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How to Replace Missing Values(NA) in R: na.omit & na.rm

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Missing values in data science arise when an observation is missing in a column of a data frame or contains a character value instead of numeric value. Missing values must be dropped or replaced in order to draw correct conclusion from the data.

In this tutorial, we will learn how to deal with missing values with the dplyr library. dplyr library is part of an ecosystem to realize a data analysis


The fourth verb in the dplyr library is helpful to create new variable or change the values of an existing variable.

We will proceed in two parts. We will learn how to:

  • exclude missing values from a data frame
  • impute missing values with the mean and median

The verb mutate() is very easy to use. We can create a new variable following this syntax:

mutate(df, name_variable_1 = condition, ...)

Exclude Missing Values (NA)

The na.omit() method from the dplyr library is a simple way to exclude missing observation. Dropping all the NA from the data is easy but it does not mean it is the most elegant solution. During analysis, it is wise to use variety of methods to deal with missing values

To tackle the problem of missing observations, we will use the titanic dataset. In this dataset, we have access to the information of the passengers on board during the tragedy. This dataset has many NA that need to be taken care of.

We will upload the csv file from the internet and then check which columns have NA. To return the columns with missing data, we can use the following code:

Let's upload the data and verify the missing data.

PATH <- ""
df_titanic <- read.csv(PATH, sep = ",")
# Return the column names containing missing observations
list_na <- colnames(df_titanic)[ apply(df_titanic, 2, anyNA) ]

Impute Missing data with the Mean and Median

We could also impute(populate) missing values with the median or the mean. A good practice is to create two separate variables for the mean and the median. Once created, we can replace the missing values with the newly formed variables.

Step 1) Earlier in the tutorial, we stored the columns name with the missing values in the list called list_na. We will use this list

Step 2) Now we need to compute of the mean with the argument na.rm = TRUE. This argument is compulsory because the columns have missing data, and this tells R to ignore them.

# Create mean
average_missing <- apply(df_titanic[,colnames(df_titanic) %in% list_na],
      na.rm =  TRUE)
Step 3) Replace the NA Values
Step 4) We can replace the missing observations with the median as well.
Step 5) A big data set could have lots of missing values and the above method could be cumbersome. We can execute all the above steps above in one line of code using sapply() method. Though we would not know the vales of mean and median.
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