MaraimElbadri · August 29, 2015 14:13 · Dec 20, 2012 · May 17, 2012
diff --git a/example-r-markdown.rmd b/example-r-markdown.rmd
@@ -33,7 +33,7 @@ To run the basic working example that produced this blog post:
 
 
 ## Prepare for analyses
-```{r setup}
+```{r }
 set.seed(1234)
 library(ggplot2)
 library(lattice)
@@ -51,12 +51,13 @@ Pressing tab when inside the braces will bring up code chunk options.
 
 The following R code chunk labelled `basicconsole` is as follows:
 
-    ```{r basicconsole}
+    ```{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}
@@ -72,7 +73,7 @@ Images generated by `knitr` are saved in a figures folder. However, they also ap
 ### Simple plot
 Here is a basic plot using base graphics:
 
-    ```{r simpleplot}
+    ```{r }
     plot(x)
     ```
 
@@ -86,7 +87,7 @@ 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 multipleplots}
+    ```{r }
     boxplot(1:10~rep(1:2,5))
     plot(x, y)
     ```
@@ -117,7 +118,7 @@ Note that unlike traditional Sweave, there is no need to print lattice plots dir
 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 dotpointprint, results='asis', echo=FALSE}
+    ```{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"))
     ```
@@ -128,7 +129,7 @@ cat(paste("* The value of y[", 1:3, "] is ", y[1:3], sep="", collapse="\n"))
 ```
 
 ### Create Markdown table code from R
-    ```{r createtable, results='asis', echo=FALSE}
+    ```{r , results='asis', echo=FALSE}
     cat("x | y", "--- | ---", sep="\n")
     cat(apply(df, 1, function(X) paste(X, collapse=" | ")), sep = "\n")
     ```
@@ -155,7 +156,7 @@ head(df)
 ### Control figure size
 The following is an example of a smaller figure using `fig.width` and `fig.height` options.
 
-    ```{r smallplot, fig.width=3, fig.height=3}
+    ```{r , fig.width=3, fig.height=3}
     plot(x)
     ```
 
@@ -171,7 +172,7 @@ 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 longanalysis, cache=TRUE}
+    ```{r , cache=TRUE}
     for (i in 1:5000) {
         lm((i+1)~i)
     }

diff --git a/example-r-markdown.rmd b/example-r-markdown.rmd
@@ -0,0 +1,298 @@
+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.
+
+<!-- more -->
+
+
+## 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 setup}
+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 basicconsole}
+    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 simpleplot}
+    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 multipleplots}
+    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 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"))
+    ```
+
+```{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 createtable, 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 smallplot, 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 longanalysis, 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 `<br/>`'s
+**Question:** I asked on the Rstudio discussion site:
+[Why does Markdown to HTML insert `<br/>` 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` .
No results found