How to Calculate Partial Correlation in R

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Partial correlation is a statistical measure used to quantify the degree of association between two variables, while controlling for the effect of one or more additional variables. In other words, it helps in understanding the relationship between two variables when the influence of other variables is removed. In this comprehensive guide, we will explore how to calculate partial correlation in R, how to interpret the results, and understand its applications and limitations.

Understanding Partial Correlation

In many practical scenarios, the relationship between two variables might be influenced by one or more additional variables. Partial correlation helps to isolate and assess the relationship between two variables while controlling for other variables.

For instance, let’s say we want to assess the relationship between academic performance and time spent studying, while controlling for intelligence. Partial correlation will give us insight into how academic performance and study time are related when the effect of intelligence is removed.

Calculating Partial Correlation in R

Step 1: Installing and Loading Necessary Packages

R does not have a built-in function for calculating partial correlations, so you will need to install and load an external package. The ppcor package is commonly used for this purpose.

Install the package.


Load the package.


Step 2: Importing and Preparing Your Data

Assuming your dataset is in a CSV file named “data.csv”, use the read.csv() function to import it.

data <- read.csv("path_to_your_file/data.csv")

View the first few rows of your data.


Step 3: Calculating Partial Correlation

Use the pcor() function from the ppcor package to calculate the partial correlation between two variables while controlling for other variables. For instance, if you want to calculate the partial correlation between variables “X” and “Y”, while controlling for variables “A” and “B”.

result <- pcor(cbind(data$X, data$Y, data$A, data$B))

Step 4: Viewing and Understanding the Results

Print the result object to view the partial correlation.


This will show you the partial correlation coefficient, the test statistic, and the p-value.

Visualizing Partial Correlation

Although there aren’t standard plots designed specifically for partial correlations, scatter plots can still provide some insights. One way to do this is by plotting the residuals of the variables involved after removing the effect of the control variables. This is rather advanced and may require a good understanding of linear regression. Here’s how you might do it.

model_X <- lm(X ~ A + B, data=data)
model_Y <- lm(Y ~ A + B, data=data)

residuals_X <- residuals(model_X)
residuals_Y <- residuals(model_Y)

plot(residuals_X, residuals_Y, main="Partial Correlation Residuals Plot",
     xlab="Residuals X", ylab="Residuals Y", pch=19)

Interpreting the Results

Like Pearson’s correlation, the partial correlation coefficient ranges from -1 to 1:

  • A coefficient close to 1 indicates a strong positive relationship.
  • A coefficient close to -1 indicates a strong negative relationship.
  • A coefficient close to 0 indicates a weak or no relationship.

The p-value is also critical; a small p-value (typically, less than 0.05) indicates that the partial correlation is statistically significant.

Applications and Limitations

Partial correlation is especially useful in fields such as economics, psychology, and social sciences, where it is important to control for confounding variables. However, it has some limitations:

  • It only captures linear relationships.
  • It requires that the control variables are relevant in explaining the association.
  • It doesn’t imply causation.


Partial correlation is a powerful statistical tool that helps in isolating the relationship between two variables while controlling for others. In R, this can be achieved using the ppcor package. While interpreting the results, it is crucial to consider the context and limitations of partial correlation. It is an essential technique, especially in multivariate data analysis, for understanding the complex relationships among variables.

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