Refactor ready for website

Author: liamjberrisford

_config.yml

@@ -91,3 +91,11 @@ execute:
       - 'individual_modules/improve_your_r_code/data_table.ipynb'
       - 'individual_modules/improve_your_r_code/parallelisation.ipynb'
       - 'individual_modules/improve_your_r_code/rcpp.ipynb'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Course_Outro.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Getting_Started_with_Markdown_in_R.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Formatted_Text.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Visual_Prelude.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_YAML_Header.md'

_static/multiple_regression_hyperplane.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#FFD700", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
+                  nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#4682B4", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#4682B4", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#4682B4", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
                   edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to HPC", "to": "Parallel Computing", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to HPC", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}]);
 
                   nodeColors = {};

_static/multiple_regression_hyperplane_2.html

@@ -282,8 +282,8 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#4682B4", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#4682B4", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis "}, {"color": "#4682B4", "id": "Python for Data Analysis ", "label": "Python for Data Analysis ", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis \nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: None"}]);
-                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis ", "width": 1}]);
+                  nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#FFD700", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#FFD700", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
+                  edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}, {"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}]);
 
                   nodeColors = {};
                   allNodes = nodes.get({ returnType: "Object" });

_static/workshops_network_hpc.html

@@ -196,15 +196,14 @@ parts:
                   - file: individual_modules/improve_your_r_code/rcpp
               - file: individual_modules/section_landing_pages/Introduction_to_Markdown_in_R
                 sections:
-                  - file: individual_modules/Introduction_to_Markdown_in_R/1_Course_Overview
-                  - file: individual_modules/Introduction_to_Markdown_in_R/2_Background_to_Markdown
-                  - file: individual_modules/Introduction_to_Markdown_in_R/3_Getting_Started_with_Markdown_in_R
-                  - file: individual_modules/Introduction_to_Markdown_in_R/4a_RMarkdown_Components_Visual_Prelude
-                  - file: individual_modules/Introduction_to_Markdown_in_R/4b_RMarkdown_Components_YAML_Header
-                  - file: individual_modules/Introduction_to_Markdown_in_R/4c_RMarkdown_Components_Formatted_Text
-                  - file: individual_modules/Introduction_to_Markdown_in_R/4d_RMarkdown_Components_Embedded_Code
-                  - file: individual_modules/Introduction_to_Markdown_in_R/5_Processing_RMarkdown_Files
-                  - file: individual_modules/Introduction_to_Markdown_in_R/6_Course_Outro
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Getting_Started_with_Markdown_in_R
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Visual_Prelude
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_YAML_Header
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Formatted_Text
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Course_Outro
           - file: course_homepages/unix
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_unix

_static/workshops_network_python_ds.html

@@ -1,12 +1,10 @@
-# Introduction to Markdown in R
+# A general background to Markdown
 
-## A general background to Markdown
-
-### What is Markdown?
+## What is Markdown?
 
 Markdown is a special type of language that can be used to create formatted text within a text editor. The concept of Markdown was created by John Gruber in 2004. Unlike programming languages which execute commands, Markdown is used to define the appearance and structure of text. It has a dedicated set of annotation sytnax (e.g. symbols) that can be used to control the formatting of text, from defining headers and boldening words, to adding hyperlinks and creating lists. While the annotation syntax is visible in the Markdown document itself, it does not actually show up in the outputted version of the document. Instead, the annotation syntax gets processed as instructions that dictate how the output content is displayed.
 
-### Why use Markdown?
+## Why use Markdown?
 
