Merge pull request #260 from coding-for-reproducible-research/markdown_r_corrections

Corrections for Markdown in R

Author: liamjberrisford

individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown.md

@@ -1,4 +1,4 @@
-# A general background to Markdown
+# A General Background to Markdown
 
 ## What is Markdown?
 

individual_modules/Introduction_to_Markdown_in_R/Getting_Started_with_Markdown_in_R.md

@@ -47,4 +47,6 @@ Completing the above four steps should result in an RStudio window that looks li
 
 ### 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.
+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 ![Floppy Disk](./Embedded_Display_Items/floppy_disk.png) 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.
+
+

individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files.md

@@ -1,4 +1,4 @@
-# Processing R Markdown 
+# Processing R Markdown Documents
 
 Throughout this workshop, the gap between what syntax looks like in a `.Rmd` file and how things appear in the final output document has been bridged using vague phrases like "*The HTML output generated upon processing the R Markdown document*...". To be more precise, the overall procedure of going from a `.Rmd` file to a final output document is called **rendering**.
 

individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code.md

@@ -1,4 +1,4 @@
-# Embedded Code - Components of an R Markdown Document
+# Components of an R Markdown Document - Embedded Code
 
 As mentioned earlier in this workshop, one of the primary benefits of R Markdown is the ability to integrate formatted plain text with R code and its outputs into a single dynamic document. Code can be embedded into R Markdown documents in two different forms:
 

individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Formatted_Text.md

@@ -1,4 +1,4 @@
-# Formatted Plain Text - Components of an R Markdown Document
+# Components of an R Markdown Document - Formatted Plain Text
 
 Many of the features that you might implement in other text-based applications like Microsoft Word can also be easily implemented in R Markdown documents. This could range from basic alterations to text aesthetics, through to the addition of tables and images, or even the inclusion of hyperlinks.
 
@@ -82,7 +82,7 @@ output: html_document
 This is my very first R Markdown document.
 ```
 
-Notice how the plain text on the line starting with the `#` now appears blue. This is an example of annotation syntax highlighting in R Markdown, which usefully makes the specific bits of text being formatted stand out. Processing the above in an R Markdown file would then generate a HTML output that displays like the following:
+Notice how the plain text on the line starting with the `#` now appears blue. This is an example of annotation syntax highlighting in R Markdown, which usefully makes the specific bits of text being formatted stand out. This is an example of annotation syntax highlighting in R Markdown, which usefully makes the specific bits of text being formatted stand out. Processing the above in an R Markdown file would then generate a HTML output that displays like the following:
 
 ![single header](Embedded_Display_Items/single_header.png)
 
@@ -387,7 +387,7 @@ The above will translate into the below output HTML when processed:
 
 ### Task
 
-Below is a HTML output generated using R Markdown that summarises how skeletal muscle adapts to different exercise types. Try to reproduce this in your open R Markdown document. You can check the formatting effects you apply in real time by toggling from `Source` view to `Visual` view in the top left corner of the RStudio script pane. The Google Scholar entry for the utilised journal article can be found [here](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Integrative+effects+of+resistance+training+and+endurance+training+on+mitochondrial+remodeling+in+skeletal+muscle&btnG=). You will need to create a `.bib` file containing the reference and also obtain the URL for the image directly from the journal article webpage.
+Below is a HTML output generated using R Markdown that summarises how skeletal muscle adapts to different exercise types. Try to reproduce this in your open R Markdown document. You can check the formatting effects you apply in real time by toggling from `Source` view to `Visual` view in the top left corner of the RStudio script pane. The Google Scholar entry for the utilised journal article can be found by searching the journal title in Google Scholar itself. You will need to create a `.bib` file containing the reference and also obtain the URL for the image directly from the journal article webpage.
 
 #### *Task HTML output:*
 

individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Visual_Prelude.md

@@ -1,4 +1,4 @@
-# A Visual Prelude - Components of an R Markdown Document
+# Components of an R Markdown Document - A Visual Prelude
 
 So far we have installed the `rmarkdown` package for producing Markdown documents in R, and used it to initialise a blank R Markdown document. It is worthwhile noting that, whereas standard Markdown files hold the `.md` file extention, raw R Markdown documents instead carry the `.Rmd` file extension. 
 

individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_YAML_Header.md

@@ -1,12 +1,12 @@
-# The YAML header - Components of an R Markdown Document
+# Components of an R Markdown Document - The YAML header
 
 ## What is the YAML header?
 
 A YAML header is the very first component worth adding to an R Markdown file. Conceptually, it is a short block of text occuring at the start of an R Markdown file that can be used to define metadata for the file as well as instructions on how the R Markdown file should be processed and how to style the output.
 
 ## What does a YAML header look like?
 
-The YAML header is itself comprised of key-value pairs that are enclosed above and below by triple-dash (---) lines. An example YAML header is as follows:
+The YAML header is itself comprised of key-value pairs that are enclosed above and below by triple-dash (`---`) lines. An example YAML header is as follows:
 
 ```r
 ---
@@ -54,7 +54,7 @@ output: word_document
 ---
 ```
 
-Some output options can be leveraged regardless of output format, whereas other are only valid for specific types of output format. The most common output types and options when defining the `output` key of a YAML header are as follows (sourced from [posit](https://posit.co/wp-content/uploads/2022/10/rmarkdown-1.pdf)):
+Some output options can be leveraged regardless of output format, whereas others are only valid for specific types of output format. The most common output types and options when defining the `output` key of a YAML header are as follows (sourced from [posit](https://posit.co/wp-content/uploads/2022/10/rmarkdown-1.pdf)):
 
 ![rmarkdown outputs](Embedded_Display_Items/rmarkdown_cheat_sheet_outputs.png)