How to Conduct an ANCOVA in R

How to conduct an ANCOVA in R

This tutorial explains how to conduct an ANCOVA (analysis of covariance) in R.

What is an ANCOVA?

To understand the ANCOVA, it first helps to understand the ANOVA.

An ANOVA (analysis of variance) is used to determine whether or not there is a statistically significant difference between the means of three or more independent groups. 

For example, suppose we want to know whether or not studying technique has an impact on exam scores for a class of students. We randomly split the class into three groups. Each group uses a different studying technique for one month to prepare for an exam. At the end of the month, all of the students take the same exam.

To find out if studying technique impacts exam scores, we can conduct a one-way ANOVA, which will tell us if if there is a statistically significant difference between the mean scores of the three groups.

One way ANOVA example

An ANCOVA (“Analysis of Covariance”) is also used to determine whether or not there is a statistically significant difference between the means of three or more independent groups. Unlike an ANOVA, however, an ANCOVA includes one or more covariates, which can help us better understand how a factor impacts a response variable after accounting for some covariate(s).

For example, suppose we want to know whether or not studying technique has an impact on exam scores, but we want to account for the grade that the student already has in the class so we use their current grade as a covariate and conduct an ANCOVA to determine if there is a statistically significant difference between the mean scores of the three groups.

This allows us to test whether or not studying technique has an impact on exam scores after the influence of the covariate has been removed. Thus, if we find that there is a statistically significant difference in exam scores between the three studying techniques, we can be sure that this difference exists even after accounting for the students current grade in the class (i.e. if they’re already doing well or not in the class).

Example of ANCOVA

Related: Understanding the Differences Between ANOVA, ANCOVA, MANOVA, and MANCOVA

How to Conduct an ANCOVA in R

We will conduct an ANCOVA to test whether or not studying technique has an impact on exam scores by using the following variables:

  • Studying technique: The independent variable we are interested in analyzing
  • Student’s current grade: The covariate that we want to take into account
  • Exam score: The response variables we are interested in analyzing

The following dataset contains information for 90 students that were randomly split into three groups of 30. The dataset shows the studying technique each student used (A, B, or C), their current grade in the class when they started using the studying technique, and their exam score they received after using the studying technique for one month to prepare for the exam:

#make this example reproducible 
set.seed(10)

#create dataset
data <- data.frame(technique = rep(c("A", "B", "C"), each = 30),
                   current_grade = runif(90, 65, 95),
                   exam = c(runif(30, 80, 95), runif(30, 70, 95), runif(30, 70, 90)))

#view first six lines of dataset
head(data)

#  technique current_grade     exam
#1         A      80.22435 87.32759
#2         A      74.20306 90.67114
#3         A      77.80723 88.87902
#4         A      85.79306 87.75735
#5         A      67.55408 85.72442
#6         A      71.76310 92.52167

Step 1: Explore the Data

Before we fit the ANCOVA model, we should first explore the data to gain a better understanding of it and verify that there aren’t any extreme outliers that could skew the results.

First, we can view a summary of each variable in the dataset:

summary(data)

# technique current_grade        exam      
# A:30      Min.   :65.43   Min.   :71.17  
# B:30      1st Qu.:71.79   1st Qu.:77.27  
# C:30      Median :77.84   Median :84.69  
#           Mean   :78.15   Mean   :83.38  
#           3rd Qu.:83.65   3rd Qu.:89.22  
#           Max.   :93.84   Max.   :94.76  

We can see that each value for studying technique (A, B, and C) shows up 30 times in the data.

We can also see how the current student scores were distributed at the beginning of the study. The minimum score in the class was 65.43, the max was 93.84, and the mean was 78.15.

Likewise, we can see that the minimum score received on the exam was 71.17, the max was 94.76, and the mean was 83.38.

Next, we can use the dplyr package to easily find the mean and the standard deviation of both the current grades and the exam scores for each studying technique:

#load dplyr
library(dplyr)

data %>%
  group_by(technique) %>%
  summarise(mean_grade = mean(current_grade),
            sd_grade = sd(current_grade),
            mean_exam = mean(exam),
            sd_exam = sd(exam))

# A tibble: 3 x 5
#  technique mean_grade sd_grade mean_exam sd_exam                      
#1 A               79.0     7.00      88.5    3.88
#2 B               78.5     8.33      81.8    7.62
#3 C               76.9     8.24      79.9    5.71

We can see that the mean and the standard deviations of the current grade for the students using each studying technique is roughly similar. 

We can also see that the mean exam score is noticeably higher for the students who used studying technique A compared to techniques and C.

