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.
In this tutorial, you will learn
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, ...) arguments: -df: Data frame used to create a new variable -name_variable_1: Name and the formula to create the new variable -...: No limit constraint. Possibility to create more than one variable inside mutate()
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 <- "https://raw.githubusercontent.com/thomaspernet/data_csv_r/master/data/titanic_csv.csv" df_titanic <- read.csv(PATH, sep = ",") # Return the column names containing missing observations list_na <- colnames(df_titanic)[ apply(df_titanic, 2, anyNA) ] list_na
##  "age" "fare"
colnames(df_titanic)[apply(df_titanic, 2, anyNA)]
Gives the name of columns that do not have data.
The columns age and fare have missing values.
We can drop them with the na.omit().
library(dplyr) # Exclude the missing observations df_titanic_drop <-df_titanic %>% na.omit() dim(df_titanic_drop)
##  1045 13
The new dataset contains 1045 rows compared to 1309 with the original dataset.
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.
We will use the apply method to compute the mean of the column with NA. Let's see an example
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], 2, mean, na.rm = TRUE) average_missing
We pass 4 arguments in the apply method.
- df: df_titanic[,colnames(df_titanic) %in% list_na]. This code will return the columns name from the list_na object (i.e. "age" and "fare")
- 2: Compute the function on the columns
- mean: Compute the mean
- na.rm = TRUE: Ignore the missing values
## age fare ## 29.88113 33.29548
We successfully created the mean of the columns containing missing observations. These two values will be used to replace the missing observations.
Step 3) Replace the NA Values
The verb mutate from the dplyr library is useful in creating a new variable. We don't necessarily want to change the original column so we can create a new variable without the NA. mutate is easy to use, we just choose a variable name and define how to create this variable. Here is the complete code
# Create a new variable with the mean and median df_titanic_replace <- df_titanic %>% mutate(replace_mean_age = ifelse(is.na(age), average_missing, age), replace_mean_fare = ifelse(is.na(fare), average_missing, fare))
We create two variables, replace_mean_age and replace_mean_fare as follow:
- replace_mean_age = ifelse(is.na(age), average_missing, age)
- replace_mean_fare = ifelse(is.na(fare), average_missing,fare)
If the column age has missing values, then replace with the first element of average_missing (mean of age), else keep the original values. Same logic for fare
##  263
Perform the replacement
##  0
The original column age has 263 missing values while the newly created variable have replaced them with the mean of the variable age.
Step 4) We can replace the missing observations with the median as well.
median_missing <- apply(df_titanic[,colnames(df_titanic) %in% list_na], 2, median, na.rm = TRUE) df_titanic_replace <- df_titanic %>% mutate(replace_median_age = ifelse(is.na(age), median_missing, age), replace_median_fare = ifelse(is.na(fare), median_missing, fare)) head(df_titanic_replace)
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.
sapply does not create a data frame, so we can wrap the sapply() function within data.frame() to create a data frame object.
# Quick code to replace missing values with the mean df_titanic_impute_mean < -data.frame( sapply( df_titanic, function(x) ifelse(is.na(x), mean(x, na.rm = TRUE), x)))
We have three methods to deal with missing values:
- Exclude all of the missing observations
- Impute with the mean
- Impute with the median
The following table summarizes how to remove all the missing observations
|base||List missing observations|
colnames(df)[apply(df, 2, anyNA)]
|dplyr||Remove all missing values|
Imputation with mean or median can be done in two ways
- Using apply
- Using sapply
|Step by step with apply||Check columns with missing, compute mean/median, store the value, replace with mutate()||You know the value of means/median||More execution time. Can be slow with big dataset|
|Quick way with sapply||Use sapply() and data.frame() to automatically search and replace missing values with mean/median||Short code and fast||Don't know the imputation values|