# Chapter 2 Vectors

*Last updated: 2024-06-24 11:04:54 *

## Aims

Our aims in this chapter are:

- Learn how to work with R code files
- Get to know the simplest data structure in R, the vector
- Learn about subsetting, one of the fundamental operations with data

## 2.1 R code files

### 2.1.1 What are code files

In Chapter 1, we typed short and simple expressions into the R console. As we progress, however, the code we write will get longer and more complex. To be able to edit and save longer code, the code is kept in code *files*. Thus there are two “methods” for executing R code:

*Typing*the code in the console and pressing**Enter**- Sending code stored in a
*code file*to the console (we will see how, in a moment)

Either way, the code is interpreted, and we get the results or outputs (Figure 2.1).

### 2.1.2 Working with plain text

Computer code is stored in code files as **plain text**. When writing computer code, we must use a plain text editor, such as **Notepad++** or **RStudio** (Section 1.2). A word processor, such as **Microsoft Word**, is not a good choice for writing code, because:

- Documents created with a word processor contain elements other than plain text (such as highlighting, font types, sizes, colors, etc.), which are not plain text and therefore ignored by the interpreter, leading to confusion.
- Word processors can automatically correct “mistakes” thereby introducing unintended changes in our code, such as capitalizing:
`max(1)`

→`Max(1)`

.

Any plain text file can be used to store R code, though, conventionally, R code files have the `*.R`

file extension.

### 2.1.3 Code files in RStudio

To start working with a code file in RStudio, we can do one of the following:

- Create a new code file, selecting
**File → New File… → R Script**from the menu (or pressing**Ctrl+Shift+N**) - Open an
*existing*code file, selecting**File → Open File…**from the menu (or pressing**Ctrl+O**)

The new file, or a modified existing file, can be saved by selecting **File → Save** from the menu (or pressing **Ctrl+S**).

Open the code file named

`volcano.R`

which is included in the book materials in RStudio.

There are several methods to execute code from a code file, by sending it to the console. The most obvious one is to copy a section of code, then paste it in the console, and press **Enter**, but this is not very convenient. Instead we usually do one of the following:

- We can send a single expression, by placing the cursor on a particular line and pressing
**Ctrl+Enter**. The expression is executed and the cursor advances to the next line, which means we can press**Ctrl+Enter**again to execute it too, and so on. - We can send a selection of several lines of code, by marking the section and pressing
**Ctrl+Enter**. - We can execute all lines from the top of the code file to the line where the cursor is, by pressing
**Ctrl+Alt+B**.

For example, we can run the file `volcano.R`

which draws a 3D image of a volcano (Figure 2.2). The file is contained in the book materials, see Appendix A for the complete list of files and the download link.

Try each of the above three methods to execute R code with the

`volcano.R`

code file. Running the entire code file, by selecting all code withCtrl+Aand pressingCtrl+Enter, produces a 3D image of a volcano in the graphical output panel (Figure 2.2).

### 2.1.4 RStudio keyboard stortcuts

RStudio has numerous keyboard shortcuts for making it easier to edit and execute code files, some of which we already mentioned in the previous section. The most useful RStudio keyboard shortcuts are given in Table 2.1.

Shortcut | Action |
---|---|

Ctrl+1 |
Moving cursor to the code editor |

Ctrl+2 |
Moving cursor to the console |

Ctrl+Enter |
Running the current selection or line |

Ctrl+Alt+B |
Running from top to current line |

Ctrl+Shift+C |
Turn comment on or off |

Tab |
Auto-complete |

Ctrl+D |
Delete line |

Ctrl+Shift+D |
Duplicate line |

Ctrl+F |
Find and replace menu |

Ctrl+S |
Save |

## 2.2 Assignment

So far we have been using R by typing expressions into the command line and observing the result on screen. That way, R functions as a “calculator”; the results are not kept in computer memory (Figure 2.3).

