# An R HTML vignette with knitr

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, 0.1, 0.1))
    plot(cars, pch = 19)

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)