Subsetting Data in R

John Muschelli

January 5, 2016
Overview

We showed one way to read data into R using read.csv. In this

module, we will show you how to:

1. Select specific elements of an object by an index or logical

condition
2. Renaming columns of a data.frame
3. Subset rows of a data.frame
4. Subset columns of a data.frame
5. Add/remove new columns to a data.frame
6. Order the columns of a data.frame
7. Order the rows of a data.frame
Setup

We will show you how to do each operation in base R then show

you how to use the dplyr package to do the same operation (if
applicable).
Many resources on how to use dplyr exist and are straightforward:

I https:
//cran.rstudio.com/web/packages/dplyr/vignettes/
I https:
//stat545-ubc.github.io/block009_dplyr-intro.html
I https://www.datacamp.com/courses/
dplyr-data-manipulation-r-tutorial
Select specific elements using an index

Often you only want to look at subsets of a data set at any given
time. As a review, elements of an R object are selected using the
brackets ([ and ]).
For example, x is a vector of numbers and we can select the second
element of x using the brackets and an index (2):

x = c(1, 4, 2, 8, 10)
x[2]

[1] 4
Select specific elements using an index

We can select the fifth or second AND fifth elements below:

x = c(1, 2, 4, 8, 10)
x[5]

[1] 10

x[c(2,5)]

[1] 2 10
Subsetting by deletion of entries
You can put a minus (-) before integers inside brackets to remove
these indices from the data.

x[-2] # all but the second

[1] 1 4 8 10

Note that you have to be careful with this syntax when dropping
more than 1 element:

x[-c(1,2,3)] # drop first 3

[1] 8 10

# x[-1:3] # shorthand. R sees as -1 to 3

x[-(1:3)] # needs parentheses

[1] 8 10
Select specific elements using logical operators
What about selecting rows based on the values of two variables?
We use logical statements. Here we select only elements of x
greater than 2:

[1] 1 2 4 8 10

x > 2

[1] FALSE FALSE TRUE TRUE TRUE

x[ x > 2 ]

[1] 4 8 10
Select specific elements using logical operators

You can have multiple logical conditions using the following:

I & : AND
I | : OR

x[ x > 2 & x < 5 ]

[1] 4

x[ x > 5 | x == 2 ]

[1] 2 8 10
which function
The which functions takes in logical vectors and returns the index
for the elements where the logical value is TRUE.

which(x > 5 | x == 2) # returns index

[1] 2 4 5

x[ which(x > 5 | x == 2) ]

[1] 2 8 10

x[ x > 5 | x == 2 ]

[1] 2 8 10
Creating a data.frame to work with

Here we create a toy data.frame named df using random data:

set.seed(2016) # reproducbility
df = data.frame(x = c(1, 2, 4, 10, 10),
x2 = rpois(5, 10),
y = rnorm(5),
z = rpois(5, 6)
)
Renaming Columns of a data.frame: base R
We can use the colnames function to directly reassign column
names of df:

colnames(df) = c("x", "X", "y", "z")

head(df)

x X y z
1 1 7 -0.2707606 6
2 2 6 -1.1179372 4
3 4 10 -1.3473558 7
4 10 13 0.4832675 10
5 10 13 0.1523950 5

colnames(df) = c("x", "x2", "y", "z") #reset

Renaming Columns of a data.frame: base R
We can assign the column names, change the ones we want, and
then re-assign the column names:

cn = colnames(df)
cn[ cn == "x2"] = "X"
colnames(df) = cn
head(df)

x X y z
1 1 7 -0.2707606 6
2 2 6 -1.1179372 4
3 4 10 -1.3473558 7
4 10 13 0.4832675 10
5 10 13 0.1523950 5

colnames(df) = c("x", "x2", "y", "z") #reset

Renaming Columns of a data.frame: dplyr

library(dplyr)

Note, when loading dplyr, it says objects can be “masked”. That

means if you use a function defined in 2 places, it uses the one that
is loaded in last.
Renaming Columns of a data.frame: dplyr

For example, if we print filter, then we see at the bottom

namespace:dplyr, which means when you type filter, it will use
the one from the dplyr package.

filter

function (.data, ...)

{
filter_(.data, .dots = lazyeval::lazy_dots(...))
}
<environment: namespace:dplyr>
Renaming Columns of a data.frame: dplyr

A filter function exists by default in the stats package, however.