Storing objects in the temporary computer memory (RAM) is called **assignment**. In an assignment expression, we are storing an object, under a certain name, in the RAM (Figure 2.4). Assignment is done using the assignment operator. Assignment is an essential operation in programming, because it makes automation possible—reaching the goal step by step, while storing intermediate products.
An assignment expression consists of:

- The
*expression*whose result we want to store - The
*assignment operator*,`=`

or`<-`

- The
*name*which will be assigned to the object

For example, the following expression assigns the result of the arithmetic calculation `(6617747987-6617746521)/10`

into a variable named `rateEstimate`

:

When we type an object name in the console, R accesses an object stored under that name in the RAM, and calls the `print`

function on the object (Figure 2.5):

What happens when we assign a new value to an existing object? The old value gets deleted, and the object is associated with a new value:

Note the difference between the `==`

and `=`

operators! `=`

is an assignment operator:

while `==`

is a conditional operator (Section 1.3.4) to test for equality:

Which user-defined objects are currently in memory? The `ls`

function returns a character *vector* (see Section 2.3 below) with their names:

Why did we write

`ls()`

and not`ls`

?

## 2.3 Vectors

### 2.3.1 What is a vector?

The vector is the simplest data structure in R, and the first data structure we learn about in this book. A vector, in R, is an *ordered* collection of values of the *same type*, such as:

**Numbers**—`numeric`

(numbers with a decimal point), or`integer`

(whole numbers)**Text**—`character`

**Logical**—`logical`

Recall that these are the same three types of “constant values” we saw in Chapter 1. In fact, R doesn’t have a special class for individual constant values. A constant value in R is actually represented by a vector of length 1.

The distinction between the `numeric`

and `integer`

classes (Section 1.3.11) is not very important for our purposes. Both of these two classes are used to represent numbers, and R automatically converts from one to another, as needed. We are mentioning both only because you may encounter either one when working with numbers. In this book, we will refer to both `numeric`

and `integer`

vectors as “numeric”, for convenience.

### 2.3.2 The `c`

function

A vector of length 1 can be created simply by typing a value, such as `600`

or `"Hello"`

, as we have already seen (Section 1.3). A vector of length >1 can be created in several ways. The most straightforward method is to use the `c`

function, which *combines* its inputs—vectors of length 1, or more—into a new vector, in the specified order. For example:

Note that the `c`

function is not restricted to combining individual values (i.e., vectors of length 1). It can be used to combine any number of vectors, of any length. For example, the following expression combines four vectors—of length 3, 1, 3 and 2—into a new vector of length 9:

Here is another example of using the `c`

function, this time to combine four `character`

values into a vector of length 4:

### 2.3.3 Vector subsetting (individual elements)

We can access individual vector *elements* using the `[`

operator and a numeric **index**. That way, we can get a subset with an individual vector element:

Note that numeric indices in R start at `1`

! This is unlike Python, C, JavaScript, and many other programming languages, where numeric indices start at `0`

.

Here is another example:

Note the three components of an expression for accessing a vector element:

- The vector being subsetted (
`counts`

`[4]`

) - Square brackets (
`counts`

`[`

`4`

)`]`

- The index (
`counts[`

`4`

`]`

)

We can also make an assignment into a vector subset, for example to replace an individual element:

In this example, we made an assignment into a subset with a *single* element. As we will see later on, we can assign values into a subset of *any* length, using the same method (Section 2.3.9).

### 2.3.4 Calling functions on a vector

There are numerous functions for calculating vector properties in R. The `length`

, `min`

, `max`

, `range`

, `mean`

, and `sum`

functions are most commonly used. Here is a demonstration of these functions:

In what way is the

`range`

function different from the other functions shown above?

Contrariwise, there are functions that operate on each vector element, *separately*, returning a vector of results having the same length as the input:

```
sqrt(x) # Square root
## Warning in sqrt(x): NaNs produced
## [1] 1.000000 2.449490 1.732051 NaN 1.414214
```

Why does the output of

`sqrt(x)`

contain`NaN`

?

Note that the last expression produced a **warning**. A warning, in R, signals to the user that something suspicious or notable has happened. A warning differs from an error (Section 1.3.7) in that when a warning is raised, the expression is executed nevertheless. Contrariwise, when an error is raised, code evaluation stops and the expression (and subsequent expressions, if any) is not executed by the interpreter.

### 2.3.5 The recycling rule (arithmetic)

Binary operations, such as arithmetic (Section 1.3.2) and conditional (Section 1.3.4) operators, when applied on two vectors, are done *element-by-element*. The result is, then, a vector of the respective results. For example, the following expression:

is interpreted as:

Here are three more examples, demonstrating the element-by-element behavior using other operators, `*`

, `>`

, and `<`

:

What happens when the input vector lengths do not match? In such case, the shorter vector gets **“recycled”**. For example, when one of the vectors is of length 3 and the other vector is of length 6, then the shorter vector (of length 3) is replicated two times, until it matches the longer vector (Figure 2.6). Thus, the expression:

is equivalent to the expression:

When one of the vectors is of length 1 and the other is of length 4, the shorter vector (of length 1) is replicated 4 times:

When one of the vectors is of length 2 and the other is of length 6, the shorter vector (of length 2) is replicated 3 times:

What happens when the longer vector length is not a multiple of the shorter vector length? In such case, recycling is “incomplete”, as indicated by a warning message. In the following example, the shorter vector is recycled “1.5 times”:

```
c(1, 2) * c(1, 2, 3)
## Warning in c(1, 2) * c(1, 2, 3): longer object length is not a multiple of
## shorter object length
## [1] 1 4 3
```

Incomplete recycling is rarely something we want to do in practice. Therefore, the latter warning is usually an indication that something is wrong in our code.

### 2.3.6 Consecutive and repetitive vectors

#### 2.3.6.1 Introduction

Other than the `c`

function (Section 2.3.2), there are three commonly used methods for creating *consecutive* or *repetitive* vectors:

#### 2.3.6.2 Consecutive vectors

The `:`

operator is used to create a vector of consecutive values in steps of `1`

:

or in steps of `-1`

:

The `seq`

function provides a more general way to create a consecutive vector with *any* step size, not necessarily `1`

or `-1`

. The three most useful parameters of the `seq`

function are:

`from`

—Where to start`to`

—When to end`by`

—Step size

For example:

The above examples of the `seq`

function are also examples of passing more than one argument in a function call (Section 1.3.6). You may also have noticed that the arguments are *named*. We are going to elaborate on the syntax rules of using more than one argument, in a function call in R, in a moment (Section 2.3.7).

#### 2.3.6.3 Repetitive vectors

The `rep`

function *replicates* its argument to create a repetitive vector:

`x`

—What to replicate`times`

—How many times to replicate the entire vector`each`

—How many times to replicate each element

For example, using `times`

we can replicate the entire vector the specified number of times:

Alternatively, we can use `each`

to replicate each element the specified number of times:

### 2.3.7 Function calls

Using the `seq`

function, we will demonstrate three properties of function calls. First, we can omit parameter names as long as the arguments are passed in the default order. For example, the following two function calls are identical, because the default order of the (first three) `seq`

function parameters is `from`

, `to`

, and `by`

:

Second, we can use any argument order as long as parameter *names* are specified. The following three function calls are identical, even though argument order is not the same, since the arguments are named:

Third, we can omit parameters that have a **default** argument, specified as part of the function definition. For example, the `by`

parameter of `seq`

has a default value of `1`

:

The parameters of a particular function, their order, and their default values (if any), can be found in the help file of every function (Section 1.3.12):

### 2.3.8 Vector subsetting (general)

So far, we created vector subsets using a `numeric`

index which consists of a single value (Section 2.3.3), as in:

We can also use a vector of length >1 as an index. For example, the following expression returns the first *and* second elements of `x`

, since the index is the vector `c(1,2)`

(which we create using the `:`

operator) (Section 2.3.6.2):

Note that the vector of indices can consist of any combination of indices whatsoever. It does not have to be consecutive, and it can even include repetitions:

`letters`

is a built-in vector of English letters, i.e.,`c('a','b','c',...)`

. What will be the result of`letters[rep(2,3)]`

?

Here is another example (Figure 2.7):

And here is one more example where the index is not consecutive:

Note, again, the components of the subsetting expression:

- The vector being subsetted (
`counts`

`[c(1:3, 7:9)]`

) - Square brackets (
`counts`

`[`

`c(1:3, 7:9)`

)`]`

- The index (
`counts[`

`c(1:3, 7:9)`

`]`

)

For the next examples, let’s create a vector of all *even* numbers between 1 and 100:

```
x = seq(2, 100, 2)
x
## [1] 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38
## [20] 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76
## [39] 78 80 82 84 86 88 90 92 94 96 98 100
```

Can you think of another way to create the above vector, using the

`:`

and`*`

operators?

What is the meaning of the numbers in square brackets when printing the vector?

