Multilevel Regression Models and Simpson’s paradox | by Dorian Drost | Aug, 2023

Avoiding false conclusions with the proper tooling

Data Analysis influences our conclusions, but we should use the proper tooling to take the right path. Photo by Brendan Church on Unsplash

Data Analysis is — as indicated by that profession’s name — an integral part of a Data Scientist’s work, ranging from descriptive statistics and simple regression models to sophisticated machine learning approaches. However, those approaches have to be handled with care, and selecting the right approach is far away from being trivial. Complex data often includes hidden structures that, if not considered appropriately, can lead to fallacies that may end up in invalid conclusions.

In this article, I want to give an example of Simpson’s paradox and show how a simple yet shortsighted analysis can lead to false conclusions that appear to be backed by the data, although they are not more than a misinterpretation. Thereby I demonstrate the usage of multilevel regression models as an appropriate way of data analysis for hierarchical, i.e. nested, data.

The problem

Let’s start already! Say we have published a smartphone app and want to learn more about our users and how satisfied they are. Hence we perform a small survey and ask some of our users to tell us how satisfied they are with our app on a scale from 1 (very unhappy) to 4 (very happy). Additionally, we measured how much time they spent in our app in the last week, and to get a rich sample, we asked users in different countries. Then our data may look like this (I am using generated data for this article):

   Satisfaction  Time_spent  Country
0 2.140440 1.585295 0
1 2.053545 0.636235 0
2 1.589258 1.468033 1
3 1.853545 0.968651 2
4 1.449286 0.967104 2
. . . .
. . . .
. . . .

We are interested in the relationship between the time spent in our app and the reported satisfaction. To be precise, we want to know whether spending more time in our app is associated with more satisfaction or less, and we want to quantify that association, i.e. we want to make a statement like “spending one hour more in our app is associated with being x times more/less satisfied”. When we look at the data, we might have a first intuition already, that more time spent in the app is correlated with lower satisfaction:

Linear regression

Let’s do a linear regression to see if we are right. With linear regression, we try to predict satisfaction given the time spent as a linear function of the form satisfaction = intercept + regression_coefficient * time_spent. We can easily do that with the statsmodels package using the OLS (Ordinary Least Squares) function.

import statsmodels.api as sm
result = sm.OLS(df["Satisfaction"], sm.add_constant(df["Time_spent"])).fit()

The add_constant method is just a technical detail we use to tell the model, that we want to have an intercept in our equation (which is required, as long as our data is not standardized). The result.params gives us two values, namely the intercept (const) and the regression_coefficient for the variable Time_spent.

const         3.229412
Time_spent -0.655470

That is, our model tells us, that satisfaction can be predicted as 3.229 –0.655*time_spent. In other words, one hour more time spent in the app leads to a decrease of 0.655 points in satisfaction (because of the minus sign). However, one doesn’t start from zero, but the mean satisfaction of a person just from their first impression (i.e. time_spent=0) is 3.229. We can also make that visible as a line with intercept 3.229 and slope -0.665:

Of course, this prediction is not perfect, but at least it gives us a trend. Okay, so the case is clear, right? Spending more time in the app leads to a decrease in satisfaction, and we can even quantify that decrease. We could now draw our conclusions from that and think about how to improve the app (we want our users to be more satisfied as they use the app more, of course), or do a more detailed survey to find out why the users are not satisfied.

Well, not so fast!

Grouping per country

Remember, that we collected data from users in different countries? What happens, if we take a look at the data separated by country? In the following plot, we see the very same data points as before, but now we highlighted each country in a different color.

There are two observations we can make from that plot. First, the countries seem to differ in their satisfaction and their time spent in the app. The subjects from the blue country spend more time in the app but are less satisfied than subjects from the other countries, on average. Even more, when we take a look at the three countries in separation, we might think that the association between time spent in the app and satisfaction is indeed positive. Isn’t that contradicting our previous analysis?

Simpson’s paradox

Well, it is actually not named after those Simpsons…Photo by Stefan Grage on Unsplash

The effect we just saw is called Simpson’s paradox. It occurs when a correlation in data is different across groups vs. within groups. While being very counterintuitive, this can happen indeed (as we just saw), and the reason for that is confounding variables. Let’s explain that with our example above. When looking at each country in isolation, we see a positive trend: more time spent in the app is associated with higher satisfaction. However, as we already saw, the countries differ in their mean satisfaction and time spent in the app. In the blue country, the mean satisfaction is lower but the mean time spent in the app is higher than in the orange or green country; a trend that is opposing the trend within the countries. However, there may be another variable causing this. E.g. one could imagine, that in the blue country, more people are bored more often, leading to less satisfaction in general (and hence less positive mood towards our app) but more time to spend in the app. Of course, that is just one possible explanation and there can be many others. However, the correct explanation doesn’t matter too much at the moment. For us, it is important to understand, that there are systematic differences between the countries.

