An R Companion for the Handbook of Biological Statistics

Salvatore S. Mangiafico

About R

R is a free, open source, and cross-platform programming language that is well suited for statistical analyses.  This means you can download R to your Windows, Mac OS, or Linux computer for free.  It also means that, in theory, you can look at the code behind any of the analyses it performs to better understand the process, or to modify the code for your own purposes.


R is being used more and more in educational, academic, and commercial settings.  A few advantages of working with R as a student, teacher, or researcher include:


  • R functions return limited output. This helps prevent students from sorting through a lot of output they may not understand, and in essence requires the user to know what output they’re asking R to produce.
  • Since all functions are open source, the user has access to see how pre-defined functions are written.
  • There are powerful packages written for specific type of analyses.
  • There are lots of free resources available online.
  • It can also be used online without installing software.


For a brief summary of some the advantages of R from the perspective of a graduate student, see https://thetarzan.wordpress.com/2011/07/15/why-use-r-a-grad-students-2-cents/.


It is also worth mentioning a few drawbacks with using R.  New users are likely to find the code difficult to understand.  Also, I think that while there are a plethora of examples for various analyses available online, it may be difficult as a beginner to adapt these examples to her own data.  One goal of this book is to help alleviate these difficulties for beginners.  I have some further thoughts below on avoiding pitfalls in R.