How can we check how many elements does `x`

have? Recall the `length`

function (Section 2.3.4):

Using this knowledge, here are two expression that return the value of the *last* element in `x`

:

Which of the last two expressions is preferable? Why?

Which index can we use to get back the entire vector? We can use an index that contains all of the vector element indices, starting from `1`

and up to `length(x)`

:

```
x[1:length(x)]
## [1] 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38
## [20] 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76
## [39] 78 80 82 84 86 88 90 92 94 96 98 100
```

What index can we use to get the entire vector

except forthe last two elements?

What index can we use to get a

reversedvector?

Note that there is a built-in function named `rev`

for reversing a vector:

```
rev(x)
## [1] 100 98 96 94 92 90 88 86 84 82 80 78 76 74 72 70 68 66 64
## [20] 62 60 58 56 54 52 50 48 46 44 42 40 38 36 34 32 30 28 26
## [39] 24 22 20 18 16 14 12 10 8 6 4 2
```

Note that, when requesting elements beyond the vector length, we get `NA`

(*Not Available*) values. For example:

### 2.3.9 The recycling rule (assignment)

Earlier, we saw how the recycling rule applies to arithmetic and conditional operators (Section 2.3.5). The rule also applies to assignment.

For example, here we assign a vector of length 1 (`NA`

) into a subset of length 6 (`c(1:3,7:9)`

). As a result, `NA`

is replicated six times, to match the subset:

Here, `c(NA,99)`

is replicated three times, also to match the subset of length 6:

### 2.3.10 Logical vectors

#### 2.3.10.1 Creating logical vectors

The third common type of vectors, in addition to `numeric`

and `character`

vectors, are `logical`

vectors. A logical vector is composed of `logical`

values (Section 1.3.4), `TRUE`

and `FALSE`

(or `NA`

). For example:

Usually, we will not be creating `logical`

vectors *manually*, but through applying a conditional operator (Section 1.3.4) on a `numeric`

or `character`

vector. For example:

Note how the recycling rule applies to conditional operators in the above expression.

An important property of `logical`

vectors is, that, when arithmetic operations are applied, the `logical`

vector is automatically *converted* to a numeric one, where `TRUE`

becomes `1`

and `FALSE`

becomes `0`

. For example:

What is the meaning of the values

`4`

and`0.4`

in the above example?

#### 2.3.10.2 Subsetting with logical vectors

So far, we used a *numeric* vector of indices when subsetting a vector (Sections 2.3.3 and 2.3.8). A `logical`

vector can also be used as an index for subsetting. When using a `logical`

vector of indices, the subset contains those elements which are in the same positions as the `TRUE`

elements in the index. This means that the `logical`

vector of indices needs to match the length of the vector being subsetted. If this is not the case, the `logical`

vector is recycled.

For example:

Here is another example, where the `logical`

vector of indices is created from the same vector being subsetted:

In this example, the logical vector `counts<3`

:

specifies whether to *include* each of the elements of `counts`

in the resulting subset (Figure 2.8).

What does the expression

`counts[counts<3]`

do, in plain language?

Here are some more examples of subsetting with a `logical`

index:

What does the output

`integer(0)`

, which we got in the last expression, mean?

The next example is slightly more complex; we select the elements of `z`

whose square is larger than 8:

Let’s go over this step-by-step. First, `z^2`

gives a vector of squared `z`

values (`2`

is recycled):

Then, each of the squares is compared to 8 (`8`

is recycled):

Finally, the `logical`

vector `z^2>8`

is used for subsetting `z`

.

### 2.3.11 Missing values

The `is.na`

function is used to detect *missing* (`NA`

) values (Section 1.3.5) in a vector. The `is.na`

function:

- accepts a vector, of any type, and
- returns a
`logical`

vector, with`TRUE`

in place of`NA`

values and`FALSE`

in place of non-`NA`

values.

For example, suppose we have a vector `x`

where some of the values are missing:

The `is.na`

function can be used to detect which values are missing:

How can we use the above expression to subset the

non-missingvalues of`x`

?

A common mistake is to use comparison with `NA`

to detect missing values, instead of `is.na`

, as in:

Can you explain the above result?

