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I was wondering how you could turn an R script into an HTML report (From the sounds of it using knitr is the way to go). I would like to do this without using RStudio if possible.

Say I have to following R script

#Load librarys + initilisation calculations
#User shouldn't see the next 2 lines
library(foo)
set.seed(42)

#User will see the next 3 lines
print("This is some text to describe what the user is about to see")
head(mtcars)
boxplot(mtcars$mpg~mtcars$cyl)


#Not shown to user:
numbers <- runif(100)
moreNumbers <- rnorm(100)
group <- c(rep("a",100), rep("b",100))
df <- data.frame(c(numbers, moreNumbers), group)
names(df) <- c("ExampleData", "g")


#Show to user 
t.test(df$ExampleData~df$g)

I've tried having a look around the internet and feel as if all the steps are just a little too far ahead of what I understand.

Do I need to make another R script which contains a stitch()/knit() function which calls the script above?

Thanks,

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  • you do not need Rstudio to use knitr. See rmarkdown.rstudio.com Commented Feb 11, 2015 at 2:12

2 Answers 2

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Call knitr::spin() on your R script. Or equivalently, click the notebook button on the RStudio toolbar.

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2 Comments

That's actually really close! Is there a way to suppress output from the lines of code if required?
@testuser Yes, you can use chunk options as usual, and the syntax is a little bit different, e.g. #+ results='hide', eval=TRUE Please see the link I included in the answer.
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The answer to your question about making another script is no. What you need to do is knit("your_script.R") or whatever it is called. But first, you have to make it conform to knitr conventions. There are many sample files here which you can use to get things correct.

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3 Comments

So it's basically just going to require re-formatting the "your_script.R"?
You just need to edit it. Look at the link, under demos then minimal examples. There is a header line for each code block which tells knitr what to do, display it or not, and many other options. Fixing your script above will take just a few minutes. And if you want html as your output you should name your script with a .Rmd extension so knitr automatically creates the html.
Correction: for html output use script.Rhtml. See ?knit.

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