jeromyanglim / example-r-markdown.rmd Created May 17, 2012

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Example of using R Markdown

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 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) using [knitr](http://yihui.name/knitr/) in Rstudio 0.96. This combination of tools provides an exciting improvement in usability for [reproducible analysis](http://stats.stackexchange.com/a/15006/183). Specifically, this post (1) discusses getting started with R Markdown and knitr in Rstudio 0.96; (2) provides a basic example of producing console output and plots using R Markdown; (3) highlights several code chunk options such as caching and controlling how input and output is displayed; (4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and (5) discusses the implications of R Markdown. This post was produced with R Markdown. The source code is available here as a gist. The post may be most useful if the source code and displayed post are viewed side by side. In some instances, I include a copy of the R Markdown in the displayed HTML, but most of the time I assume you are reading the source and post side by side.       ## Getting started To work with R Markdown, if necessary:   * Install [R](http://www.r-project.org/) * Install the lastest version of [RStudio](http://rstudio.org/download/) (at time of posting, this is 0.96) * Install the latest version of the knitr package: install.packages("knitr")   To run the basic working example that produced this blog post:   * Open R Studio, and go to File - New - R Markdown * If necessary install ggplot2 and lattice packages: install.packages("ggplot2"); install.packages("lattice")  * Paste in the contents of this gist (which contains the R Markdown file used to produce this post) and save the file with an .rmd extension * Click Knit HTML         ## Prepare for analyses {r } set.seed(1234) library(ggplot2) library(lattice)      ## Basic console output To insert an R code chunk, you can type it manually or just press Chunks - Insert chunks or use the shortcut key. This will produce the following code chunk:   {r}    Pressing tab when inside the braces will bring up code chunk options.   The following R code chunk labelled basicconsole is as follows:   {r } x <- 1:10 y <- round(rnorm(10, x, 1), 2) df <- data.frame(x, y) df  The code chunk input and output is then displayed as follows:   {r basicconsole} x <- 1:10 y <- round(rnorm(10, x, 1), 2) df <- data.frame(x, y) df    ## Plots Images generated by knitr are saved in a figures folder. However, they also appear to be represented in the HTML output using a [data URI scheme]( http://en.wikipedia.org/wiki/Data_URI_scheme). This means that you can paste the HTML into a blog post or discussion forum and you don't have to worry about finding a place to store the images; they're embedded in the HTML.   ### Simple plot Here is a basic plot using base graphics:   {r } plot(x)    {r simpleplot} plot(x)    Note that unlike traditional Sweave, there is no need to write fig=TRUE.     ### Multiple plots Also, unlike traditional Sweave, you can include multiple plots in one code chunk:   {r } boxplot(1:10~rep(1:2,5)) plot(x, y)    {r multipleplots} boxplot(1:10~rep(1:2,5)) plot(x, y)    ### ggplot2 plot Ggplot2 plots work well:   {r ggplot2ex} qplot(x, y, data=df)    ### lattice plot As do lattice plots:   {r latticeex} xyplot(y~x)    Note that unlike traditional Sweave, there is no need to print lattice plots directly.   ## R Code chunk features ### Create Markdown code from R The following code hides the command input (i.e., echo=FALSE), and outputs the content directly as code (i.e., results=asis, which is similar to results=tex in Sweave).     {r , results='asis', echo=FALSE} cat("Here are some dot points\n\n") cat(paste("* The value of y[", 1:3, "] is ", y[1:3], sep="", collapse="\n"))    {r dotpointprint, results='asis', echo=FALSE} cat("Here are some dot points\n\n") cat(paste("* The value of y[", 1:3, "] is ", y[1:3], sep="", collapse="\n"))    ### Create Markdown table code from R {r , results='asis', echo=FALSE} cat("x | y", "--- | ---", sep="\n") cat(apply(df, 1, function(X) paste(X, collapse=" | ")), sep = "\n")    {r createtable, results='asis', echo=FALSE} cat("x | y", "--- | ---", sep="\n") cat(apply(df, 1, function(X) paste(X, collapse=" | ")), sep = "\n")    ### Control output display The folllowing code supresses display of R input commands (i.e., echo=FALSE) and removes any preceding text from console output (comment=""; the default is comment="##").   {r echo=FALSE, comment="", echo=FALSE} head(df)    {r echo=FALSE, comment="", echo=FALSE} head(df)        ### Control figure size The following is an example of a smaller figure using fig.width and fig.height options.   {r , fig.width=3, fig.height=3} plot(x)    {r smallplot, fig.width=3, fig.height=3} plot(x)    ### Cache analysis Caching analyses is straightforward. Here's example code. On the first run on my computer, this took about 10 seconds. On subsequent runs, this code was not run.   