Many of the functions that summarize vector properties (Section 2.3.4), such as `sum`

and `mean`

, have a parameter called `na.rm`

. The `na.rm`

parameter is used to determine whether `NA`

values are *excluded* from the calculation. The default is `na.rm=FALSE`

, meaning that `NA`

values are *not* excluded. For example:

Why do we get

`NA`

in the first expression?

What do you think will be the result of

`length(x)`

:`NA`

or`7`

? Execute the expression to check your answer.

How can we replace the

`NA`

values in`x`

with the mean of its non-`NA`

values?

## 2.4 Additional useful functions

### 2.4.1 `any`

and `all`

Sometimes we want to figure out whether a `logical`

vector:

- contains
*at least one*`TRUE`

value; or - is
*entirely*composed of`TRUE`

values.

We can use the `any`

and `all`

functions, respectively, to do those things.

The `any`

function returns `TRUE`

if at least *one* of the input vector values is `TRUE`

, otherwise it returns `FALSE`

. For example, let’s take a numeric vector `x`

:

The expression `any(x > 5)`

returns `TRUE`

, which means that the vector `x > 5`

contains at least one `TRUE`

value, i.e., at least one element of `x`

is greater than `5`

:

The expression `any(x > 88)`

returns `FALSE`

, which means that the vector `x > 88`

contains no `TRUE`

values, i.e., none of the elements of `x`

are greater than `88`

:

The `all`

function returns `TRUE`

if *all* of the input vector values are `TRUE`

, otherwise it returns `FALSE`

. For example, the expression `all(x > 5)`

returns `FALSE`

, which means that the vector `x > 5`

contains at least one `FALSE`

value, i.e., *not* all elements of `x`

are greater than `5`

:

The expression `all(x > -1)`

returns `TRUE`

, which means that `x > -1`

is composed entirely of `TRUE`

values, i.e., all elements of `x`

are greater than `-1`

:

In a way, `any`

and `all`

are *inverse*:

`any`

determines if the logical vector contains at least one`TRUE`

value.`all`

determines if the logical vector contains at least one`FALSE`

value.

Which expression can we use to get

`TRUE`

if vector`x`

contains at least one`NA`

value, or`FALSE`

if it does not?

### 2.4.2 `which`

The `which`

function converts a `logical`

vector to a `numeric`

one, with the *indices* of `TRUE`

values. That way, we can find out the index of values that satisfy a given condition. For example, considering the vector `x`

:

the expression `which(x > 2.3)`

returns the indices of `TRUE`

elements in `x > 2.3`

, i.e., the indices of `x`

elements which are greater than `2.3`

:

### 2.4.3 `which.min`

and `which.max`

Related to `which`

(Section 2.4.2) are functions `which.min`

and `which.max`

. The latter two functions return the index of the (first!) *minimal* or *maximal* value in a vector, respectively. For example, considering the vector `x`

:

using `which.min`

we can find out that the *minimal* value of `x`

is in the 5^{th} position:

while using `which.max`

we can find out that the *maximal* value of `x`

is in the 2^{nd} position:

What expression can we use to find

allindices (`2`

,`7`

) of the maximal value in`x`

?

Keep in mind that `which`

, `which.min`

, and `which.max`

ignore `NA`

values. For example:

### 2.4.4 The `order`

function

The `order`

function returns ordered vector indices, based on the order of vector values. In other words, `order`

gives the index of the smallest value, the index of the second smallest value, etc., up to the index of the largest value. For example, given the vector `x`

:

`order(x)`

returns the indices `1:length(x)`

, ordered from smallest to largest value:

This result tells us that the 5^{th} element of `x`

is the smallest, the 6^{th} is the second smallest, and so on.

We can also get the *reverse* order with `decreasing=TRUE`

:

How can we get a

sortedvector of elements from`x`

, as shown below, using the`order`

function?

`## [1] 0 1 2 2 3 6 6`

### 2.4.5 `paste`

and `paste0`

The `paste`

function is used to “paste” text values. Its `sep`

parameter determines the separating character(s), with the default being `sep=" "`

(a space). For example:

Non-character vectors are automatically converted to `character`

before pasting:

The recycling rule applies in `paste`

too:

```
paste("image", 1:5, ".tif", sep = "")
## [1] "image1.tif" "image2.tif" "image3.tif" "image4.tif" "image5.tif"
```

Finally, the `paste0`

function is a shortcut for `paste`

with `sep=""`

: