(1) Explanatory Notes. The terms package and library tend to be used interchangeably in R literature. These terms refer to the compiled chunks of downloadable content that developers and users create to increase the functionality of R. These packages are what make R so attractive and so capable. As an example, consider a fictional researcher, Dr. Smarty Pants at the University of Jupiter’s Moon. Dr. Smarty Pants wants to do a new statistical technique, called the Wiz-Magic Decomposition analysis or WMD for short. Unfortunately, because WMD is so new, Dr. Smarty Pants can not find WMD in any of the existing statistical software available. But, Dr. Smarty Pants is an R user. So, no matter who Dr. Smarty Pants happens to be, where he or she happens to be, and no matter what analysis he or she wants to perform; any individual, like Dr. Smarty Pants, can write the code to perform the desired analysis and send it to CRAN as a new package. CRAN will then check it to make sure it works, has proper documentation, and post it so that everyone can then use the newest most advanced techniques, like WMD. You might think this process takes a great deal of time, but it does not. As of this writing, according to CRAN there are 9000 packages available and it is very likely that within a week, new packages will be available. Remember, packages are not just new analysis; many are very specific and may include better ways to do existing functions (e.g. the AMORE package is described as “A MORE flexible neural network package”). Furthermore, packages get updated to increase functionality or ease of use. Keep in mind, all packages and all new versions of R are completely free. So, you’re now likely wondering, how do I get and use these packages? First, open R if it is not already.

(2) To download and install packages, you must have R open and you must have an internet connection. Next, click on ‘Packages’ at the top of the R Console.

Take note of the options here, you will likely use two of them most frequently; ‘Install Package(s)…’ and ‘Update packages…’ The base install of R comes with a few core packages. We are interested in installing new/different packages; so, click on ‘Install Package(s)…’ You will then be prompted to select a CRAN mirror site from which to download packages. I suggest selecting a location close to the physical location of your computer. Once you select a mirror site, you will be presented with an alphabetical list of all the available packages. Before you choose, please take a minute to read the following paragraph.

The first time you install R on your machine, it is recommended you install all the packages used on this site. Fortunately, you do not need to point and click each of these packages to install them. You can use THIS script. If you simply open that script in your browser and copy - paste its contents into your R console and run it, it will install all the package used on this site (and their dependent packages). Depending on your internet connection speed, this operation may take several minutes.

(3) Now choose the Hmisc package; then click ‘OK’. You will notice in the R Console, packages will be downloaded first, in the appropriate location, and then they will be installed—which gives the message “package ‘Hmisc’ successfully unpacked and MD5 sums checked”. You will also notice a message telling you where the temporary file is located which contains the downloaded package(s). You could delete this temp file after all the packages are installed, but it can be useful to take note of it in the unlikely event your internet connection gets interrupted during download. If your connection is interrupted, you can still install the packages that were downloaded successfully by clicking on ‘Packages’ then ‘Install package(s) from local zip files…’.

(4) Updating packages. Now that you have the Hmisc package installed, you need to update. This may seem silly because you just installed it, but remember with a few thousand packages it becomes time consuming to update all of them when a new version of R is released and you may not have the most recent version of a package. So, click on ‘Packages’ and then ‘Update packages…’. If you have not done so already in this session of R (e.g. if you closed R and just re-opened it), you will need to choose a mirror site. You will then be prompted with a list of packages that can be updated. I generally choose all the available packages to make sure I have the most functionally up-to-date software. Once you choose which/all packages, click ‘Ok’ and you will notice a similar series of messages in the console showing the download and install of the updated packages.

 We will be using the Hmisc package/library in the next set of notes on using a package/library; but in future notes/tutorials we will need a variety of package—again, it is highly recommended you download and install all of the packages used on this site.