# Introduction: Adding Partial Residuals to Marginal Effects Plots

#### Daniel Lüdecke

#### 2023-11-29

Source:`vignettes/introduction_partial_residuals.Rmd`

`introduction_partial_residuals.Rmd`

Plotting partial residuals on top of the estimated marginal means
allows detecting missed modeling, like unmodeled non-linear
relationships or unmodeled interactions. In a nutshell, it allows
*Visualizing Fit and Lack of Fit in Complex Regression Models with
Predictor Effect Plots and Partial Residuals* (Fox & Weisberg
2018).

To add partial residuals to a plot, add
`show_residuals = TRUE`

to the `plot()`

function
call. Unlike plotting raw data, partial residuals are much better in
detecting spurious patterns of relationships between predictors and
outcome.

### Detecting non-linear relationship

Let’s look at an example with a non-linear relationship. The missed pattern is not obvious when looking at the raw data:

```
library(ggeffects)
set.seed(1234)
x <- rnorm(200)
z <- rnorm(200)
# quadratic relationship
y <- 2 * x + x^2 + 4 * z + rnorm(200)
d <- data.frame(x, y, z)
m <- lm(y ~ x + z, data = d)
pr <- ggpredict(m, "x [all]")
plot(pr, show_data = TRUE)
```

However, it becomes more obvious with partial residuals:

`plot(pr, show_residuals = TRUE)`

It is even more obvious, when a local polynomial regression line
(loess) is added to the plot. This can be achieved using
`show_residuals_line = TRUE`

.

`plot(pr, show_residuals = TRUE, show_residuals_line = TRUE)`

### Detecting missed interactions

Here is another example, which shows that the partial residuals plot suggests modeling an interaction:

```
set.seed(1234)
x <- rnorm(300, mean = 10)
z <- rnorm(300)
v <- rnorm(300)
y <- (4 * z + 2) * x - 40 * z + 5 * v + rnorm(300, sd = 3)
d <- data.frame(x, y, z)
m <- lm(y ~ x + z, data = d)
pr <- ggpredict(m, c("x", "z"))
# raw data, no interaction
plot(pr, show_data = TRUE)
```

Again, it is recommended to add a loess-fit line to the residuals:

`plot(pr, show_residuals = TRUE, grid = TRUE, show_residuals_line = TRUE)`

Modeling the interaction clearly catches the pattern in the data better.

### Using the complete range of values

*ggeffects* usually “prettyfies” the data and tries to find a
pretty sequence over a range of a focal predictor, to avoid too lengthy
output, particularly for continuous variables (see section *pretty
value ranges* in this
vignette).

This, however, might be misleading in some cases when creating residual plots. In the next example, we have a sinus-curve pattern for the residuals, which is hidden by default:

```
set.seed(1234)
x <- seq(-100, 100, length.out = 1e3)
z <- rnorm(1e3)
y <- 5 * sin(x / 2) + x / 2 + 10 * z
m <- lm(y ~ x + z)
pr <- ggpredict(m, "x")
plot(pr, residuals = TRUE)
```

In such cases, it is recommended to use the `all`

-tag in
the `terms`

-argument.

## References

Fox J, Weisberg S. *Visualizing Fit and Lack of Fit in Complex
Regression Models with Predictor Effect Plots and Partial
Residuals*. Journal of Statistical Software 2018;87. https://www.jstatsoft.org/article/view/v087i09