R Nuts and Bolts Part-II

4.8 Explicit Coercion

Objects can be explicitly coerced from one class to another using the as.* functions, if available.

> x <- 0:6
> class(x)
[1] "integer"
> as.numeric(x)
[1] 0 1 2 3 4 5 6
> as.logical(x)
[1] FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
> as.character(x)
[1] "0" "1" "2" "3" "4" "5" "6"

Sometimes, R can’t figure out how to coerce an object and this can result in NAs being produced.

> x <- c("a", "b", "c")
> as.numeric(x)
Warning: NAs introduced by coercion
[1] NA NA NA
> as.logical(x)
[1] NA NA NA
> as.complex(x)
Warning: NAs introduced by coercion
[1] NA NA NA

When nonsensical coercion takes place, you will usually get a warning from R.

4.9 Matrices

Matrices are vectors with a dimension attribute. The dimension attribute is itself an integer vector of length 2 (number of rows, number of columns)

> m <- matrix(nrow = 2, ncol = 3) 
> m
     [,1] [,2] [,3]
[1,]   NA   NA   NA
[2,]   NA   NA   NA
> dim(m)
[1] 2 3
> attributes(m)
$dim
[1] 2 3

Matrices are constructed column-wise, so entries can be thought of starting in the “upper left” corner and running down the columns.

> m <- matrix(1:6, nrow = 2, ncol = 3) 
> m
     [,1] [,2] [,3]
[1,]    1    3    5
[2,]    2    4    6

Matrices can also be created directly from vectors by adding a dimension attribute.

> m <- 1:10 
> m
 [1]  1  2  3  4  5  6  7  8  9 10
> dim(m) <- c(2, 5)
> m
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    3    5    7    9
[2,]    2    4    6    8   10

Matrices can be created by column-binding or row-binding with the cbind() and rbind() functions.

> x <- 1:3
> y <- 10:12
> cbind(x, y)
     x  y
[1,] 1 10
[2,] 2 11
[3,] 3 12
> rbind(x, y) 
  [,1] [,2] [,3]
x    1    2    3
y   10   11   12

4.10 Lists

Lists are a special type of vector that can contain elements of different classes. Lists are a very important data type in R and you should get to know them well. Lists, in combination with the various “apply” functions discussed later, make for a powerful combination.

Lists can be explicitly created using the list() function, which takes an arbitrary number of arguments.

> x <- list(1, "a", TRUE, 1 + 4i) 
> x
[[1]]
[1] 1

[[2]]
[1] "a"

[[3]]
[1] TRUE

[[4]]
[1] 1+4i

We can also create an empty list of a prespecified length with the vector() function

> x <- vector("list", length = 5)
> x
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

[[5]]
NULL

4.11 Factors

Factors are used to represent categorical data and can be unordered or ordered. One can think of a factor as an integer vector where each integer has a label. Factors are important in statistical modeling and are treated specially by modelling functions like lm() and glm().

Using factors with labels is better than using integers because factors are self-describing. Having a variable that has values “Male” and “Female” is better than a variable that has values 1 and 2.

Factor objects can be created with the factor() function.

> x <- factor(c("yes", "yes", "no", "yes", "no")) 
> x
[1] yes yes no  yes no 
Levels: no yes
> table(x) 
x
 no yes 
  2   3 
> ## See the underlying representation of factor
> unclass(x)  
[1] 2 2 1 2 1
attr(,"levels")
[1] "no"  "yes"

Often factors will be automatically created for you when you read a dataset in using a function like read.table(). Those functions often default to creating factors when they encounter data that look like characters or strings.

The order of the levels of a factor can be set using the levels argument to factor(). This can be important in linear modelling because the first level is used as the baseline level.

> x <- factor(c("yes", "yes", "no", "yes", "no"))
> x  ## Levels are put in alphabetical order
[1] yes yes no  yes no 
Levels: no yes
> x <- factor(c("yes", "yes", "no", "yes", "no"),
+             levels = c("yes", "no"))
> x
[1] yes yes no  yes no 
Levels: yes no

4.12 Missing Values

Missing values are denoted by NA or NaN for q undefined mathematical operations.

• is.na() is used to test objects if they are NA

• is.nan() is used to test for NaN

• NA values have a class also, so there are integer NA, character NA, etc.

• A NaN value is also NA but the converse is not true

> ## Create a vector with NAs in it
> x <- c(1, 2, NA, 10, 3)  
> ## Return a logical vector indicating which elements are NA
> is.na(x)    
[1] FALSE FALSE  TRUE FALSE FALSE
> ## Return a logical vector indicating which elements are NaN
> is.nan(x)   
[1] FALSE FALSE FALSE FALSE FALSE

> ## Now create a vector with both NA and NaN values
> x <- c(1, 2, NaN, NA, 4)
> is.na(x)
[1] FALSE FALSE  TRUE  TRUE FALSE
> is.nan(x)
[1] FALSE FALSE  TRUE FALSE FALSE

4.13 Data Frames

Data frames are used to store tabular data in R. They are an important type of object in R and are used in a variety of statistical modeling applications. Hadley Wickham’s package dplyr has an optimized set of functions designed to work efficiently with data frames.

Data frames are represented as a special type of list where every element of the list has to have the same length. Each element of the list can be thought of as a column and the length of each element of the list is the number of rows.

Unlike matrices, data frames can store different classes of objects in each column. Matrices must have every element be the same class (e.g. all integers or all numeric).

In addition to column names, indicating the names of the variables or predictors, data frames have a special attribute called row.names which indicate information about each row of the data frame.

Data frames are usually created by reading in a dataset using the read.table() or read.csv(). However, data frames can also be created explicitly with the data.frame() function or they can be coerced from other types of objects like lists.

Data frames can be converted to a matrix by calling data.matrix(). While it might seem that the as.matrix() function should be used to coerce a data frame to a matrix, almost always, what you want is the result of data.matrix().

> x <- data.frame(foo = 1:4, bar = c(T, T, F, F)) 
> x
  foo   bar
1   1  TRUE
2   2  TRUE
3   3 FALSE
4   4 FALSE
> nrow(x)
[1] 4
> ncol(x)
[1] 2

4.14 Names

R objects can have names, which is very useful for writing readable code and self-describing objects. Here is an example of assigning names to an integer vector.

> x <- 1:3
> names(x)
NULL
> names(x) <- c("New York", "Seattle", "Los Angeles") 
> x
   New York     Seattle Los Angeles 
          1           2           3 
> names(x)
[1] "New York"    "Seattle"     "Los Angeles"

Lists can also have names, which is often very useful.

> x <- list("Los Angeles" = 1, Boston = 2, London = 3) 
> x
$`Los Angeles`
[1] 1

$Boston
[1] 2

$London
[1] 3
> names(x)
[1] "Los Angeles" "Boston"      "London"     

Matrices can have both column and row names.

> m <- matrix(1:4, nrow = 2, ncol = 2)
> dimnames(m) <- list(c("a", "b"), c("c", "d")) 
> m
  c d
a 1 3
b 2 4

Column names and row names can be set separately using the colnames() and rownames() functions.

> colnames(m) <- c("h", "f")
> rownames(m) <- c("x", "z")
> m
  h f
x 1 3
z 2 4

Note that for data frames, there is a separate function for setting the row names, the row.names() function. Also, data frames do not have column names, they just have names (like lists). So to set the column names of a data frame just use the names() function. Yes, I know its confusing. Here’s a quick summary:

Object	Set column names	Set row names
data frame	names()	row.names()
matrix	colnames()	rownames()