Lesson 3

Mastering ANOVA in R: Analyzing Variance in Grouped Data

Introduction to ANOVA

Welcome, friend! Today, we're learning about the Analysis of Variance or ANOVA. It's a method used to determine if there are significant differences between the means (or averages) of three or more groups. This tool is handy in fields such as biology, manufacturing, and education.

Let's unwrap the mystery of ANOVA together!

What is ANOVA?

ANOVA is like a detective. It solves a mystery: are the means of certain groups equal? It does this by examining how the individual data values deviate from the group means and the grand mean. Just imagine that you have three apples of different types, and you want to know if they weigh the same. ANOVA would be like a scale that helps determine this!

ANOVA makes three assumptions:

  1. Normality: The data from each group follow a normal distribution.
  2. Homogeneity of Variance: Each group has the same variance.
  3. Independence: Each data point is independent of the others.

Today, we’ll study the ANOVA test in R.

One-way ANOVA

Think of the One-way ANOVA as a game in which you're comparing the average scores (means) of several teams (groups). The ultimate goal is to figure out if there is at least one team scoring differently than the others.

The output of the One-way ANOVA test is a value called F-statistic. A simple way to think about the F-statistic is as a signal-to-noise ratio:

  • Signal: The extent to which the group means differ from each other.
  • Noise: The extent to which the group members differ among themselves.

If the teams' scores are all similar, we would have a low signal and a high noise, yielding an F-statistic close to 1.0. However, if the average score of one of the teams is substantially different from the others, the signal increases compared to the noise, resulting in an F-statistic greater than 1.0.

Introducing Apple Dataset

We have gathered weight data for three different types of apples. Now, we are curious if the average weight is the same for each kind of apple. Below is how we would create a sample dataset:

1# Sample weights for 3 different apple types 2data <- data.frame( 3 apple_type = c(rep("Apple1", 5), rep("Apple2", 5), rep("Apple3", 5)), 4 weight = c(162.5, 165.0, 167.5, 160.0, 158.5, 175.0, 177.5, 172.5, 170.0, 160.5, 182.5, 185.0, 180.0, 177.5, 165.5) 5)

Here's our sample data with weights for three types of apples: Apple1, Apple2, and Apple3.

Performing One-way ANOVA

We can now put the data to the test. We will use the One-way ANOVA method to see if these apple types differ in weight:

1# Perform One-way ANOVA 2anova_result <- aov(weight ~ apple_type, data = data) 3 4# Print the ANOVA table 5print(summary(anova_result))

The aov function from the stats package in R is used to fit an ANOVA model.

The summary of the aov function provides the F-value and the P-value (represented as Pr(>F)) in the output ANOVA table. Here is how the output looks like:

1 Df Sum Sq Mean Sq F value Pr(>F) 2apple_type 2 594.5 297.27 7.845 0.00662 ** 3Residuals 12 454.7 37.89 4--- 5Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Take a look at the function's arguments. The data argument is simply our data frame. Let's discuss the first argument in more detail. In the context of the aov (Analysis of Variance) function in R, weight ~ apple_type is a formula that specifies the statistical model to be estimated.

Here, weight is the dependent variable (or response variable), and apple_type is the independent variable (or predictor variable). The tilde (~) operator can be read as "is modeled as a function of".

So weight ~ apple_type implies that the analysis aims to understand how weight varies as a function of apple_type. One-way ANOVA is a type of statistical model used to compare the means of weight for different apple_types.


Let's consider the obtained table's columns:

1 Df Sum Sq Mean Sq F value Pr(>F) 2apple_type 2 594.5 297.27 7.845 0.00662 ** 3Residuals 12 454.7 37.89

Here's a concise explanation of each column in the ANOVA table output from the aov function in R:

  • Df (Degrees of Freedom): Counts the number of levels in the group variable and observations, helping to quantify the sample's size and variability.
  • Sum Sq (Sum of Squares): Total variation attributed to each source – between groups (variation due to the difference in group means) and within groups (variation within each group).
  • Mean Sq (Mean Square): Average variation for each source, calculated by dividing Sum of Squares by the corresponding Degrees of Freedom.
  • F value: Ratio of between-group variance to within-group variance, indicating how strongly the groups differ.
  • Pr(>F) (P-value): Probability of observing the given results (or more extreme) under the null hypothesis. A small value suggests significant differences between group means.

Our One-way ANOVA test yielded two main results: the F-value and the P-value. Let's understand how to interpret them.

The F-value tells us how much the apple types differ in weight compared to how much the weights fluctuate within each apple type. A higher F-value suggests that the differences in group weights are probably not due to random chance.

The P-value (0.0066 in our case) is well below the typical threshold of 0.05, indicating a statistically significant difference. This suggests that the likelihood of getting our observed data if all apple types had the same average weight is very low - only 0.66%.

Given these results, we can confidently reject the hypothesis that all apple types have the same average weight. The average weight of the apple types in our data is significantly different.


This was an exciting journey through the land of ANOVA! We unveiled the mystery of testing group means in R using the nifty tool aov from the stats package!

These lessons become more helpful with practice. So, up next are some fun exercises. You'll get hands-on experience performing One-way ANOVA on real-world datasets. Get ready, set, and code on!

Enjoy this lesson? Now it's time to practice with Cosmo!

Practice is how you turn knowledge into actual skills.