index.qmd

---
title: "Design and Analysis of Experiments"
date: 2024/09/17
categories: BDSI Workshop
engine: knitr
filters:
  - webr2
webr: 
  show-startup-message: false    
  packages:
    - tidyverse
    - edibble
---


## 👋 Welcome 

This is a training workshop for BIOL8001 students but extended to also 
staff and students affiliated with the Australian National University (ANU) offered by the ANU Biological Data Science Institute (BDSI). 

This workshop provides a comprehensive introduction to the principles of experimental design and the analysis of experimental data. Participants are expected to have a basic understanding of R and linear models prior to the start of the workshop. 


## 🎯 Learning objectives 

Upon completion of this workshop, participants should be able to:

{{< include slides/_learning-objectives.qmd >}}


## 🔧 Preparation 

Please ensure that you download and install 

- the latest version of [R](https://cran.csiro.au/),
- the latest version of [RStudio Desktop](https://posit.co/download/rstudio-desktop/) or [Positron](https://github.com/posit-dev/positron/releases), and 
- the following packages by opening RStudio Desktop or Positron, then copy and paste the command below in the Console section, pushing Enter after pasting.

```r
install.packages(c("edibble", "broom"))
```

- For Window users, you may need to [install Rtools](https://cran.r-project.org/bin/windows/Rtools/) to install R packages.




```{r setup, include = FALSE}
library(webexercises)
library(tidyverse)
ex_tabset <- function(id) {
  paste0("[<i class='fas fa-pen-square'></i> Self test with Exercise ", id, "](#tabset-1-", id, "-tab){onclick=",
         'document.getElementById(', "'tabset-1-", id, "-tab').click();",
         '}')
}
slide_title <- function(id) {
  paste0("[", 
         rmarkdown::yaml_front_matter(paste0("slides/slide", id, ".qmd"))$title,
         "](slides/slide", id, ".html){target='_blank'}")
}

LOs <- readLines("slides/_learning-objectives.qmd")
LOs <- LOs[LOs!=""]
LOs <- stringr::str_replace(LOs, "- ", "")

checklist <- function(x) {
  paste0("::: {.callout-note}\n\n", 
         "## Reflect on learning objectives \n\n",
         "You should be able to:\n",
         paste0("<ul class='checkbox'>", paste(paste0("<li><input type='checkbox'> ", x, "</li>"), collapse = "\n\n"), "</ul>\n\n:::"))

}

```


## 📚 Slides

[![](images/by-nc-sa.svg)](https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en)

Click on the heading to open the slides in a new tab, or click on details to see the slides on this page.

###  `r slide_title(1)`

<details>

<iframe class="slide-deck" src="slides/slide1.html"></iframe>

`r ex_tabset(1)`

</details>

###  `r slide_title(2)`

<details>

<iframe class="slide-deck" src="slides/slide2.html"></iframe>

`r ex_tabset(2)`

</details>

### `r slide_title(3)`

<details>
   
<iframe class="slide-deck" src="slides/slide3.html"></iframe>

`r ex_tabset(3)`

</details>

## 📑 Resources

- Ruxton & Colegrave (2006) Experimental design for the life sciences. 2nd Edition. _(This book has a number of practical advices.)_
- Glass (2007) Experimental design for biologists. 1st Edition. _(This book is more philosophical.)_
- Chapters 1, 3, 4 and 7 from Welham et al. (2015) Statistical Methods in Biology: Design and Analysis of Experiments and Regression. See <http://www.stats4biol.info/> for the data and code in the book. _(This book is more statistical.)_

## 🏋️‍♀️ Self-paced exercises

The following self-paced exercises are designed to check your understanding of the material. After completing each exercise, review your answers and assess your grasp of the concepts.


::: {.panel-tabset}

## Exercise 1

`r checklist(LOs[1:2])`


{{< include "exercises/_exercise1.qmd" >}}



## Exercise 2

`r checklist(LOs[3:4])`


{{< include "exercises/_exercise2.qmd" >}}



## Exercise 3

`r checklist(LOs[5])`


{{< include "exercises/_exercise3.qmd" >}}





:::