If you want to rerun cached code chunks, just [delete the contents of the cache folder](http://stackoverflow.com/a/10629121/180892)   {r , cache=TRUE} for (i in 1:5000) { lm((i+1)~i) }    ## Basic markdown functionality For those not familiar with standard [Markdown](http://daringfireball.net/projects/markdown/), the following may be useful. See the source code for how to produce such points. However, RStudio does include a Markdown quick reference button that adequatly covers this material.   ### Dot Points Simple dot points:   * Point 1 * Point 2 * Point 3   and numeric dot points:   1. Number 1 2. Number 2 3. Number 3   and nested dot points:   * A * A.1 * A.2 * B * B.1 * B.2     ### Equations Equations are included by using LaTeX notation and including them either between single dollar signs (inline equations) or double dollar signs (displayed equations). If you hang around the Q&A site [CrossValidated](http://stats.stackexchange.com) you'll be familiar with this idea.   There are inline equations such as $y_i = \alpha + \beta x_i + e_i$.   And displayed formulas:   $$\frac{1}{1+\exp(-x)}$$     knitr provides self-contained HTML code that calls a Mathjax script to display formulas. However, in order to include the script in my blog posts I [took the script](https://gist.github.com/2716053) and incorporated it into my blogger template. If you are viewing this post through syndication or an RSS reader, this may not work. You may need to view this post on my website.   ### Tables Tables can be included using the following notation   A | B | C --- | --- | --- 1 | Male | Blue 2 | Female | Pink   ### Hyperlinks   * If you like this post, you may wish to subscribe to [my RSS feed](http://feeds.feedburner.com/jeromyanglim).   ### Images Here's an example image:   ![image from redmond barry building unimelb](http://i.imgur.com/RVNmr.jpg)     ### Code Here is Markdown R code chunk displayed as code:   {r} x <- 1:10 x      And then there's inline code such as x <- 1:10.   ### Quote Let's quote some stuff:   > To be, or not to be, that is the question: > Whether 'tis nobler in the mind to suffer > The slings and arrows of outrageous fortune,     ## Conclusion   * R Markdown is awesome. * The ratio of markup to content is excellent. * For exploratory analyses, blog posts, and the like R Markdown will be a powerful productivity booster. * For journal articles, LaTeX will presumably still be required. * The RStudio team have made the whole process very user friendly. * RStudio provides useful shortcut keys for compiling to HTML, and running code chunks. These shortcut keys are presented in a clear way. * The incorporated extensions to Markdown, particularly formula and table support, are particularly useful. * Jump-to-chunk feature facilitates navigation. It helps if your code chunks have informative names. * Code completion on R code chunk options is really helpful. See also [chunk options documentation on the knitr website](http://yihui.name/knitr/options). * Other recent posts on R markdown include those by : * [Christopher Gandrud](http://christophergandrud.blogspot.com.au/2012/05/dynamic-content-with-rstudio-markdown.html) * [Markcus Gesmann](http://lamages.blogspot.com.au/2012/05/interactive-reports-in-r-with-knitr-and.html) * [Rstudio on R Markdown](http://rstudio.org/docs/authoring/using_markdown) * [Yihui Xie](http://yihui.name/knitr/): I really want to thank him for developing knitr. He has also posted [this example of R Markdown](https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rmd).     ## Questions The following are a few questions I encountered along the way that might interest others. ### Annoying
's **Question:** I asked on the Rstudio discussion site: [Why does Markdown to HTML insert
 on new lines?](http://support.rstudio.org/help/discussions/problems/2329-why-does-r-markdown-to-html-insert-br-when-there-is-a-new-line-of-text)   **Answer:** I just do a find and delete on this text for now.   ### Temporarily disable caching **Question:** I asked on StackOverflow about [How to set cache=FALSE for a knitr markdown document and override code chunk settings?](http://stackoverflow.com/q/10628665/180892)   **Answer:** Delete the cache folder. But there are other possible workflows.   ### Equivalent of Sexpr **Question:** I asked on Stack Overvlow about [whether there an R Markdown equivalent to Sexpr in Sweave?](http://stackoverflow.com/q/10629416/180892).   **Answer:** Include the code between brackets of "backick r space" and "backtick". E.g., in the source code I have calculated 2 + 2 = r 2 + 2 . 

Thank you! It's very useful.

commented

Line 298 has a type, missing "t" in first "backick"

But why (for all plots) is there no image for all plot chunks which do NOT start at the beginning of the line? although R DOES execute the R-code + renders the images ...

Very useful, thank you

Incredibly useful! You should ask Rmarkdown to post this on their page! A horrible lack of examples...