The Difference Between Link Functions and

Data Transformations
by Kim Love 1 Comment

Generalized linear models—and generalized linear mixed models—are

called generalized linear because they connect a model’s outcome to its
predictors in a linear way. The function used to make this connection is called
a link function. Link functions sounds like an exotic term, but they’re actually
much simpler than they sound.

For example, Poisson regression (commonly used for outcomes that are

counts) makes use of a natural log link function as follows:

Clearly, there is not a direct linear relationship of the x variables to the

average count, but there is a “sort of linear” relationship happening: a function
of the mean of y is related to a linear combination of x variables. In other
words, the linear model has now been generalized to a bigger type of
situation.

This can lead to confusion, though, because on the surface it looks very
similar to what happens when we transform the dependent variable in a linear
model, like a linear regression.

The key thing to understand is that the natural log link function is a function of
the mean of y, not the y values themselves.

Transformations of Y
Below is a linear model equation where the original dependent variable, y, has
been natural log transformed. That is, the natural log has been taken of each
individual value of y, and that is being used as the dependent variable.
The linear model with the log transformation is providing an equation for an
individual value of ln(y). We could also write it as follows, where we are
modeling the mean of ln(y) (note the error term is no longer present):

This makes the difference a bit clearer. When we transform the data in a
linear model, we are no longer claiming that y is normally distributed around a
mean, given the x values — we are claiming that our new outcome variable,
ln(yi), is normally distributed.

In fact, we often make this transformation specifically because the values of y

do not appear to be normally distributed around their average.

In the case of the Poisson model, however, the link function does not change
the distribution of the actual observations in some way to make them
something other than Poisson distributed. Instead, the link function defines the
relationship of the x variables directly to the mean of the Poisson distributed y.
The individual observations then vary around this expected value accordingly.

The mean of the log is not the log of the mean

As you may know, if you have used this kind of data transformation in a linear
model before, you cannot simply take the exponent of the mean of ln(y) to get
the mean of y.

You might be surprised to know, though, that you can do this with a link
function. If you have specific values of your x variables, you can calculate the
predicted average count, μy based on those x values by inversing the natural
log:
This ability to back-transform means (and regression coefficients) to a more
intuitive scale is part of what makes generalized linear models so useful.