2 Basic Introduction to R

This tutorial offers an introduction to the basics of R. R is a general platform for performing statistical and programming tasks. R offers a wide variety of network functionality, making it possible to do everything from simple network construction and graphing to sophisticated statistical models, all under one platform. Through a series of R tutorials, we will offer R code and examples for each major topic covered in the main text. In this tutorial, we offer a very brief overview of R and R packages, just enough to make sure that everyone can run and follow the tutorials that follow.

Note that we do not offer a dedicated tutorial on R programming. All tutorials (except this one) are motivated by a problem related to network analysis. It will be useful to have some basic familiarity with R and its syntax (or be willing to learn as we go along!) but this is not strictly necessary. Each tutorial includes both R code and results, making it easier for readers to follow along, even without detailed knowledge of R. Readers interested in learning R in more depth should consider one of the many introductory R textbooks.

2.1 Preliminaries

The first step is to gain access to R, which is free and available on the R website: http://cran.r-project.org/. Simply go to the R website, select the appropriate location and operating system, and follow the instructions to download the base distribution of R. RStudio offers a user friendly environment to run R and is recommended.

Once R is opened we can begin to run commands. R commands can be run directly from the console, from the R script editor or from a text editor separate from R. For example, the following does a bit of simple math:

5 + 5

## [1] 10

The two ## are printed for convenience, and indicate that everything that follows is a result shown in the R console. As another example, here we sum up a series of numbers using a sum() function.

sum(5, 5, 4)

## [1] 14

R offers detailed help files for each function. To access help, type ?name_of_function. For example, for help on the sum() function, run:

?sum

All lines proceeded by a # are comments and will not run. For example:

# This is a comment. R will not recognize this as a command.

2.2 Packages

The functionality of R is extended by loading packages that researchers have contributed to the R community. Packages are sets of useful functions that accomplish a set of tasks, such as graphing a network. In this book we will primarily make use of: igraph (Csardi and Nepusz 2006), sna (Butts 2023b), network (Butts 2015), networkDynamic (Butts et al. 2023), ndtv (Bender-deMoll 2022), egor (Krenz et al. 2023), ergm (Handcock et al. 2023), ergm.ego (Krivitsky 2023), ergm.count (Krivitsky 2022), tergm (Krivitsky and Handcock 2023), relevent (Butts 2023a), EpiModel (Jenness, Goodreau, and Morris 2018), netdiffuseR (Vega Yon and Valente 2022), and RSiena (Ripley et al. 2023). igraph, network and sna perform similar tasks related to network construction, graphing and network measurement. sna and network work in tandem while igraph is a fairly stand alone package. Note that igraph and sna/network construct networks in very different manners and there is little overlap in syntax. We will present the code for performing different calculations and tasks in both igraph and sna/network, where appropriate. The other packages, like ergm, tergm, and RSiena, estimate more advanced statistical models and we will cover them later in the book. Each package of interest must be installed and loaded before it can be used. The packages will not be immediately available when R is opened. A package only has to be installed once on a computer, but the package will have to be loaded every time R is restarted. To install all of the packages used in this book, run the following:

source("https://github.com/JeffreyAlanSmith/Integrated_Network_Science/raw/master/R/setup.R")

It is also possible to install each package individually as we need them. For example, to install igraph, sna, and network, we would do:

install.packages("igraph")
install.packages("sna")
install.packages("network")

Now that we have our packages successfully installed, we can go ahead and load them into R. Here we will load the network package as an example. We can use of all the functions available in that package once it is loaded into R. We load packages by using a library() function. The input is the name of the package, not in quotes.

library(network)

We can look up all of the functions within a package by using a help() function. For example, let’s look at the functions available in the network package.

help(package = network)

Note that the package argument is necessary to look up all of the functions. We can also detach a package if we no longer want it loaded. This is sometimes useful if two packages do not play well together. Here we will use a detach() function.

detach(package:network)

For simplicity, we will assume that the reader has restarted R at the beginning of each tutorial. This will ensure that the code will run without any complications. We will now turn to the basics of data management and network construction in R, covered in Chapter 3.