How to Fix: Invalid factor level, NA generated in R

In this article, we will be looking at the approaches with the examples to fix the error: invalid factor level, NA generated.

Such type of warning message is produced by the compiler when a programmer tries to add a value to a factor variable in R that doesn’t have any existence at the beforehand as a defined level. The complete warning message is given below:

Warning message:
In `[<-.factor`(`*tmp*`, iseq, value = "C") :
  invalid factor level, NA generated 

When error might occur

Let’s create a data frame.

R

# Create a data frame
dataframe < - data.frame(team=factor(c('Alpha', 'Alpha',
                                       'Beta', 'Beta',
                                       'Charlie', 'Charlie',
                                       'Charlie')),
                         points=c(96, 91, 86, 89, 93, 87, 91))

# Display the data frame
dataframe

# Display the structure of the data frame
str(dataframe)

Output:

In this example, the team variable has the three types of values only: “Alpha”, “Beta”, “Charlie”. Now, we will try to insert an additional row at the end of the data frame having the team name equal to “Gamma”.

Example:

R

# Create a data frame
dataframe <- data.frame(team=factor(c('Alpha', 'Alpha',
                                      'Beta', 'Beta',
                                      'Charlie', 'Charlie',
                                      'Charlie')),
                 points=c(96, 91, 86, 89, 93, 87, 91))

#add new row to end of data frame
dataframe[nrow(dataframe) + 1,] = c('Gamma', 99)

Output:

Output

The compiler produces the warning message. This is because the value “Gamma” is not already present under the team column. Note that it is just a warning message and the compiler will automatically insert a new row at the end of the data frame but instead of “Gamma” the cell would have the value equal to NA.

R

# Create a data frame
dataframe <- data.frame(team=factor(c('Alpha', 'Alpha',
                                      'Beta', 'Beta',
                                      'Charlie', 'Charlie',
                                      'Charlie')),
                 points=c(96, 91, 86, 89, 93, 87, 91))

# add new row to end of data frame
dataframe[nrow(dataframe) + 1,] = c('Gamma', 99)

# Display the dataframe
dataframe

Output:

How the warning can be avoided:

We can get rid of this warning by firstly transforming the factor variable to a character variable and then we can transform it again to a factor variable just after adding the additional row.

Example:

R

# Create a data frame
dataframe <- data.frame(team=factor(c('Alpha', 'Alpha',
                                      'Beta', 'Beta',
                                      'Charlie', 'Charlie',
                                      'Charlie')),
                 points=c(96, 91, 86, 89, 93, 87, 91))

# Convert team variable to character
dataframe$team <- as.character(dataframe$team)

# Insert a new row to end of data frame
dataframe[nrow(dataframe) + 1,] = c('Gamma', 99)

# Transform team variable back to factor
dataframe$team <- as.factor(dataframe$team)

# Display the data frame
dataframe

Output:

As you can see in the output, the warning, as well as the “NA” thing, have been eliminated from the dataframe. Now let’s display the structure of the modified dataframe once:

R

# Create a data frame
dataframe <- data.frame(team=factor(c('Alpha', 'Alpha',
                                      'Beta', 'Beta',
                                      'Charlie', 'Charlie',
                                      'Charlie')),
                 points=c(96, 91, 86, 89, 93, 87, 91))

# Convert team variable to character
dataframe$team <- as.character(dataframe$team)

# Insert a new row to end of data frame
dataframe[nrow(dataframe) + 1,] = c('Gamma', 99)

# Transform team variable back to factor
dataframe$team <- as.factor(dataframe$team)

# Display the structure of the data frame
str(dataframe)

Output: