Modern R Programming Cookbook: Recipes to simplify your statistical applications

To start this recipe, you will need to know your version of the Windows operating system, for example, whether it is Windows 7, 8, or 10. Also, you need to know specific architecture, such as 32-bit or 64-bit. Once you know the particulars of the operating system, you are ready to install base R by following the steps in the next section. Another thing that you need to check is whether R is already installed on your computer or not. You can easily check by inspecting the Start menu or task bar or desktop icon. Now, let's assume that you did not install R previously in your computer and this is the first time you are going to do so.

Once you get detailed information about your operating system, you will need to download the executable file for the Windows operating system. To find the latest version of R, you can visit the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/. On this web page, you will get to know the latest release of R and other related information.

To download the latest release of R for Windows, perform the following steps:

Once you have downloaded the executable file, you are ready to install it on your computer. Perform the following steps and choose the options accordingly. The screenshots are for your convenience only:

Once you follow the steps described in the How to do it… section, the R software will be installed, and it's ready to use. You can open R using either the desktop icon or quick launch icon, or from the Start menu.

However, to do some advanced-level work in R or if you want to open the R console from the Windows Command Prompt, you need to do some configuration that is specific to the operating system. In this subsection, you will see how the configuration works.

If you want to access the R terminal from the Windows Command Prompt, then you must open the Windows Command Prompt, and then type R and press Enter. However, without correctly configuring R, you won't be able to open the R terminal in this way. The following are the steps to configure R:

Once you have performed the preceding steps, it is the time to check whether you have correctly configured environment variables by performing the following steps:

If you want to customize the R console, its display font, font size, and others, you can edit the preferences from the menu. For example, navigate to Edit | GUI preference…. You will see the following screen. You are now able to change anything you want to customize your R console and other things:

In this recipe, you have gone through the steps based on the Windows operating system. If you want to install and configure R for Linux, see the next recipe Installing and configuring base R in Linux.

To install R in the Linux operating system, first, you need to know the version of Linux you are using. To know the version of Linux installed on your computer, there are many options. One of the options is the following command:

lsb_release -a

This command will give the release information as shown in the following screenshot:

In this recipe, you will see the example from the Ubuntu 14.04 release.

Once you have the version number, you simply need to install base R onto your computer. The step-by-step procedure is as follows:

        deb <cran mirror address>/bin/linux/ubuntu trusty/

      sudo apt-get update
      sudo apt-get install r-base

      sudo apt-get install r-base-dev

In this recipe, you have installed base R into Ubuntu 14.04 release. If your operating system has another release of Linux, then visit https://cran.r-project.org/, select Download R for Linux, and follow the steps outlined there.

To understand how to install an IDE into either Windows or Linux, follow the next recipe.

To install an IDE, the first step is to install base R; that is, you need to make sure R has been installed prior to installing RStudio IDE. RStudio is an open source and enterprise-ready professional software for R. Now, let's take a look at the following few steps to download and install RStudio IDE:

The following steps will help you go through the installation process:

Once you run the executable file of RStudio, it then checks whether there is any base R installed in the computer. If you do not already have R installed, then you will be given a message stating that base R is required to install RStudio. Once you have made sure that base R is already installed, it will install the IDE without any errors by following the steps mentioned in the How to do it… section.

The following screenshot is the initial user interface of RStudio where you will see four major components:

Let's take a look at the following four major components shown in the preceding screenshot:

There is another similar IDE available, R tools for Visual Studio. This is another IDE developed and released by Microsoft. You will come into this recipe in this chapter.

To install RStudio IDE, the prior requirement is to install base R. Let's assume that base R is already installed on the computer. Now, visit the following web page and download the appropriate installer from the available list at https://www.rstudio.com/products/rstudio/ and store it in the home directory for convenience. Depending on the version of Linux, the executable file comes with the various formats. In this recipe, you will download the .deb file and store it in the home directory. Also, you can directly install it from the internet using the wget command with the appropriate link to the file such as https://download1.rstudio.org/rstudio-1.0.136-amd64.deb.

Once you have downloaded the appropriate executable file, you are ready to install it. Since, you have downloaded the .deb file, you will require gdebi-core to execute that file. Here are the steps to install gdebi-core and then install RStudio IDE:

      sudo apt-get install gdebi-core

      wget https://download1.rstudio.org/rstudio-1.0.136-amd64.deb

The preceding command would generate the following output:

      sudo gdebi rstudio-1.0.136-amd64.deb

The preceding command will generate the following output:

First, the sudo apt-get install gdebi-core command helps you download and install the gdebi-core package into the Linux system. By using the wget command, you are actually downloading the necessary file to install RStudio from the RStudio website. After that when you enter the sudo gdebi rstudio-1.0.136-amd64.deb command, it installs the software for you, and after completing this step, you are ready to use it.

To know more about RStudio, you can visit the RStudio website for more documentation, but this recipe covered the most basic steps to install the software.

To install RTVS, your computer needs to fulfill some of the following prerequisites:

Let's take a look at the following steps:

Once the installation is completed, the user interface is similar to RStudio. Here is the screenshot of RTVS:

Here are the relevant links for more information about RTVS. It is suggested that you take a look at them for updated information:

Suppose you are interested in visualizing your data using the ggplot2 library, but when you call the library using the library(ggplot2) code, you end up getting an error saying that ggplot2 is not found. Now, you need to install ggplot2. In this recipe, you will install the following libraries from the sources mentioned:

Under the default utils library, there is a function called install.packages() to install a package from within the R console. You can use the command install.packages(). This command will prompt you to select the appropriate server CRAN.

      install.packages("ggplot2")

      install.packages("ggplot2")
      --- Please select a CRAN mirror for use in this session ---

    library(devtools)
    install_github("hadley/dplyr")

    source(https://bioconductor.org/biocLite.R)
    biocLite("GenomicFeatures")

In any of the commands to install a library, either install.packages(), install_github(), or biocLite(), first, it connects with the mirror server where the source code / binary-released version of the specified library is located. Then, it checks whether the dependent libraries are installed onto the computer or not. If the required dependent library is absent, then it will download and install those required libraries before installing the one you specified through the command. The command will also search for the location where the installed library will be stored. You can explicitly specify the location or you can use the default. The recommended approach is to specify a location and install all customized libraries into that folder.

To specify the installation location, you can use the lib= option within the function. Make sure you have created the folder that you are going to use as the destination folder. Here is an example:

    install.packages("ggplot2", lib="c:/rPackages")

Using devtools, you can install from either CRAN or from GitHub or even from the BioC repository. There are specific functions available within the devtools library as follows:

The user might need a specific version of a library to do a certain task, and that version could be an older one. To install the specific version of the library, see the next recipe that talks about it.

To install a specific version of an R library, there is another facility available. The necessary functions are bound into the versions library to do this job. You need to install versions before using the function within it. To get ready, you have to run the following command:

    install.packages("versions")

Take a look at the following steps:

        library(versions)
        installed.versions("ggplot2")

The preceding command will show the following output on the console screen:

        > installed.versions("ggplot2")
        Checking package in 'C:/rPackages'
        (as 'lib' is unspecified)
        [1] "2.2.0"
        > 

      install.versions("ggplot2", versions = "2.2.0")

Whenever you call the installed.versions() function, it looks at the DESCRIPTION file of that library and extracts the version number and displays it on the console.

Alternatively, whenever you call install.versions() to install the specified version of a library, it checks the date of that version and runs the install.dates() function internally to download the appropriate version onto the computer.