If you want to make sure you use that one, you use
PackageName::Function with the colon-colon (“::”) operator.

head(stats::filter,2)

1 function (x, filter, method = c("convolution", "recursive

2 sides = 2L, circular = FALSE, init = NULL)

This is important when loading many packages, and you may have
some conflicts/masking:
Renaming Columns of a data.frame: dplyr

To rename columns in dplyr, you use the rename command

df = dplyr::rename(df, X = x2)
head(df)

x X y z
1 1 7 -0.2707606 6
2 2 6 -1.1179372 4
3 4 10 -1.3473558 7
4 10 13 0.4832675 10
5 10 13 0.1523950 5

df = dplyr::rename(df, x2 = X) # reset
Subset columns of a data.frame:

We can grab the x column using the $ operator.

df$x

[1] 1 2 4 10 10
Subset columns of a data.frame:
We can also subset a data.frame using the bracket [, ]
subsetting.
For data.frames and matrices (2-dimensional objects), the
brackets are [rows, columns] subsetting. We can grab the x
column using the index of the column or the column name (“x”)

df[, 1]

[1] 1 2 4 10 10

df[, "x"]

[1] 1 2 4 10 10
Subset columns of a data.frame:

We can select multiple columns using multiple column names:

df[, c("x", "y")]

x y
1 1 -0.2707606
2 2 -1.1179372
3 4 -1.3473558
4 10 0.4832675
5 10 0.1523950
Subset columns of a data.frame: dplyr

The select command from dplyr allows you to subset

select(df, x)

x
1 1
2 2
3 4
4 10
5 10
Select columns of a data.frame: dplyr
The select command from dplyr allows you to subset columns of

select(df, x, x2)

x x2
1 1 7
2 2 6
3 4 10
4 10 13
5 10 13

select(df, starts_with("x"))

x x2
1 1 7
2 2 6
3 4 10
4 10 13
Subset rows of a data.frame with indices:

Let’s select rows 1 and 3 from df using brackets:

df[ c(1, 3), ]

x x2 y z
1 1 7 -0.2707606 6
3 4 10 -1.3473558 7
Subset rows of a data.frame:

Let’s select the rows of df where the x column is greater than 5 or

is equal to 2. Without any index for columns, all columns are
returned:

df[ df$x > 5 | df$x == 2, ]

x x2 y z
2 2 6 -1.1179372 4
4 10 13 0.4832675 10
5 10 13 0.1523950 5
Subset rows of a data.frame:

We can subset both rows and colums at the same time:

df[ df$x > 5 | df$x == 2, c("y", "z")]

y z
2 -1.1179372 4
4 0.4832675 10
5 0.1523950 5
Subset rows of a data.frame: dplyr

The command in dplyr for subsetting rows is filter. Try

?filter

filter(df, x > 5 | x == 2)

x x2 y z
1 2 6 -1.1179372 4
2 10 13 0.4832675 10
3 10 13 0.1523950 5

Note, no $ or subsetting is necessary. R “knows” x refers to a

column of df.
Subset rows of a data.frame: dplyr

By default, you can separate conditions by commas, and filter

assumes these statements are joined by &

filter(df, x > 2 & y < 0)

x x2 y z
1 4 10 -1.347356 7

filter(df, x > 2, y < 0)

x x2 y z
1 4 10 -1.347356 7
Combining filter and select

You can combine filter and select to subset the rows and
columns, respectively, of a data.frame:

select(filter(df, x > 2 & y < 0), y, z)

y z
1 -1.347356 7

In R, the common way to perform multiple operations is to wrap

functions around each other in a nested way such as above
Assigning Temporary Objects

One can also create temporary objects and reassign them:

df2 = filter(df, x > 2 & y < 0)

df2 = select(df2, y, z)
Piping - a new concept

There is another (newer) way of performing these operations, called

“piping”. It is becoming more popular as it’s easier to read:

df %>% filter(x > 2 & y < 0) %>% select(y, z)

y z
1 -1.347356 7

It is read: “take df, then filter the rows and then select y, z”.
Adding new columns to a data.frame: base R

You can add a new column, called newcol to df, using the $
operator:

df$newcol = 5:1
df$newcol = df$x + 2
Removing columns to a data.frame: base R

You can remove a column by assigning to NULL:

df$newcol = NULL

or selecing only the columns that were not newcol:

df = df[, colnames(df) != "newcol"]

Adding new columns to a data.frame: base R

You can also “column bind” a data.frame with a vector (or series
of vectors), using the cbind command:

cbind(df, newcol = 5:1)

x x2 y z newcol
1 1 7 -0.2707606 6 5
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 3
4 10 13 0.4832675 10 2
5 10 13 0.1523950 5 1
Adding columns to a data.frame: dplyr
The mutate function in dplyr allows you to add or replace columns
of a data.frame:

mutate(df, newcol = 5:1)

x x2 y z newcol
1 1 7 -0.2707606 6 5
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 3
4 10 13 0.4832675 10 2
5 10 13 0.1523950 5 1

print({df = mutate(df, newcol = x + 2)})

x x2 y z newcol
1 1 7 -0.2707606 6 3
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 6
Removing columns to a data.frame: dplyr

The NULL method is still very common.

