This lesson is in the early stages of development (Alpha version)

r-novice-inflammation

This repository is a way for me to test out the new features in {sandpaper} on a real repository. It’s derived from Programming With R and hopefully, I can get it to a point where it will be identical without using Jekyll.

To render this lesson, first clone it and then use {sandpaper} to render it

remotes::install_github("zkamvar/sandpaper", dep = TRUE)
usethis::create_from_github("zkamvar/miniature-octo-waffle", "~/Desktop")
## you will be moved to that directory

sandpaper::build_lesson()

I converted this site by using the {dovetail} package:

remotes::install_github("zkamvar/sandpaper", dep = TRUE)
remotes::install_github("carpentries/dovetail") # contains script to convert lessons
remotes::install_github("carpentries/pegboard") # for converting 

# Download the repo from github
usethis::create_from_github("swcarpentry/r-novice-inflammation", "~/Desktop")

# convert the materials
source(system.file("convert", "convert.R", package = "dovetail"))

# Create sandpaper repo
sandpaper::create_lesson("~/Desktop/new-rni")

system("cp -R ~/Desktop/rni/_episodes_rmd/* ~/Desktop/new-rni/episodes")

## change ../fig to fig
## change latex link to latex equation

After that was done, I had to make a couple of changes like making sure the hard-coded figures were no longer sourcing above their current directory, by changing all instances of ../fig to fig and changing the reference to the latex equation in episode 8 to actual latex code.

I could then build the lesson inside of the new-rni directory

sandpaper::build_lesson()

	Setup	Download files and setup software required for this lesson
00:00	1. Analyzing Patient Data	How do I read data into R? How do I assign variables? What is a data frame? How do I access subsets of a data frame? How do I calculate simple statistics like mean and median? Where can I get help? How can I plot my data?
00:45	2. Creating Functions	How do I make a function? How can I test my functions? How should I document my code?
01:15	3. Analyzing Multiple Data Sets	How can I do the same thing to multiple data sets? How do I write a `for` loop?
01:45	4. Making Choices	How do I make choices using `if` and `else` statements? How do I compare values? How do I save my plots to a PDF file?
02:15	5. Command-Line Programs	How do I write a command-line script? How do I read in arguments from the command-line?
02:45	6. Best Practices for Writing R Code	How can I write R code that other people can understand and use?
02:55	7. Dynamic Reports with knitr	How can I put my text, code, and results all in one document? How do I use `knitr`? How do I write in Markdown?
03:15	8. Making Packages in R	How do I collect my code together so I can reuse it and share it? How do I make my own packages?
03:45	9. Introduction to RStudio	How do I use the RStudio graphical user interface?
04:00	10. Addressing Data	What are the different methods for accessing parts of a data frame?
04:20	11. Reading and Writing CSV Files	How do I read data from a CSV file into R? How do I write data to a CSV file?
04:50	12. Understanding Factors	How is categorical data represented in R? How do I work with factors?
05:10	13. Data Types and Structures	What are the different data types in R? What are the different data structures in R? How do I access data within the various data structures?
05:55	14. The Call Stack	What is the call stack, and how does R know what order to do things in? How does scope work in R?
06:10	15. Loops in R	How can I do the same thing multiple times more efficiently in R? What is vectorization? Should I use a loop or an `apply` statement?
06:40	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

r-novice-inflammation

Schedule