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---
title: "Reproducible research with Quarto"
categories: BDSI workshop
date: 04/12/2024
engine: knitr
---
## Welcome 👋
This is a training workshop for staff and students affiliated with the Australian National University (ANU) offered by the ANU Biological Data Science Institute (BDSI).
The goal of the workshop is to provide participants with the proficiency to author reproducible research documents using Quarto, an open-source system for scientific and technical publishing. Prior familiarity and usage of at least one of the programming languages such as Python, R, or Julia is assumed to get the most out of the workshop.
## 🎯 Learning objectives
Upon completion of this workshop, participants should be able to:
{{< include slides/_learning-objectives.qmd >}}
## 🔧 Preperation
Please ensure that you download and install
- the latest version of [Quarto](https://quarto.org/docs/get-started/),
- bring your own dataset for technical report writing _(note: the teaching team can't help with the analysis or writing content -- you are recommended to do the analysis and writing up the results before the workshop)_,
- (Optional) make a free account at [Quarto Pub](https://quartopub.com/), and
- (Optional) [Slack](https://slack.com/intl/en-au) (alternatively you can use the web version).
### For **R** users
- It is assumed that you already have R installed.
- Please install the latest version of [RStudio Desktop](https://posit.co/download/rstudio-desktop/),
- And install the following R packages:
```r
install.packages(c("tidyverse", "rmarkdown", "quarto", "tinytex"))
# then install tinytex
tinytex::install_tinytex()
```
### For **Python** users
- It is assumed that you already have Python installed.
- Run the following command in the terminal:
```bash
quarto install tinytex
```
- Please install [Jupyter](https://jupyter.org/install).
- Optionally (but preferred), follow the same instruction as the R users and install the following R package:
```r
install.packages("reticulate")
```
### For **Julia** users
- It is assumed that you already have Julia installed.
- Run the following command in the terminal:
```bash
quarto install tinytex
```
- Please install [Jupyter](https://jupyter.org/install).
- Optionally (but preferred), follow the same instruction as the R users and install the following R package:
```r
install.packages("JuliaCall")
```
### For **other language** users
Other languages are possible as well (e.g. E-Views, SAS and Stata) but it may not work as seamlessly as above languages. Other languages that is supported via the knitr engine are listed below.
```{r}
names(knitr::knit_engines$get())
```
### {{< fa hand-holding-medical >}} Issues
If you are having issues, see also [here](https://learnr.numbat.space/chapter1) or talk to the teaching team.
<i class='fas fa-exclamation-circle'></i> Please note that the teaching team primarily consists of R users, so we may not be able to provide help for other languages.
::: {.callout-note icon=false style="width:100%"}
## <i class='fab fa-slack'></i> [Slack workspace (Optional)]{#slack}
We use Slack to facilitate communication between workshop participants and the teaching team.
::: w-100
[<button class="button">Join ANU Learning Data Slack Community</button>](https://join.slack.com/t/anulearningdata/signup){.no-decoration}
:::
- You must use your ANU email to sign up.
- Use your full name.
- By joining, you agree to abide by this [**code of conduct**](/slack.html).
- Please **don't direct message the teaching team** in Slack. Your questions are more likely to be answered in the Slack channels rather than in direct messages.
Please note that the teaching team does not necessarily actively monitor or attend to the Slack workspace outside of the workshop.
:::
## Teaching team
```{css}
#| echo: false
.nav-link.active {
background-color: #F5EDDE!important;
border-bottom-color: #F5EDDE!important;
}
.tab-content {
background-color: #F5EDDE!important;
}
```
`r photo_path <- "slides/"`
{{< include slides/_team.qmd >}}
## Materials
The materials can be found [here](/materials.html).
   
These materials are shared under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-nc-sa/4.0/).