Programming with R

Addressing data

Objectives

Understand the 3 different ways R can address data inside a data frame.

Combine different methods for addressing data with the assignment operator to update subsets of data

R is a powerful language for data manipulation. There are 3 main ways for addressing data inside R objects.

By index (slicing)
By logical vector
By name (columns only)

Lets start by loading some sample data:

dat<-read.csv(file='data/sample.csv',header=TRUE, stringsAsFactors=FALSE)

Tip

The first row of this csv file is a list of column names. We used the header=TRUE argument to read.csv so that R can interpret the file correctly. We are using the stringsAsFactors=FALSE argument to override the default behaviour for R. Using factors in R is covered in a separate lesson.

Lets take a look at this data.

class(dat)

[1] "data.frame"

R has loaded the contents of the .csv file into a variable called dat which is a data frame.

dim(dat)

[1] 100   9

The data has 100 rows and 9 columns.

head(dat)

      ID Gender      Group BloodPressure  Age Aneurisms_q1 Aneurisms_q2
1 Sub001      m    Control           132 16.0          114          140
2 Sub002      m Treatment2           139 17.2          148          209
3 Sub003      m Treatment2           130 19.5          196          251
4 Sub004      f Treatment1           105 15.7          199          140
5 Sub005      m Treatment1           125 19.9          188          120
6 Sub006      M Treatment2           112 14.3          260          266
  Aneurisms_q3 Aneurisms_q4
1          202          237
2          248          248
3          122          177
4          233          220
5          222          228
6          320          294

The data is the results of an (not real) experiment, looking at the number of aneurisms that formed in the eyes of patients who undertook 3 different treatments.

Addressing by index

We have already seen how square brackets [ can be used to subset (slice) data. The generic format is dat[row_numbers,column_numbers].

Challenge - Selecting values 1

What will be returned by dat[1,1]?

dat[1,1]

[1] "Sub001"

If we leave out a dimension R will interpret this as a request for all values in that dimension.

Challenge - Selecting values 2

What will be returned by dat[,2]?

The colon : can be used to create a sequence of integers.

6:9

[1] 6 7 8 9

Creates a vector of numbers from 6 to 9.

This can be very useful for addressing data.

Challenge - Subsetting with sequences

Use the colon operator to index just the aneurism count data (columns 6 to 9).

Finally we can use the c() (combine) function to address non-sequential rows and columns.

dat[c(1,5,7,9),1:5]

      ID Gender      Group BloodPressure  Age
1 Sub001      m    Control           132 16.0
5 Sub005      m Treatment1           125 19.9
7 Sub007      f    Control           173 17.7
9 Sub009      m Treatment2           131 19.4

Returns the first 5 columns for patients in rows 1,5,7 & 9

Challenge - Subsetting non-sequential data

Return the Age and Gender values for the first 5 patients.

Addressing by name

Columns in an R data frame are named.

names(dat)

[1] "ID"            "Gender"        "Group"         "BloodPressure"
[5] "Age"           "Aneurisms_q1"  "Aneurisms_q2"  "Aneurisms_q3" 
[9] "Aneurisms_q4"

Tip

If names are not specified e.g. using headers=FALSE in a read.csv() function, R assigns default names V1,V2,...,Vn

We usually use the $ operator to address a column by name

dat$Gender

  [1] "m" "m" "m" "f" "m" "M" "f" "m" "m" "f" "m" "f" "f" "m" "m" "m" "f"
 [18] "m" "m" "F" "f" "m" "f" "f" "m" "M" "M" "f" "m" "f" "f" "m" "m" "m"
 [35] "m" "f" "f" "m" "M" "m" "f" "m" "m" "m" "f" "f" "M" "M" "m" "m" "m"
 [52] "f" "f" "f" "m" "f" "m" "m" "m" "f" "f" "f" "f" "M" "f" "m" "f" "f"
 [69] "M" "m" "m" "m" "F" "m" "m" "f" "M" "M" "M" "f" "m" "M" "M" "m" "m"
 [86] "f" "f" "f" "m" "m" "f" "m" "F" "f" "m" "m" "F" "m" "M" "M"

Named addressing can also be used in square brackets.

head(dat[,c('Age','Gender')])

   Age Gender
1 16.0      m
2 17.2      m
3 19.5      m
4 15.7      f
5 19.9      m
6 14.3      M

Best Practice

Best practice is to address columns by name, often you will create or delete columns and the column position will change.

Logical indexing

A logical vector contains only the special values TRUE & FALSE.

c(TRUE,TRUE,FALSE,FALSE,TRUE)

[1]  TRUE  TRUE FALSE FALSE  TRUE

Tip

Note the values TRUE and FALSE are all capital letters and are not quoted.

Logical vectors can be created using relational operators e.g. <, >, ==, !=, %in%.

x<-c(1,2,3,11,12,13)
x < 10

[1]  TRUE  TRUE  TRUE FALSE FALSE FALSE

x %in% 1:10

[1]  TRUE  TRUE  TRUE FALSE FALSE FALSE

We can use logical vectors to select data from a data frame.

index <- dat$Group == 'Control'
dat[index,]$BloodPressure

 [1] 132 173 129  77 158  81 137 111 135 108 133 139 126 125  99 122 155
[18] 133  94  98  74 116  97 104 117  90 150 116 108 102

Often this operation is written as one line of code:

plot(dat[dat$Group=='Control',]$BloodPressure)

plot of chunk logical_vectors_indexing2

Challenge - Using logical indexes

Create a scatterplot showing BloodPressure for subjects not in the control group.
How many ways are there to index this set of subjects?

Combining indexing and assignment

The assignment operator <- can be combined with indexing.

x<-c(1,2,3,11,12,13)
x[x < 10] <- 0
x

[1]  0  0  0 11 12 13

Challenge - Updating a subset of values

In this dataset, values for Gender have been recorded as both uppercase M, F and lowercase m,f. Combine the indexing and assignment operations to convert all values to lowercase.