Programming with R

Dynamic reports with knitr

Learning Objectives

To discover knitr and the generation of dynamic reports

Knitr is an R package that makes your code neat, pretty, and shows your notes, code, and output simultaneously in an html document. You create these documents in .Rmd files. You can write in LateX or md.

knitr extracts R code in the input document (.Rmd), evaluates it and writes the results to the output document (html). There are two types of R code: chunks (code as separate paragraphs) and inline R code.

install.packages("knitr")

library(knitr)

Restart RStudio. Open a new Rmd file.

In Rmd, anything between lines that start and end with triple quotes ``` will be run as R code.

summary(cars)

     speed           dist       
 Min.   : 4.0   Min.   :  2.00  
 1st Qu.:12.0   1st Qu.: 26.00  
 Median :15.0   Median : 36.00  
 Mean   :15.4   Mean   : 42.98  
 3rd Qu.:19.0   3rd Qu.: 56.00  
 Max.   :25.0   Max.   :120.00

Challenge - Using KnitR to produce a report

Open an new .Rmd script and save it as inflammation_report.Rmd
Copy and paste the code as embedded R chunks to read in the data and plot average inflammation, or the heat map that we created.
Add a few notes describing what the code does and what the main findings are.
KNIT and view the html