Writing html from within R using knitr

Question

Maybe I am missing the obvious, but I have been struggling with finding an example for the following: I would like to write reports of my analysis in R to a html file using the knitr package. I have found the stitch() function, however it would be nice to have more control about which results & plots are written to html and which are not. In principal I would like to be able to code the following:

# some dummy code
library(ggplot)
data <- read.table('/Users/mydata', header=TRUE)
model <- lm(Y~X*Y, data)

# write this result to html:
summary(model)

thanks for the hint. But doesnt this example show how you embed R-code within a html file. I would rather like to create a html file and write content to it WITHIN R. Just like stitch() does, only that I would like to have more flexibility than just write everything to the html file. — jokel
– jokel, Commented Apr 28, 2012 at 12:00

dready · Accepted Answer · 2012-04-28 17:22:57Z

I guess I do not understand exactly what you are lacking, but here is a minimal examples I cooked up. To run this

library(knitr)
knit("r-report.html")

And the example.

<HTML>
<HEAD>
  <TITLE>Analyzing Diamonds!</TITLE>
</HEAD>

<BODY>
<H1>Diamonds are everywhere!</H1>

<!--begin.rcode echo=FALSE

## Load libraries, but do not show this
library(ggplot2)
library(plyr)
testData <- rnorm(1)
end.rcode-->

This is an analysis of diamonds, load the data.<p>
<!--begin.rcode echo=TRUE, fig.keep="all"
# Load the data
data(diamonds)
# Preview
head(diamonds)
end.rcode-->

Generate a figure, don't show code <p>
<!--begin.rcode echo=FALSE, fig.align="center", dev="png"
# This code is not shown, but figure will output
qplot(diamonds$color, fill=diamonds$color) + 
  opts(title="A plot title")
end.rcode-->

Show some code, don't output the figure<p>
<!--begin.rcode echo=TRUE, fig.keep="none"
# Show the code for this one, but don't write out the figure
ggplot(diamonds, aes(carat, price, colour=cut)) + 
  geom_point(aes(alpha=0.9))
end.rcode-->


And the value testData: <!--rinline testData --> inside a text block.

</BODY>
</HTML>

Yihui Xie · Accepted Answer · 2012-04-28 20:26:35Z

6

Writing HTML within R is much more laborious in my eyes than writing a template and knit() it (@dready has given a decent example). The code will be rather ugly, and you will see lots of "cats" jumping around. You may end up with something like this:

sink('test.html') # redirect output to test.html
cat('<h1>First level header</h1>\n')
cat('<pre>')
summary(mtcars)
cat('</pre>\n')
sink()
browseURL('test.html')

Anyway, there is another package R2HTML which may be more suitable in this case.

answered Apr 28, 2012 at 20:26

Yihui Xie

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