We can also visualize the distribution of exam scores based on studying technique by using boxplots:

boxplot(exam ~ technique,
data = data,
main = "Exam Score by Studying Technique",
xlab = "Studying Technique",
ylab = "Exam Score",
col = "steelblue",
border = "black"
)

Checking ANCOVA Assumptions with boxplots

Similarly, we can also use boxplots to visualize the distribution of current grades based on studying technique:

boxplot(current_grade ~ technique,
data = data,
main = "Current Grade by Studying Technique",
xlab = "Studying Technique",
ylab = "Current Grade",
col = "steelblue",
border = "black"
)

Distribution using boxplots in R

Step 2: Check the Model Assumptions

Once we’ve done some basic data exploration and are familiar with the data, we need to verify that the following assumptions for ANCOVA are met:

  • The covariate and the treatment are independent – we need to verify that the covariate (current grade) and the treatment (studying technique) are independent of each other, since adding a covariate term into the model only makes sense if the covariate and the treatment act independently on the response variable (exam). 
  • Homogeneity of variance – we need to verify that the variances among the groups is equal

To verify that the covariate and the treatment are independent, we can run an ANOVA using current grade as the response variable and studying technique as the predictor variable:

#fit anova model
anova_model <- aov(current_grade ~ technique, data = data)
#view summary of anova model
summary(anova_model)

#            Df Sum Sq Mean Sq F value Pr(>F)
#technique    2     74   37.21   0.599  0.552
#Residuals   87   5406   62.14    

The p-value is greater than 0.05, so the covariate (current grade) and the treatment (studying technique) seem to be independent.

Next, to verify that there is homogeneity of variance among the groups, we can conduct Levene’s Test:

#load car library to conduct Levene's Test
libary(car)

#conduct Levene's Test
leveneTest(exam~technique, data = data)

#Levene's Test for Homogeneity of Variance (center = median)
#      Df F value    Pr(>F)    
#group  2  9.4324 0.0001961 ***
#      87   

The p-value from the test is equal to .0001961, which indicates that the variances among the groups are not equal. Although we could attempt a transformation on the data to correct this problem, we won’t worry too much about the differences in variance for the time being.

Step 3: Fit the ANCOVA Model

Next, we’ll fit the ANCOVA model using exam score as the response variable, studying technique as the predictor (or “treatment”) variable, and current grade as the covariate.

We’ll use the Anova() function in the car package to do so, just so we can specify that we’d like to use type III sum of squares for the model, since type I sum of squares is dependent upon the order that the predictors are entered into the model:

#load car library
library(car)

#fit ANCOVA model
ancova_model <- aov(exam ~ technique + current_grade, data = data)

#view summary of model
Anova(ancova_model, type="III") 

#Response: exam
#              Sum Sq Df  F value    Pr(>F)    
#(Intercept)   7161.2  1 201.4621 < 2.2e-16 ***
#technique     1242.9  2  17.4830 4.255e-07 ***
#current_grade   12.3  1   0.3467    0.5576    
#Residuals     3057.0 86         

We can see that the p-value for technique is extremely small, which indicates that studying technique has a statistically significant effect on exam scores, even after controlling for the current grade.

Step 4: Post Hoc Tests

Although the ANCOVA results told us that studying technique had a statistically significant effect on exam scores, we need to run post hoc tests to actually find out which studying techniques differ from each other.

To do so, we can use the glht() function within the multcomp package in R to perform Tukey’s Test for multiple comparisons:

#load the multcomp library
library(multcomp)

#fit the ANCOVA model
ancova_model <- aov(exam ~ technique + current_grade, data = data)

#define the post hoc comparisons to make
postHocs <- glht(ancova_model, linfct = mcp(technique = "Tukey"))

#view a summary of the post hoc comparisons
summary(postHocs)

#Multiple Comparisons of Means: Tukey Contrasts
#
#Fit: aov(formula = exam ~ technique + current_grade, data = data)
#
#Linear Hypotheses:
#           Estimate Std. Error t value Pr(>|t|)    
#B - A == 0   -6.711      1.540  -4.358 0.000109 ***
#C - A == 0   -8.736      1.549  -5.640  < 1e-04 ***
#C - B == 0   -2.025      1.545  -1.311 0.393089    

#view the confidence intervals associated with the multiple comparisons
confint(postHocs)

#	 Simultaneous Confidence Intervals
#
#Multiple Comparisons of Means: Tukey Contrasts
#
#Fit: aov(formula = exam ~ technique + current_grade, data = data)
#
#Quantile = 2.3845
#95% family-wise confidence level
#
#Linear Hypotheses:
#           Estimate lwr      upr     
#B - A == 0  -6.7112 -10.3832  -3.0392
#C - A == 0  -8.7364 -12.4302  -5.0426
#C - B == 0  -2.0252  -5.7091   1.6588

From the output, we can see that there is a statistically significant difference (at α = .05) in exam scores between studying technique A and studying technique B (p-value: .000109) as well as between technique A and technique C (p-value: <1e-04).

We can also see that there is not a statistically significant difference (at α = .05) between techniques B and CThe confidence intervals between the techniques confirm these conclusions as well.

Thus, we can conclude that using studying technique leads to a statistically significantly greater exam score for students compared to techniques and C, even after controlling for the student’s current grade in the class.

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