C An R primer

What follows is a highly condensed guide to the basic features of the R programming language and some of its most useful general purpose packages. Use this primer as a quick introduction to the language, or as a reference when reading the rest of the book. You should also read at a minimum the chapters on “Data Structures” and “Subsetting” from Advanced R, since understanding those concepts are crucial to working effectively in R.24

C.1 Values

A value is the most basic piece of data. There are several kinds of values.

Doubles are positive or negative numbers that can have a decimal point. Integers are positive or negative whole numbers. Even if a value does not have a decimal point, it is a double unless it is suffixed with L.

10.42
#> [1] 10.4
-8.67
#> [1] -8.67
10L
#> [1] 10
-8L
#> [1] -8

Text is stored in character vectors (usually called strings in other programming langauges). Characters are marked by surrounding single or double quotation marks.

"Everything is awesome"
#> [1] "Everything is awesome"
"1" # not the same as 1
#> [1] "1"
identical(1, "1")
#> [1] FALSE

Logical values, or booleans, can be either true or false.

TRUE
#> [1] TRUE
FALSE
#> [1] FALSE

Factors are a special kind of text value, where the values must be part of a predefined set of options. Factors are usually used for categorical data.

factor(c("correct", "correct", "incorrect"), levels = c("correct", "incorrect"))
#> [1] correct   correct   incorrect
#> Levels: correct incorrect

Each of these kinds of values has a corresponding missing value, NA. These are used for missing or unrecorded data.

NA
#> [1] NA
NA_character_
#> [1] NA
NA_integer_
#> [1] NA
NA_real_
#> [1] NA

C.2 Variables and assignment

Values can be stored in variables. A value is placed into a variable using the assignment operator, <-.25

x <- 1
x
#> [1] 1
y <- -3.14
y
#> [1] -3.14
result <- "The results are positive"
result
#> [1] "The results are positive"

C.3 Comparison

Values can be compared to one another. The result is always a vector of TRUE and FALSE values indicating whether the condition was met or not.

x <- 1:6 # a vector of numbers 1 to 6
x > 3
#> [1] FALSE FALSE FALSE  TRUE  TRUE  TRUE
x >= 3
#> [1] FALSE FALSE  TRUE  TRUE  TRUE  TRUE
x < 3
#> [1]  TRUE  TRUE FALSE FALSE FALSE FALSE
x == 3
#> [1] FALSE FALSE  TRUE FALSE FALSE FALSE
x != 3
#> [1]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE

Comparison also works with character vectors.

"Is this the same?" == "as this?"
#> [1] FALSE
"Is this the same?" == "Is this the same?"
#> [1] TRUE

Notice that equality is tested with the == operater, not with =.

Often it is helpful to test whether elements of one vector are contained in another vector with the %in% function. Notice that the resulting vector is the same length as the vector on the left-hand side.

c(1, 4, 2, 8, 0, 10) %in% c(1, 2, 3)
#> [1]  TRUE FALSE  TRUE FALSE FALSE FALSE

# Are these states a part of New England?
states <- c("VA", "CT", "MA", "SD", "GA", "AL", "ND", "SD", "VT") 
new_england <-  c("MA", "ME", "CT", "RI", "NH", "VT")
states %in% new_england
#> [1] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE

C.4 Functions

R is a functional programming language, so knowing how to apply functions to problems, and to write them yourself, is essential to doing your work. Functions are the verbs of R programming.

C.4.1 Using functions

Functions can be called on many different kinds of R vectors and objects. A function takes an input and produces an output. In this case we will use sum() to add up a vector of numbers.

x <- c(1, 5, 2, 4, 2, 5)
sum(x)
#> [1] 19

Notice that calls to functions are always followed by parentheses, containing the function arguments. In the example above, x was the only argument to the function; it was the means by which we passed data into the function. Functions can often take many arguments that specify options to function. For instance, if we have a vector of numbers that contains an missing value (NA), then the function sum() will return NA, because NA has no value. But by using the na.rm argument to sum(), we can instruct it to ignore NA values.

y <- c(1, NA, 2, 4, 2, 5)
sum(y)
#> [1] NA
sum(y, na.rm = TRUE)
#> [1] 14

R has many built-in functions. For instance, the sort() function can sort many different kinds of values.

x
#> [1] 1 5 2 4 2 5
sort(x)
#> [1] 1 2 2 4 5 5
sort(x, decreasing = TRUE)
#> [1] 5 5 4 2 2 1

states
#> [1] "VA" "CT" "MA" "SD" "GA" "AL" "ND" "SD" "VT"
sort(states)
#> [1] "AL" "CT" "GA" "MA" "ND" "SD" "SD" "VA" "VT"
sort(states, decreasing = TRUE)
#> [1] "VT" "VA" "SD" "SD" "ND" "MA" "GA" "CT" "AL"

It is important to note that most functions you use to work with data are pure functions. The results of pure functions depend only on their inputs: the same input will always produce the same output. And in general, R functions do not modify their inputs directly, but instead return a copy they modify their inputs. Notice that in this example the original states vector remains unsorted, even after it has been passed through the sort() function, and a new copy of the data, now sorted, is stored in the variable states_sorted. This makes it easier to reason about what a function will do.

states
#> [1] "VA" "CT" "MA" "SD" "GA" "AL" "ND" "SD" "VT"
states_sorted <- sort(states)

states
#> [1] "VA" "CT" "MA" "SD" "GA" "AL" "ND" "SD" "VT"
states_sorted
#> [1] "AL" "CT" "GA" "MA" "ND" "SD" "SD" "VA" "VT"

C.4.2 Writing your own functions

You will often have to write your own functions. You can think of a function as encapsulating some action that you take on your data. Consider the following few sentences, each of which includes a year. How can we turn the year in each of these sentences into a number?

dates <- c("The Louisiana Purchase happened in 1803.",
           "The Mexican-American war began in 1846.",
           "The Compromise of 1850 was drafted by Henry Clay.")

We can write a function that does this work for us. The function will be named extract_year. It will have a single argument, sent, which will be a sentence containing a year. The body of the function, between { and }, does the work of finding the 4-character string of digits then turning that into an integer. The last value in the function will be returned as its output.

extract_year <- function(sent) {
  require(stringr) # Make sure that the stringr package is loaded
  year_char <- str_extract(sent, "\\d{4}") # Pull out the 4 digit year
  year_int <- as.integer(year_char) # Turn the year (a character) into an integer
  year_int # This is the value that will be returned
}

Now we can call the function on our data and get the desired result:

extract_year(dates)
#> Loading required package: stringr
#> [1] 1803 1846 1850

C.5 Data structures and subsetting

If functions are the verbs of R programming, data are the nouns. And data can be stored in many different kinds of data structures, including vectors, lists, data frames, and matrices. These kinds of data structures share a set of operators for subsetting them, that is, for pulling out pieces of the data.

C.5.1 Vectors

The most basic data structure is a vector. Consider this vector of 10 names.

people <- c("Adam", "Betsy", "Charles", "Dana", "Edward", "Felicity", "George",
            "Hannah", "Ian", "Julia")

In R, elements of a vector are numbered, starting from 1 to the length of the vector. (Most programming languages have a 0-based indexing.) We can get individual elements of the vector using a numeric vector and the [ subsetting operator. For example, we can get the fifth element, or the first, eighth, tenth, and sixth elements together.

people[5]
#> [1] "Edward"
people[c(1, 8, 10, 6)]
#> [1] "Adam"     "Hannah"   "Julia"    "Felicity"

We can also subset a vector by using a logical vector. When we use a logical vector, we get back the elements that correspond to the TRUE values. It is usually a good idea to use a logical vector which has same length as the original vector. In this example, we use a function to test whether the names in our people vector have a lowercase e in them. Then we use that logical vector and the [ subset operator to return only the names that have that letter in them.

library(stringr)
# The result of this function call is a logical vector
str_detect(people, "e") 
#>  [1] FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE

people[str_detect(people, "e")]
#> [1] "Betsy"    "Charles"  "Felicity" "George"

It is possible for a vector to have names, which we can also use for subsetting. Suppose we have a set of numbers from 1 to 10 that correspond to a rank for each person. At first our vector does not have any names.

rank <- c(9, 8, 4, 10, 7, 3, 2, 5, 1, 6)
names(rank)
#> NULL

But we can use our people vector to give it names.

names(rank) <- people

Now we can get the fifth rank and see the corresponding name.

rank[5]
#> Edward 
#>      7

We can use a character vector to subset rank to using those names.

rank[c("Adam", "Hannah")]
#>   Adam Hannah 
#>      9      5

And we can sort rank and see that the names are also sorted, or get only the elements of rank which are above a certain value (another example of logical subsetting).

sort(rank)
#>      Ian   George Felicity  Charles   Hannah    Julia   Edward    Betsy 
#>        1        2        3        4        5        6        7        8 
#>     Adam     Dana 
#>        9       10
rank[rank <= 3]
#> Felicity   George      Ian 
#>        3        2        1

C.5.2 Lists

Lists are conceptually an extension of vectors. They are a vector which can contain other vectors, each of which can contain a different kind of information. Lists can thus have an arbitrary structure. Let’s create a list that models a historical event, recording certain key pieces of information. Notice that some of the information is numeric and some is text; some of the fields have a single entry, and some are a vector of values.

event <- list(
  name = "Louisiana Purchase",
  date = 1803,
  price = 15000000,
  nations = c("France", "United States"),
  negotiators = c("Napoleon", "Thomas Jefferson")
)

Because lists can have an arbitrary structure, you can use the str() function to see what a list contains. (This function works on any R object.) Notice that this is a list that has five elements, and that each of those elements has a name (date, price, and so on).

str(event)
#> List of 5
#>  $ name       : chr "Louisiana Purchase"
#>  $ date       : num 1803
#>  $ price      : num 1.5e+07
#>  $ nations    : chr [1:2] "France" "United States"
#>  $ negotiators: chr [1:2] "Napoleon" "Thomas Jefferson"

Just like a regular vector, you can subset a list with a numerical index.

event[2]
#> $date
#> [1] 1803

But notice that the resulting value is a list containing the date. We have selected an element of the list, but that element still comes wrapped in the list. We can get what is contained inside each element by using the double bracket subset operator, [[. Notice that the value returned is now the number that corresponds to the date.

event[[2]]
#> [1] 1803

Just like with regular vectors, you can also subset a list by its names if it has them.

event["date"]
#> $date
#> [1] 1803

The single bracket subset operator [ gives us a list, but we can get a named element itself with the double bracked subset operator [[.

event[["date"]]
#> [1] 1803

There is a special syntax for accessing a named element of a list using the $ operator. This is the equivalent of event[["date"]].

event$date
#> [1] 1803

C.5.3 Data frames

A data frame is like a spreadsheet, since it is a table with columns and rows. It is the data structure that we will use most in this book, though we will mostly use the dplyr package instead of base R to manipulate tabular data. Technically a data frame is a list where the constituent vectors are all the same length, and so you can use the same subset operators on data frames. Even if you mostly use dplyr, it is still important to understand how data frames work in base R.26

We can load a data frame of historical state populations from the historydata package. In an interactive session, you can get a nice view of the data frame by running View(us_state_populations).

library(historydata)
library(tidyverse)
us_state_populations
#> # A tibble: 983 × 4
#>   GISJOIN  year         state population
#>     <chr> <int>         <chr>      <int>
#> 1    G090  1790   Connecticut     237655
#> 2    G100  1790      Delaware      59096
#> 3    G130  1790       Georgia      82548
#> 4    G240  1790      Maryland     319728
#> 5    G250  1790 Massachusetts     475199
#> 6    G330  1790 New Hampshire     141899
#> # ... with 977 more rows

You can get the vector for any column by using the column name with $.

head(us_state_populations$state)
#> [1] "Connecticut"   "Delaware"      "Georgia"       "Maryland"     
#> [5] "Massachusetts" "New Hampshire"

You can also subset a data frame using [. But because data frames are two dimensional, you should specify a subset index for both rows and columns. Leave either one blank to specify all columns or all rows. In the examples below there are extra spaces to make it clear where we are subsetting by rows and where by columns.