 Markdown offers several broad advantages, such as:
 

_toc.yml

@@ -1,25 +1,23 @@
-# Introduction to Markdown in R
+# Summary
 
-## Outro
-
-### Final take-homes
+## Final take-homes
 
 - The Markdown language is a useful tool for altering the format and structure of plain text
 - Markdown is best implemented in R *via* RStudio using the `rmarkdown` R package
 - R Markdown documents permit dynamic integration of formatted plain text, R code and its outputs, in turn supporting reproducible software development, data analysis and workflows
 
-### Acknowledgements and additional resources
+## Acknowledgements and additional resources
 
 This workshop shares some thoughts and ideas from the following resources:
 
 - The [Reproducible Research in R](https://monashdatafluency.github.io/r-rep-res/index.html) course developed for the Monash Bioinformatics Platform
 - The [R Markdown Cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/) developed by Yihui Xie, Christophe Dervieux and Emily Riederer
-- The [Introduction to Markdown in Python]() workshop offered by University of Exeter's Coding for Reproducable Research programme
+- The [Introduction to Markdown in Python](../../programme_information/python.ipynb) workshop offered by University of Exeter's Coding for Reproducable Research programme
 - The [R Markdown "cheat sheet"](https://posit.co/wp-content/uploads/2022/10/rmarkdown-1.pdf) available through [posit](https://posit.co/).
 
 Creation of this workshop was also supported by [ChatGPT](https://openai.com/index/chatgpt/).
 
-### Bonus task
+## Bonus task
 
 Below are links to some tutorials from the `microbiome` R package for analysis of microbiome data (Bioconductor landing page [here](https://www.bioconductor.org/packages/release/bioc/html/microbiome.html)):
 

individual_modules/Introduction_to_Markdown_in_R/1_Course_Overview.md

@@ -1,8 +1,6 @@
-# Introduction to Markdown in R
+# Getting Started 
 
-## Getting started with Markdown in R
-
-### What are the benefits of using Markdown in R?
+## What are the benefits of using Markdown in R?
 
 Implementing Markdown in R provides many benefits, for example:
 
@@ -13,11 +11,11 @@ Implementing Markdown in R provides many benefits, for example:
 |Felixble outputs| Through implementation of Markdown in R, your R code and plain text can be integrated together in a variety of different output formats, from interactive HTML reports that can be viewed in a browser, to print-friendly PDF files, editable Microsoft Word documents and even Microsoft Powerpoint Presentation format. As such, you have the flexibility to be able to present and share your R code in a way that you most prefer or that is best suited to the context at hand. |
 |Multiple languages| While the most logical implementation of Markdown in R is to produce dynamic documents of R code alongside formatted text, it is also possible to integrate and run other programming languages through Markdown in R, such a Python. This can be very useful in cases where you might need to leverage functions or libraries in the same pipeline that are native to different coding languages. |
 
-### How is Markdown implemented in R?
+## How is Markdown implemented in R?
 
 Markdown is predominantly implemented in R *via* RStudio using a dedicated R package called `rmarkdown`.
 
-#### Installing the `rmarkdown` package:
+### Installing the `rmarkdown` package:
 
 The `rmarkdown` package is available for download and installation through the Comprehensive R Archive Network (CRAN). This process can be undertaken by first opening RStudio and then performing the following click-button steps:
 
@@ -35,7 +33,7 @@ Alternitively, after opening RStudio, `rmarkdown` can be downloaded and installe
 install.packages('rmarkdown')
 ```
 
-#### Creating a new R Markdown document:
+### Creating a new R Markdown document:
 
 Once the `rmarkdown` package has been installed, a new, blank R Markdown document can be created in RStudio by:
 
@@ -47,6 +45,6 @@ Once the `rmarkdown` package has been installed, a new, blank R Markdown documen
 Completing the above four steps should result in an RStudio window that looks like the following:
 ![Blank RMarkdown file](Embedded_Display_Items/Blank_RMarkdown_View.png)
 
-#### Saving a (new) R Markdown document:
+### Saving a (new) R Markdown document:
 
 After initialising a new R Markdown document, it can be saved by clicking `File` at the top of the screen and selecting `Save`. Alternatively, the save process can be performed by clicking the <img src = "Embedded_Display_Items/floppy_disk.png" alt = "floppy disk" width = "25" style = "vertical-align:middle;"> button. It is also good practice to repeat the save process regularly when putting together an R Markdown document so that no progress is lost.