The select function can remove a column with a minus (-), much
like removing rows:

select(df, -newcol)

x x2 y z
1 1 7 -0.2707606 6
2 2 6 -1.1179372 4
3 4 10 -1.3473558 7
4 10 13 0.4832675 10
5 10 13 0.1523950 5
Removing columns to a data.frame: dplyr

Remove newcol and y

select(df, -one_of("newcol", "y"))

x x2 z
1 1 7 6
2 2 6 4
3 4 10 7
4 10 13 10
5 10 13 5
Ordering the columns of a data.frame: base R

We can use the colnames function to get the column names of df

and then put newcol first by subsetting df using brackets:

cn = colnames(df)
df[, c("newcol", cn[cn != "newcol"]) ]

newcol x x2 y z
1 3 1 7 -0.2707606 6
2 4 2 6 -1.1179372 4
3 6 4 10 -1.3473558 7
4 12 10 13 0.4832675 10
5 12 10 13 0.1523950 5
Ordering the columns of a data.frame: dplyr

The select function can reorder columns. Put newcol first, then
select the rest of columns:

select(df, newcol, everything())

newcol x x2 y z
1 3 1 7 -0.2707606 6
2 4 2 6 -1.1179372 4
3 6 4 10 -1.3473558 7
4 12 10 13 0.4832675 10
5 12 10 13 0.1523950 5
Ordering the rows of a data.frame: base R

We use the order function on a vector or set of vectors, in

increasing order:

df[ order(df$x), ]

x x2 y z newcol
1 1 7 -0.2707606 6 3
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 6
4 10 13 0.4832675 10 12
5 10 13 0.1523950 5 12
Ordering the rows of a data.frame: base R

The decreasing argument will order it in decreasing order:

df[ order(df$x, decreasing = TRUE), ]

x x2 y z newcol
4 10 13 0.4832675 10 12
5 10 13 0.1523950 5 12
3 4 10 -1.3473558 7 6
2 2 6 -1.1179372 4 4
1 1 7 -0.2707606 6 3
Ordering the rows of a data.frame: base R

You can pass multiple vectors, and must use the negative (using -)
to mix decreasing and increasing orderings (sort increasing on x and
decreasing on y):

df[ order(df$x, -df$y), ]

x x2 y z newcol
1 1 7 -0.2707606 6 3
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 6
4 10 13 0.4832675 10 12
5 10 13 0.1523950 5 12
Ordering the rows of a data.frame: dplyr

The arrange function can reorder rows By default, arrange orders

in ascending order:

arrange(df, x)

x x2 y z newcol
1 1 7 -0.2707606 6 3
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 6
4 10 13 0.4832675 10 12
5 10 13 0.1523950 5 12
Ordering the rows of a data.frame: dplyr

Use the desc to arrange the rows in descending order:

arrange(df, desc(x))

x x2 y z newcol
1 10 13 0.4832675 10 12
2 10 13 0.1523950 5 12
3 4 10 -1.3473558 7 6
4 2 6 -1.1179372 4 4
5 1 7 -0.2707606 6 3
Ordering the rows of a data.frame: dplyr

It is a bit more straightforward to mix increasing and decreasing

orderings:

arrange(df, x, desc(y))

x x2 y z newcol
1 1 7 -0.2707606 6 3
2 2 6 -1.1179372 4 4
3 4 10 -1.3473558 7 6
4 10 13 0.4832675 10 12
5 10 13 0.1523950 5 12
Transmutation

The transmute function in dplyr combines both the mutate and

select functions. One can create new columns and keep the only
the columns wanted:

transmute(df, newcol2 = x * 3, x, y)

newcol2 x y
1 3 1 -0.2707606
2 6 2 -1.1179372
3 12 4 -1.3473558
4 30 10 0.4832675
5 30 10 0.1523950