So, why didn’t we find that out in our previous analysis? Did we do a mistake when performing the linear regression? Well, yes, as it was wrong to perform a linear regression at all because one of the core assumptions of the linear regression was violated: A linear regression assumes, that all data points are sampled independently and from the same distribution. That is not the case in our example, though! Obviously, the distributions of time spent in the app and satisfaction are different across the different countries. Now, if the assumptions of linear regression are violated, linear regression is not the right tool for data analysis.

Hierarchical models

What can we do now, to analyze our data in a more appropriate way? Luckily, statistical models are available that extend the idea of linear regression to hierarchical data. We speak of hierarchical data if the data points we sampled are nested in a hierarchical structure, like in our case, where the people we asked are nested in the countries. Those statistical models are called hierarchical linear models, multilevel models, or linear mixed effect models. Such models account for the group structures by introducing so-called fixed effects and random effects. In a simple example, where we want to predict one variable given a single other variable (as we want to predict satisfaction given the time spent in the app), the fixed effects consist of one intercept and one slope for all groups together. So far that is the very same as in the linear regression.

Now the random effects can introduce a deviation from that intercept for each group separately. For example, the intercept for the blue country may be a little lower and the intercept for the green country may be a little higher than the fixed intercept. That would account for the differences in the countries’ mean levels of satisfaction.

Additionally, the random effects can introduce a deviation of the slope for each group. For example, in the orange group, the slope may be higher than the fixed slope (i.e. the association between satisfaction and time spent is stronger), and in the green country, it may be lower.

Hierarchical models in action

Let’s see that in action to understand what really happens. We conduct a new analysis, but now we use statsmodels’ mixedlm function. We clarify that we want to predict satisfaction given the time_spent (and not vice versa) by the formula “Satisfaction ~ Time_spent” and we indicate that the “Country” column of our dataframe is determining the different groups. Additionally, the parameter re_formula=”Time_spent” tells the model that we want to have a separate slope for each group. Without that, the random effects would consider a group-specific intercept only, but not a group-specific slope.

import statsmodels.formula.api as smf

result = smf.mixedlm("Satisfaction ~ Time_spent", data=df, groups=df["Country"], re_formula="Time_spent").fit()

If we print the fixed_effects (fe_params) and the random_effects, we get values like these:

Fixed effects
Intercept 2.286638
Time_spent 0.497657
Random Effects
{0: Group -0.958805, Time_spent -0.018178,
1: Group 0.155233, Time_spent 0.274222,
2: Group 0.803572, Time_spent -0.256044}

So, what does that mean? For the fixed effects, we have one value for the intercept and one value for our variable time_spent. For the random effects, however, we have two values per country (0,1,2): one for the intercept (Group), and one for the slope of our variable (Time_spent). As we saw above, the random effects describe the deviation from the mean effects for each group. For our three groups, we can construct three different linear equations by adding the random effects to the fixed effects for the intercept and the slope each.

satisfaction_0 = (2.286638 - 0.958805) + (0.497657 - 0.018178) * time_spent = 1.327833 + 0.479479 * time_spent
satisfaction_1 = (2.286638 + 0.155233) + (0.497657 + 0.274222) * time_spent = 2.441871 + 0.771879 * time_spent
satisfaction_2 = (2.286638 + 0.803572) + (0.497657 - 0.256044) * time_spent = 3.090210 + 0.241613 * time_spent

We see that the random intercept for group 0 is negative (-0.958) and the random intercept for group 2 is positive (0.803), so group 0 is below the fixed intercept, and group 2 is above. Consequently, group 0 has the lowest intercept in its linear function (1.327) and group 2 has the highest (3.090). In other words, in country 0, satisfaction starts at a lower level than in country 2.

We also see that the slopes differ between the groups. In group 1, the slope is highest with 0.771, while for group 2 it is only 0.241. That means the association between satisfaction and time spent in the app is much higher in country 1 than in country 2. In other words, in country 1 an increase of one hour of time spent in the app leads to 0.771 points more in satisfaction (in the mean), while for country 2 it only adds another 0.241 points in satisfaction. In addition, all slopes are positive, which we expected from the plot above, but which is contradicting the negative slope of the linear regression we did at the beginning.

We can plot one regression line for each country now:

Now we clearly see the positive trend in each country and the different intercepts (i.e. the positions where the lines would be at time_spent=0).


In the above example, we saw how a short-sighted analysis can easily lead us to false conclusions. Ignoring the nested structure of the data, i.e. users coming from different countries, we could have easily stopped after the linear regression and would have concluded, that more time spent in the app was associated with lower satisfaction. Only by understanding that our data is not fulfilling the core assumptions of linear regression, as the data points are not sampled from the same distribution, we were motivated to do further analyses that revealed, that indeed the opposite is the case: More time spent in the app is indeed associated with higher satisfaction.

So, let’s formulate some takeaways from this example:

  • Before using a statistical method for analysis, its assumptions should be validated with the data.
  • For nested data, the assumption that all data points are sampled from the same distribution may not always be the case.
  • It can happen, that a trend in the data overall is different from a trend inside single groups that form that data altogether. This is called Simpson’s paradox.
  • Multilevel linear models are one way to cope with nested data structures and avoid false conclusions from Simpson’s paradox.

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