Content from Using RMarkdown

Last updated on 2024-10-22 | Edit this page

Estimated time: 12 minutes

Overview

Questions

  • How do you write a lesson using R Markdown and sandpaper?

Objectives

  • Explain how to use markdown with the new lesson template
  • Demonstrate how to include pieces of code, figures, and nested challenge blocks

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson template:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can also include figures generated from R Markdown:

R 

pie(
  c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of pyramid" = 5), 
  init.angle = 315, 
  col = c("deepskyblue", "yellow", "yellow3"), 
  border = FALSE
)
pie chart illusion of a pyramid
Sun arise each and every morning

Or you can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Callout

Callout sections can highlight information.

They are sometimes used to emphasise particularly important points but are also used in some lessons to present “asides”: content that is not central to the narrative of the lesson, e.g. by providing the answer to a commonly-asked question.

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Virtual Environments

Last updated on 2024-10-24 | Edit this page

Estimated time: 0 minutes

Overview

Questions

  • What are are virtual environements and how are they used?
  • How do I create and work with virtual environments in R?

Objectives

SH 

- define the term virtual environment and explain how virtual environments are used
- create a virtual environment that uses a specific version of a package using renv
- restore a virtual environment using renv
- explore the history of a virtual environment using renv

Key Points

  • Virtual environments help programmers to manage the packages installed in their workspace.
  • In R, you can use the renv package to control the packages that are included in your environment.

Content from Creating a Package

Last updated on 2024-10-24 | Edit this page

Estimated time: 54 minutes

Overview

Questions

  • How do you create a package in R?

Objectives

  • identify how package are organized and store on a user’s machine
  • explain the differences between each of the
  • describe the iterative steps in the package creation process
  • use devtools::create_package() to intialize the package development environment
  • convert scripts into a package that can be used by others

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

Packages structure and states alt=‘A diagram depicting the structures and states of a package’

Challenge 1: What is the correct order of these steps?

Organize the steps involved in the creation of a package * __ binary
* __ source
* __ bundle
* __ in-memory
* __ installed

  • __ source
  • __ bundle
  • __ binary
  • __ installed
  • __ in-memory

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can also include figures generated from R Markdown:

R 

pie(
  c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of pyramid" = 5), 
  init.angle = 315, 
  col = c("deepskyblue", "yellow", "yellow3"), 
  border = FALSE
)
pie chart illusion of a pyramid
Sun arise each and every morning

Or you can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Callout

Callout sections can highlight information.

They are sometimes used to emphasise particularly important points but are also used in some lessons to present “asides”: content that is not central to the narrative of the lesson, e.g. by providing the answer to a commonly-asked question.

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Code Styling and Linters

Last updated on 2024-10-24 | Edit this page

Estimated time: 54 minutes

Overview

Questions

  • What is Code Styling?
  • What are linters?

Objectives

  • describe what is code styling and what are linters
  • run linting on existing code

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson template:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can also include figures generated from R Markdown:

R 

pie(
  c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of pyramid" = 5), 
  init.angle = 315, 
  col = c("deepskyblue", "yellow", "yellow3"), 
  border = FALSE
)
pie chart illusion of a pyramid
Sun arise each and every morning

Or you can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Callout

Callout sections can highlight information.

They are sometimes used to emphasise particularly important points but are also used in some lessons to present “asides”: content that is not central to the narrative of the lesson, e.g. by providing the answer to a commonly-asked question.

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally