Introduction to R

Creating objects

You can get output from R simply by typing in math in the console

3 + 5
12/7

However, to do useful and interesting things, we need to assign values to objects. To create an object, we need to give it a name followed by the assignment operator <-, and the value we want to give it:

weight_kg <- 55

Objects can be given any name such as x, current_temperature, or subject_id. You want your object names to be explicit and not too long. They cannot start with a number (2x is not valid, but x2 is). R is case sensitive (e.g., weight_kg is different from Weight_kg). There are some names that cannot be used because they are the names of fundamental functions in R (e.g., if, else, for, see here for a complete list). In general, even if it’s allowed, it’s best to not use other function names (e.g., c, T, mean, data, df, weights). In doubt check the help to see if the name is already in use. It’s also best to avoid dots (.) within a variable name as in my.dataset. There are many functions in R with dots in their names for historical reasons, but because dots have a special meaning in R (for methods) and other programming languages, it’s best to avoid them. It is also recommended to use nouns for variable names, and verbs for function names. It’s important to be consistent in the styling of your code (where you put spaces, how you name variable, etc.). In R, two popular style guides are Hadley Wickham’s and Google’s.

When assigning a value to an object, R does not print anything. You can force to print the value by using parentheses or by typing the name:

weight_kg <- 55    # doesn't print anything
(weight_kg <- 55)  # but putting parenthesis around the call prints the value of `weight_kg`
weight_kg          # and so does typing the name of the object

Now that R has weight_kg in memory, we can do arithmetic with it. For instance, we may want to convert this weight in pounds (weight in pounds is 2.2 times the weight in kg):

2.2 * weight_kg

We can also change a variable’s value by assigning it a new one:

weight_kg <- 57.5
2.2 * weight_kg

This means that assigning a value to one variable does not change the values of other variables. For example, let’s store the animal’s weight in pounds in a new variable, weight_lb:

weight_lb <- 2.2 * weight_kg

and then change weight_kg to 100.

weight_kg <- 100

What do you think is the current content of the object weight_lb? 126.5 or 200?

mass <- 47.5            # mass?
age  <- 122             # age?
mass <- mass * 2.0      # mass?
age  <- age - 20        # age?
mass_index <- mass/age  # mass_index?

Vectors and data types

A vector is the most common and basic data structure in R, and is pretty much the workhorse of R. It’s a group of values, mainly either numbers or characters. You can assign this list of values to a variable, just like you would for one item. For example we can create a vector of animal weights:

weight_g <- c(50, 60, 65, 82)
weight_g

A vector can also contain characters:

animals <- c("mouse", "rat", "dog")
animals

The quotes around “mouse”, “rat”, etc. are essential here. Without the quotes R will assume there is a variable called mouse, rat, etc.

There are many functions that allow you to inspect the content of a vector. length() tells you how many elements are in a particular vector:

length(weight_g)
length(animals)

An important feature of a vector, is that all of the elements are the same type of data. The function class() indicates the class (the type of element) of an object:

class(weight_g)
class(animals)

The function str() provides an overview of the object and the elements it contains. It is a really useful function when working with large and complex objects:

str(weight_g)
str(animals)

You can add elements to your vector by using the c() function:

weight_g <- c(weight_g, 90) # adding at the end of the vector
weight_g <- c(30, weight_g) # adding at the beginning of the vector
weight_g

What happens here is that we take the original vector weight_g, and we are adding another item first to the end of the other ones, and then another item at the beginning. We can do this over and over again to grow a vector, or assemble a dataset. As we program, this may be useful to add results that we are collecting or calculating.

We just saw 2 of the 6 atomic vector types that R uses: "character" and "numeric". These are the basic building blocks that all R objects are built from. The other 4 are:

• "logical" for TRUE and FALSE (the boolean data type)
• "integer" for integer numbers (e.g., 2L, the L indicates to R that it’s an integer)
• "complex" to represent complex numbers with real and imaginary parts (e.g., 1+4i) and that’s all we’re going to say about them
• "raw" that we won’t discuss further

Vectors are one of the many data structures that R uses. Other important ones are lists (list), matrices (matrix), data frames (data.frame) and factors (factor).

num_char <- c(1, 2, 3, 'a')
num_logical <- c(1, 2, 3, TRUE)
char_logical <- c('a', 'b', 'c', TRUE)
tricky <- c(1, 2, 3, '4')

Subsetting vectors

If we want to extract one or several values from a vector, we must provide one or several indices in square brackets. For instance:

animals <- c("mouse", "rat", "dog", "cat")
animals[2]

#> [1] "rat"

animals[c(3, 2)]

#> [1] "dog" "rat"

We can also repeat the indices to create an object with more elements than the original one:

more_animals <- animals[c(1, 2, 3, 2, 1, 4)]
more_animals

#> [1] "mouse" "rat"   "dog"   "rat"   "mouse" "cat"

R indexes start at 1. Programming languages like Fortran, MATLAB, and R start counting at 1, because that’s what human beings typically do. Languages in the C family (including C++, Java, Perl, and Python) count from 0 because that’s simpler for computers to do.

weight_g <- c(21, 34, 39, 54, 55)
weight_g[c(TRUE, FALSE, TRUE, TRUE, FALSE)]

#> [1] 21 39 54

weight_g > 50    # will return logicals with TRUE for the indices that meet the condition

#> [1] FALSE FALSE FALSE  TRUE  TRUE

## so we can use this to select only the values above 50
weight_g[weight_g > 50]

#> [1] 54 55

weight_g[weight_g < 30 | weight_g > 50]

#> [1] 21 54 55

weight_g[weight_g >= 30 & weight_g == 21]

#> numeric(0)

animals <- c("mouse", "rat", "dog", "cat")
animals[animals == "cat" | animals == "rat"] # returns both rat and cat

#> [1] "rat" "cat"

animals %in% c("rat", "cat", "dog", "duck")

#> [1] FALSE  TRUE  TRUE  TRUE

animals[animals %in% c("rat", "cat", "dog", "duck")]

#> [1] "rat" "dog" "cat"

Missing data

As R was designed to analyze datasets, it includes the concept of missing data (which is uncommon in other programming languages). Missing data are represented in vectors as NA.

planets <- c("Mercury", "Venus", "Earth", "Mars", "Jupiter", "Saturn", "Uranus",
             "Neptune", NA)

The default setting for most base functions that read data into R is to interpret NA as a missing value. If there are multiple types of missing values in your dataset, you can extend what R considers a missing value when it reads the file in. To do this you supply additional values to the “na.strings” argument of the command to read in the data. For instance, if you wanted to read in a CSV file named planets.csv that had missing values represented as empty cell, a single blank space, and the value -999, you would use:

planets_df <- read.csv(file = "planets.csv", na.strings = c("", " ", "-999"))

When doing operations on numbers, most functions will return NA if the data you are working with include missing values. It is a safer behavior as otherwise you may overlook the fact that you are dealing with missing data. You can add the argument na.rm=TRUE to calculate the result while ignoring the missing values.

heights <- c(2, 4, 4, NA, 6)
mean(heights)
max(heights)
mean(heights, na.rm = TRUE)
max(heights, na.rm = TRUE)

If your data include missing values, you may want to become familiar with the functions is.na(), na.omit(), and complete.cases(). See below for examples.

## Extract those elements which are not missing values.
heights[!is.na(heights)]

## Returns the object with incomplete cases removed. The returned object is atomic.
na.omit(heights)

## Extract those elements which are complete cases.
heights[complete.cases(heights)]

sample <- c(2, 4, 4, "NA", 6)
mean(sample, na.rm = TRUE)

#> Warning in mean.default(sample, na.rm = TRUE): argument is not numeric or
#> logical: returning NA