Dealing with Missing Values

A common task in data analysis is dealing with missing values. In R, missing values are often represented by NA or some other value that represents missing values (i.e. 99). We can easily work with missing values and in this section you will learn how to:

Test for missing values

To identify missing values use is.na() which returns a logical vector with TRUE in the element locations that contain missing values represented by NA.is.na() will work on vectors, lists, matrices, and data frames.

# vector with missing data
x <- c(1:4, NA, 6:7, NA)
x
## [1]  1  2  3  4 NA  6  7 NA

is.na(x)
## [1] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE

# data frame with missing data
df <- data.frame(col1 = c(1:3, NA),
                 col2 = c("this", NA,"is", "text"), 
                 col3 = c(TRUE, FALSE, TRUE, TRUE), 
                 col4 = c(2.5, 4.2, 3.2, NA),
                 stringsAsFactors = FALSE)

# identify NAs in full data frame
is.na(df)
##       col1  col2  col3  col4
## [1,] FALSE FALSE FALSE FALSE
## [2,] FALSE  TRUE FALSE FALSE
## [3,] FALSE FALSE FALSE FALSE
## [4,]  TRUE FALSE FALSE  TRUE

# identify NAs in specific data frame column
is.na(df$col4)
## [1] FALSE FALSE FALSE  TRUE

To identify the location or the number of NAs we can leverage the which() and sum() functions:

# identify location of NAs in vector
which(is.na(x))
## [1] 5 8

# identify count of NAs in data frame
sum(is.na(df))
## [1] 3

For data frames, a convenient shortcut to compute the total missing values in each column is to use colSums():

colSums(is.na(df))
## col1 col2 col3 col4
##    1    1    0    1

Recode missing values

To recode missing values; or recode specific indicators that represent missing values, we can use normal subsetting and assignment operations. For example, we can recode missing values in vector x with the mean values in x by first subsetting the vector to identify NAs and then assign these elements a value. Similarly, if missing values are represented by another value (i.e. 99) we can simply subset the data for the elements that contain that value and then assign a desired value to those elements.

# recode missing values with the mean
# vector with missing data
x <- c(1:4, NA, 6:7, NA)
x
## [1]  1  2  3  4 NA  6  7 NA

x[is.na(x)] <- mean(x, na.rm = TRUE)

round(x, 2)
## [1] 1.00 2.00 3.00 4.00 3.83 6.00 7.00 3.83

# data frame that codes missing values as 99
df <- data.frame(col1 = c(1:3, 99), col2 = c(2.5, 4.2, 99, 3.2))

# change 99s to NAs
df[df == 99] <- NA
df
##   col1 col2
## 1    1  2.5
## 2    2  4.2
## 3    3   NA
## 4   NA  3.2

If we want to recode missing values in a single data frame variable we can subset for the missing value in that specific variable of interest and then assign it the replacement value. For example, here we recode the missing value in col4 with the mean value of col4.

# data frame with missing data
df <- data.frame(col1 = c(1:3, NA),
                 col2 = c("this", NA,"is", "text"), 
                 col3 = c(TRUE, FALSE, TRUE, TRUE), 
                 col4 = c(2.5, 4.2, 3.2, NA),
                 stringsAsFactors = FALSE)
                 
df$col4[is.na(df$col4)] <- mean(df$col4, na.rm = TRUE)
df
##   col1 col2  col3 col4
## 1    1 this  TRUE  2.5
## 2    2 <NA> FALSE  4.2
## 3    3   is  TRUE  3.2
## 4   NA text  TRUE  3.3

Exclude missing values

We can exclude missing values in a couple different ways. First, if we want to exclude missing values from mathematical operations use the na.rm = TRUEargument. If you do not exclude these values most functions will return an NA.

# A vector with missing values
x <- c(1:4, NA, 6:7, NA)

# including NA values will produce an NA output
mean(x)
## [1] NA

# excluding NA values will calculate the mathematical operation for all non-missing values
mean(x, na.rm = TRUE)
## [1] 3.833333

We may also desire to subset our data to obtain complete observations, those observations (rows) in our data that contain no missing data. We can do this a few different ways.

# data frame with missing values
df <- data.frame(col1 = c(1:3, NA),
                 col2 = c("this", NA,"is", "text"), 
                 col3 = c(TRUE, FALSE, TRUE, TRUE), 
                 col4 = c(2.5, 4.2, 3.2, NA),
                 stringsAsFactors = FALSE)

df
##   col1 col2  col3 col4
## 1    1 this  TRUE  2.5
## 2    2 <NA> FALSE  4.2
## 3    3   is  TRUE  3.2
## 4   NA text  TRUE   NA

First, to find complete cases we can leverage the complete.cases() function which returns a logical vector identifying rows which are complete cases. So in the following case rows 1 and 3 are complete cases. We can use this information to subset our data frame which will return the rows which complete.cases()found to be TRUE.

complete.cases(df)
## [1]  TRUE FALSE  TRUE FALSE

# subset with complete.cases to get complete cases
df[complete.cases(df), ]
##   col1 col2 col3 col4
## 1    1 this TRUE  2.5
## 3    3   is TRUE  3.2

# or subset with `!` operator to get incomplete cases
df[!complete.cases(df), ]
##   col1 col2  col3 col4
## 2    2 <NA> FALSE  4.2
## 4   NA text  TRUE   NA

An shorthand alternative is to simply use na.omit() to omit all rows containing missing values.

# or use na.omit() to get same as above
na.omit(df)
##   col1 col2 col3 col4
## 1    1 this TRUE  2.5
## 3    3   is TRUE  3.2

Exercises

  1. How many missing values are in the built-in data set airquality?
  2. Which variables are the missing values concentrated in?
  3. How would you impute the mean or median for these values?
  4. How would you omit all rows containing missing values?
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