This is an R HTML vignette. The file extension is *.Rhtml, and it has to include a special comment to tell R that this file needs to be compiled by knitr:

<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{The Title of Your Vignette}
-->

Now you can write R code chunks:

summary(cars)

##      speed           dist    
##  Min.   : 4.0   Min.   :  2  
##  1st Qu.:12.0   1st Qu.: 26  
##  Median :15.0   Median : 36  
##  Mean   :15.4   Mean   : 43  
##  3rd Qu.:19.0   3rd Qu.: 56  
##  Max.   :25.0   Max.   :120

fit=lm(dist~speed, data=cars)
summary(fit)

## 
## Call:
## lm(formula = dist ~ speed, data = cars)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -29.07  -9.53  -2.27   9.21  43.20 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  -17.579      6.758   -2.60    0.012 *  
## speed          3.932      0.416    9.46  1.5e-12 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 15.4 on 48 degrees of freedom
## Multiple R-squared:  0.651,	Adjusted R-squared:  0.644 
## F-statistic: 89.6 on 1 and 48 DF,  p-value: 1.49e-12

You can also embed plots, for example:

par(mar=c(4,4,.1,.1))
plot(cars, pch=19)
plot of chunk cars-plot

For package vignettes, you need to encode images in base64 strings using the knitr::image_uri() function so that the image files are no longer needed after the vignette is compiled. For example, you can add this chunk in the beginning of a vignette:

library(knitr)
# to base64 encode images
opts_knit$set(upload.fun = image_uri)