R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports that use R plots and data analysis. It combines the core syntax of markdown (an easy-to-write plain text format) with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).

Requirements:

You need to have R and RStudio installed before installing RMarkdown.

How to install?

Type the following command in your RStudio to install RMarkdown library. To activate RMarkdown you’ll need to install “knitr” R package.

install.packages(“rmarkdown”)
install.packages(“knitr”)

To create a new R Markdown file, go to File | New | and select R Markdown. A new file is create with a default template to get you oriented:
(Or)

open R markdown

Type in the title for your markdown file as shown in the picture below:

create a title

The new markdown file comes with a default template which can be reused/removed.

defaultpage for R markdown

To embed the code in R markdown:

```{r, echo= TRUE/FALSE}  #Start code
Write code here
``` #End of code

Here is an example using one of datasets in R.

head(mtcars)

##                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
summary(mtcars)
##       mpg             cyl             disp             hp       
##  Min.   :10.40   Min.   :4.000   Min.   : 71.1   Min.   : 52.0  
##  1st Qu.:15.43   1st Qu.:4.000   1st Qu.:120.8   1st Qu.: 96.5  
##  Median :19.20   Median :6.000   Median :196.3   Median :123.0  
##  Mean   :20.09   Mean   :6.188   Mean   :230.7   Mean   :146.7  
##  3rd Qu.:22.80   3rd Qu.:8.000   3rd Qu.:326.0   3rd Qu.:180.0  
##  Max.   :33.90   Max.   :8.000   Max.   :472.0   Max.   :335.0  
##       drat             wt             qsec             vs        
##  Min.   :2.760   Min.   :1.513   Min.   :14.50   Min.   :0.0000  
##  1st Qu.:3.080   1st Qu.:2.581   1st Qu.:16.89   1st Qu.:0.0000  
##  Median :3.695   Median :3.325   Median :17.71   Median :0.0000  
##  Mean   :3.597   Mean   :3.217   Mean   :17.85   Mean   :0.4375  
##  3rd Qu.:3.920   3rd Qu.:3.610   3rd Qu.:18.90   3rd Qu.:1.0000  
##  Max.   :4.930   Max.   :5.424   Max.   :22.90   Max.   :1.0000  
##        am              gear            carb      
##  Min.   :0.0000   Min.   :3.000   Min.   :1.000  
##  1st Qu.:0.0000   1st Qu.:3.000   1st Qu.:2.000  
##  Median :0.0000   Median :4.000   Median :2.000  
##  Mean   :0.4062   Mean   :3.688   Mean   :2.812  
##  3rd Qu.:1.0000   3rd Qu.:4.000   3rd Qu.:4.000  
##  Max.   :1.0000   Max.   :5.000   Max.   :8.000

You can also embed plots, for example:

plot(x=mtcars$mpg,y=mtcars$wt)

image of an R plot

Note that the echo = FALSE parameter can be added to the code chunk to prevent printing of the R code that generated the plot.

You could click on Knit HTML to see the output it gives.

To Knit PDF, you’ll have to download the MiKTeX package separately by going to the following site:

Windows: MiKTeX (Complete)

(NOTE: Be sure to download the Complete rather than Basic installation)

Mac OS X: TexLive 2013 (Full)

(NOTE: Download with Safari rather than Chrome _strongly_ recommended)

After downloading , run the .exe file to install the COMPLETE version of MiKTeX .

You should now be able to knit the output in a PDF format.

For more on Rmarkdown, please use the following links for reference:

  1. Markdown Basics
  2. Cheat Sheet [PDF]
  3. Reference Guide [PDF]
  4. Interactive Documents

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