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Getting Start With R

The best way to learn R is by doing. In case you are just getting started with R, this free introduction to R tutorial by DataCamp is a great resource as well the successor Intermediate R programming (subscription required). Both courses teach you R programming and data science interactively, at your own pace, in the comfort of your browser. You get immediate feedback during exercises with helpful hints along the way so you don’t get stuck.

Another free online interactive learning tutorial for R is available by O’reilly’s code school website called try R. An offline interactive learning resource isswirl, an R package that makes if fun and easy to become an R programmer. You can take a swirl course by (i) installing the package in R, and (ii) selecting a course from the course library. If you want to start right away without needing to install anything you can also choose for the online version of Swirl.

There are also some very good MOOC’s available on edX and Coursera that teach you the basics of R programming. On edX you can find Introduction to R Programming by Microsoft, an 8 hour course that focuses on the fundamentals and basic syntax of R. At Coursera there is the very popular R Programming course by Johns Hopkins. Both are highly recommended!

If you instead prefer to learn R via a written tutorial or book there is plenty of choice. There is the introduction to R manual by CRAN, as well as some very accessible books like Jared Lander’s R for Everyone or R in Action by Robert Kabacoff.

Setting up your machine

You can download a copy of R from the Comprehensive R Archive Network (CRAN). There are binaries available for Linux, Mac and Windows.

Once R is installed you can choose to either work with the basic R console, or with an integrated development environment (IDE). RStudio is by far the most popular IDE for R and supports debugging, workspace management, plotting and much more (make sure to check out the RStudio shortcuts).

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Next to RStudio you also have Architect, and Eclipse-based IDE for R. If you prefer to work with a graphical user interface you can have a look at R-commander  (aka as Rcmdr), or Deducer.

R packages

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R packages are the fuel that drive the growth and popularity of R. R packages are bundles of code, data, documentation, and tests that are easy to share with others. Before you can use a package, you will first have to install it. Some packages, like the base package, are automatically installed when you install R. Other packages, like for example the ggplot2 package, won’t come with the bundled R installation but need to be installed.

Many (but not all) R packages are organized and available from CRAN, a network of servers around the world that store identical, up-to-date, versions of code and documentation for R. You can easily install these package from inside R, using the install.packages function. CRAN also maintains a set of Task Views that identify all the packages associated with a particular task such as for example TimeSeries.

Next to CRAN you also have bioconductor which has packages for the analysis of high-throughput genomic data, as well as for example the github andbitbucket repositories of R package developers. You can easily install packages from these repositories using the devtools package.

Finding a package can be hard, but luckily you can easily search packages from CRAN, github and bioconductor usingRdocumentation, inside-R, or you can have a look at this quick list of useful R packages.

To end, once you start working with R, you’ll quickly find out that R package dependencies can cause a lot of headaches. Once you get confronted with that issue, make sure to check out packrat (see video tutorial) or checkpoint. When you’d need to update R, if you are using Windows, you can use the updateR() function from theinstallr package.

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