Merge pull request #117 from elixir-europe-training/clement-lee-patch-2

Clement lee patch 2

Author: clement-lee

README.md

@@ -1,48 +1,13 @@
-# Elixir Training Lesson template
+# Elixir Training Lesson: Literate Programming in R
 
-[![DOI](https://zenodo.org/badge/564252010.svg)](https://zenodo.org/badge/latestdoi/564252010)
+(placeholder for badge) 
 
+This repository contains the scripts and source files for the [Elixir Training Lesson: Literate Programming in R](https://elixir-europe-training.github.io/ELIXIR-TrP-LiterateProgrammingR-CodeRep/), using the template from [this repository](https://elixir-europe-training.github.io/ELIXIR-TrP-LessonTemplateInstructions-MkDocs/)
 
-For instruction on how to use the template, please follow this documentation: 
-https://elixir-europe-training.github.io/ELIXIR-TrP-LessonTemplateInstructions-MkDocs/
-
-
-**Any issues?** Contact Geert van Geest (@GeertvanGeest) 
-
-
-
-## If working locally
-
-This website is generated with [MkDocs](https://www.mkdocs.org/), with the theme [Material](https://squidfunk.github.io/mkdocs-material/).
-
-To host it locally, install MkDocs:
-```bash
-pip install mkdocs
-```
-
-and Material with some plugins:
-```bash
-pip install mkdocs-material
-pip install mkdocs-video
-pip install mkdocs-bibtex 
-pip install neoteroi-mkdocs
-```
-
-Clone this repository to your local computer. Then, make the repository your current directory and type:
-
-```bash
-mkdocs serve
-```
-
-To host it locally.
-
-Check it out with your browser at [http://localhost:8000/](http://localhost:8000/).
-
+While the training can be completed without referring to this repository at all, comprehension of how the source files lead to the webpages is an indicator of successful completion of the training, as the content i.e. literate programming **is** the way the webpages have been written.
 
 ## Citation
 
 Please cite as
 
-> Geert van Geest, Elin Kronander, Jose Alejandro Romero Herrera, Nadja Žlender, & Alexia Cardona. (2023). 
-> The ELIXIR Training Lesson Template - Developing Training Together (v1.0.0-alpha). Zenodo. 
-> https://doi.org/10.5281/zenodo.7913092
+(placeholder for citation)

docs/chapters/Chapter_04.md

@@ -21,18 +21,18 @@ Check out the [Quarto gallery](https://quarto.org/docs/gallery/) to see its capa
 In this part of the tutorial, we'll focus on using Quarto with R. But remember, Quarto isn't limited to [R](https://quarto.org/docs/computations/r.html) — it also works with Python, Julia, and Observable JS!
 
 ### Installation Guide 
-Before we start, it's essential to set up our environment. Here's what you need:
+Before we start, it's essential to set up our environment. Here's what you need (you should already have the first three from the [software setup](../../#software-setup)):
 
 1. **RStudio Installation**: Ensure you have the latest version of RStudio. This will provide the best compatibility with Quarto.
 
-2. **Quarto Installation:** Visit the [Quarto website](https://quarto.org/) for installation instructions. For a more detailed guide, check out the [Quarto guide]([https://quarto.org/](https://quarto.org/docs/guide/)). Make sure to follow the steps appropriate for your operating system.
+2. **Quarto Installation**: Visit the [Quarto website](https://quarto.org/) for installation instructions. For a more detailed guide, check out the [Quarto guide]([https://quarto.org/](https://quarto.org/docs/guide/)). Make sure to follow the steps appropriate for your operating system.
 
-3. **TinyTeX Setup**
+3. **TinyTeX Setup**:
 TinyTeX is a minimal TeX distribution specifically tailored for Quarto, which you'll need for generating PDFs. Here's how to install it:
 - Open RStudio, navigate to *Tools* > *Terminal* > *New Terminal*.
 - In the terminal, type *quarto install tinytex* to start the installation process.
 
-4. **Update R Packages**
+4. **Update R Packages**:
 To ensure smooth operation with Quarto, update the following R packages by running this command in RStudio:
 
 ```R