us_state_populations[5:8,    ]    # rows 5-8, all columns
#> # A tibble: 4 × 4
#>   GISJOIN  year         state population
#>     <chr> <int>         <chr>      <int>
#> 1    G250  1790 Massachusetts     475199
#> 2    G330  1790 New Hampshire     141899
#> 3    G340  1790    New Jersey     184139
#> 4    G360  1790      New York     340241
us_state_populations[   , 2:3]    # all rows, columns 2-3
#> # A tibble: 983 × 2
#>    year         state
#>   <int>         <chr>
#> 1  1790   Connecticut
#> 2  1790      Delaware
#> 3  1790       Georgia
#> 4  1790      Maryland
#> 5  1790 Massachusetts
#> 6  1790 New Hampshire
#> # ... with 977 more rows
us_state_populations[5:8, 2:3] # rows 5-8, colums 2-3
#> # A tibble: 4 × 2
#>    year         state
#>   <int>         <chr>
#> 1  1790 Massachusetts
#> 2  1790 New Hampshire
#> 3  1790    New Jersey
#> 4  1790      New York

You can subset a data frame using a logical operator. Here we use a common idiom to find create a logical vector where we check whether each row in the state column is equal to "Massachusetts", and then use that vector to subset the data frame’s rows. (Notice the space after the ,.) The result is that we have filtered the data frame to just the Massachusetts population. This is much less verbose in dplyr, but there are times when you will need to manipulate a data frame in base R.

us_state_populations[us_state_populations$state == "Massachusetts", ]
#> # A tibble: 23 × 4
#>   GISJOIN  year         state population
#>     <chr> <int>         <chr>      <int>
#> 1    G250  1790 Massachusetts     475199
#> 2    G250  1800 Massachusetts     574564
#> 3    G250  1810 Massachusetts     700745
#> 4    G250  1820 Massachusetts     523287
#> 5    G250  1830 Massachusetts     610408
#> 6    G250  1840 Massachusetts     737699
#> # ... with 17 more rows

C.5.4 Matrices

A matrix is a very common data structure in computational history, useful for holding counts of words in documents, similarities between texts, distances between points, and the like. A matrix is a vector where all of the elements are of the same type, but it is arranged in two dimensions. Consider this matrix, which could represent how similar documents are to one another.

m <- matrix(c(NA, NA, NA, NA, NA, 0.31, NA, NA, NA, NA, 0.29, 0.95, NA,
              NA, NA, 0.66, 0.7, 0.18, NA, NA, 0.41, 0.3, 0.49, 0.7, NA),
            nrow = 5, ncol = 5)
rownames(m) <- letters[1:5]
colnames(m) <- letters[1:5]
m
#>    a    b    c    d    e
#> a NA 0.31 0.29 0.66 0.41
#> b NA   NA 0.95 0.70 0.30
#> c NA   NA   NA 0.18 0.49
#> d NA   NA   NA   NA 0.70
#> e NA   NA   NA   NA   NA

Notice that we only need the upper triangle of the matrix because presumably the similarities of two documents are the same in either direction, and the similarity of a document to itself is not a very meaningful question. You can subset a matrix with [ by rows and columns. Here we get the similarity of a to c, and then the similarity of a to every text.

m["a", "c"] 
#> [1] 0.29
m["a", ]
#>    a    b    c    d    e 
#>   NA 0.31 0.29 0.66 0.41

Notice that the [ operator simplifies the results to a one-dimensional vector or single number if possible, rather than giving us a matrix back. This is sometimes undesirable, and we can avoid it by using the drop = FALSE argument to [.

m["a", "c", drop = FALSE]
#>      c
#> a 0.29
m["a", , drop = FALSE]
#>    a    b    c    d    e
#> a NA 0.31 0.29 0.66 0.41

  1. Wickham, Advanced R, chs. 2–3.

  2. I’m calling certain parts of R syntax operators, but technically they are special functions with syntactic sugar.

  3. The tibble package, part of the tidyverse, changes a few things about how data frames function in R. It makes them print in a more friendly way, but it also changes the [ and [[ operators so that they do not use the argument drop = TRUE by default. See that package’s documentation for more detail.