Queensland and Monash, check the commit log!)
_quarto.yml file required for this workshop
project:
execute-dir: "project"
_quarto.yml suggested further settings
project:
execute-dir: "project" # Working directory always the same.
output-dir: "output" # HTML files go in this directory.
# render: # Specify order of rendering.
# - "report/preprocess.qmd"
# - "report/my-report.qmd"
format:
html:
toc: true # Table of contents.
code-fold: true # Initially hide code.
fontsize: "10pt" # Smaller font.
embed-resources: true # Ensure HTML files are fully self-contained.After editing _quarto.yml, you may need to close and re-open your project in RStudio.
If you specify the order of rendering, the whole project can be run in the correct order in a single step. In RStudio this can be done in the “Build” pane with the “Render Project” button. On the command line it can be done with:
quarto render
Nice looking tables
The default appearance of tables produced by code chunks is a bit plain. Try these instead, and look at their documentation for how to customize the output further.
knitr::kable(mtcars)| mpg | cyl | disp | hp | drat | wt | qsec | vs | am | gear | carb | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.620 | 16.46 | 0 | 1 | 4 | 4 |
| Mazda RX4 Wag | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.875 | 17.02 | 0 | 1 | 4 | 4 |
| Datsun 710 | 22.8 | 4 | 108.0 | 93 | 3.85 | 2.320 | 18.61 | 1 | 1 | 4 | 1 |
| Hornet 4 Drive | 21.4 | 6 | 258.0 | 110 | 3.08 | 3.215 | 19.44 | 1 | 0 | 3 | 1 |
| Hornet Sportabout | 18.7 | 8 | 360.0 | 175 | 3.15 | 3.440 | 17.02 | 0 | 0 | 3 | 2 |
| Valiant | 18.1 | 6 | 225.0 | 105 | 2.76 | 3.460 | 20.22 | 1 | 0 | 3 | 1 |
| Duster 360 | 14.3 | 8 | 360.0 | 245 | 3.21 | 3.570 | 15.84 | 0 | 0 | 3 | 4 |
| Merc 240D | 24.4 | 4 | 146.7 | 62 | 3.69 | 3.190 | 20.00 | 1 | 0 | 4 | 2 |
| Merc 230 | 22.8 | 4 | 140.8 | 95 | 3.92 | 3.150 | 22.90 | 1 | 0 | 4 | 2 |
| Merc 280 | 19.2 | 6 | 167.6 | 123 | 3.92 | 3.440 | 18.30 | 1 | 0 | 4 | 4 |
| Merc 280C | 17.8 | 6 | 167.6 | 123 | 3.92 | 3.440 | 18.90 | 1 | 0 | 4 | 4 |
| Merc 450SE | 16.4 | 8 | 275.8 | 180 | 3.07 | 4.070 | 17.40 | 0 | 0 | 3 | 3 |
| Merc 450SL | 17.3 | 8 | 275.8 | 180 | 3.07 | 3.730 | 17.60 | 0 | 0 | 3 | 3 |
| Merc 450SLC | 15.2 | 8 | 275.8 | 180 | 3.07 | 3.780 | 18.00 | 0 | 0 | 3 | 3 |
| Cadillac Fleetwood | 10.4 | 8 | 472.0 | 205 | 2.93 | 5.250 | 17.98 | 0 | 0 | 3 | 4 |
| Lincoln Continental | 10.4 | 8 | 460.0 | 215 | 3.00 | 5.424 | 17.82 | 0 | 0 | 3 | 4 |
| Chrysler Imperial | 14.7 | 8 | 440.0 | 230 | 3.23 | 5.345 | 17.42 | 0 | 0 | 3 | 4 |
| Fiat 128 | 32.4 | 4 | 78.7 | 66 | 4.08 | 2.200 | 19.47 | 1 | 1 | 4 | 1 |
| Honda Civic | 30.4 | 4 | 75.7 | 52 | 4.93 | 1.615 | 18.52 | 1 | 1 | 4 | 2 |
| Toyota Corolla | 33.9 | 4 | 71.1 | 65 | 4.22 | 1.835 | 19.90 | 1 | 1 | 4 | 1 |
| Toyota Corona | 21.5 | 4 | 120.1 | 97 | 3.70 | 2.465 | 20.01 | 1 | 0 | 3 | 1 |
| Dodge Challenger | 15.5 | 8 | 318.0 | 150 | 2.76 | 3.520 | 16.87 | 0 | 0 | 3 | 2 |
| AMC Javelin | 15.2 | 8 | 304.0 | 150 | 3.15 | 3.435 | 17.30 | 0 | 0 | 3 | 2 |
| Camaro Z28 | 13.3 | 8 | 350.0 | 245 | 3.73 | 3.840 | 15.41 | 0 | 0 | 3 | 4 |
| Pontiac Firebird | 19.2 | 8 | 400.0 | 175 | 3.08 | 3.845 | 17.05 | 0 | 0 | 3 | 2 |
| Fiat X1-9 | 27.3 | 4 | 79.0 | 66 | 4.08 | 1.935 | 18.90 | 1 | 1 | 4 | 1 |
| Porsche 914-2 | 26.0 | 4 | 120.3 | 91 | 4.43 | 2.140 | 16.70 | 0 | 1 | 5 | 2 |
| Lotus Europa | 30.4 | 4 | 95.1 | 113 | 3.77 | 1.513 | 16.90 | 1 | 1 | 5 | 2 |
| Ford Pantera L | 15.8 | 8 | 351.0 | 264 | 4.22 | 3.170 | 14.50 | 0 | 1 | 5 | 4 |
| Ferrari Dino | 19.7 | 6 | 145.0 | 175 | 3.62 | 2.770 | 15.50 | 0 | 1 | 5 | 6 |
| Maserati Bora | 15.0 | 8 | 301.0 | 335 | 3.54 | 3.570 | 14.60 | 0 | 1 | 5 | 8 |
| Volvo 142E | 21.4 | 4 | 121.0 | 109 | 4.11 | 2.780 | 18.60 | 1 | 1 | 4 | 2 |
DT::datatable(mtcars)