When using classification models in machine learning, a common metric that we use to assess the quality of the model is the F1 Score.
This metric is calculated as:
F1 Score = 2 * (Precision * Recall) / (Precision + Recall)
- Precision: Correct positive predictions relative to total positive predictions
- Recall: Correct positive predictions relative to total actual positives
For example, suppose we use a logistic regression model to predict whether or not 400 different college basketball players get drafted into the NBA.
The following confusion matrix summarizes the predictions made by the model:
Here is how to calculate the F1 score of the model:
Precision = True Positive / (True Positive + False Positive) = 120/ (120+70) = .63157
Recall = True Positive / (True Positive + False Negative) = 120 / (120+40) = .75
F1 Score = 2 * (.63157 * .75) / (.63157 + .75) = .6857
The following example shows how to calculate the F1 score for this exact model in R.
Example: Calculating F1 Score in R
The following code shows how to use the confusionMatrix() function from the caret package in R to calculate the F1 score (and other metrics) for a given logistic regression model:
library(caret) #define vectors of actual values and predicted values actual <- factor(rep(c(1, 0), times=c(160, 240))) pred <- factor(rep(c(1, 0, 1, 0), times=c(120, 40, 70, 170))) #create confusion matrix and calculate metrics related to confusion matrix confusionMatrix(pred, actual, mode = "everything", positive="1") Reference Prediction 0 1 0 170 40 1 70 120 Accuracy : 0.725 95% CI : (0.6784, 0.7682) No Information Rate : 0.6 P-Value [Acc > NIR] : 1.176e-07 Kappa : 0.4444 Mcnemar's Test P-Value : 0.005692 Sensitivity : 0.7500 Specificity : 0.7083 Pos Pred Value : 0.6316 Neg Pred Value : 0.8095 Precision : 0.6316 Recall : 0.7500 F1 : 0.6857 Prevalence : 0.4000 Detection Rate : 0.3000 Detection Prevalence : 0.4750 Balanced Accuracy : 0.7292 'Positive' Class : 1
We can see that the F1 score is 0.6857. This matches the value that we calculated earlier by hand.
Note: We must specify mode = “everything” in order to get the F1 score to be displayed in the output.
If you use F1 score to compare several models, the model with the highest F1 score represents the model that is best able to classify observations into classes.
For example, if you fit another logistic regression model to the data and that model has an F1 score of 0.85, that model would be considered better since it has a higher F1 score.
How to Perform Logistic Regression in R
F1 Score vs. Accuracy: Which Should You Use?