`remotes::install_github("vincentarelbundock/marginaleffects")`

# Machine Learning

`marginaleffects`

offers several “model-agnostic” functions to interpret statistical and machine learning models. This vignette highlights how the package can be used to extract meaningful insights from models trained using the `mlr3`

and `tidymodels`

frameworks.

Make sure to restart `R`

after installation. Then, load a few libraries:

```
library("marginaleffects")
library("fmeffects")
library("ggplot2")
library("mlr3verse")
library("modelsummary")
library("ggokabeito")
library("tidymodels") |> suppressPackageStartupMessages()
theme_set(theme_bw())
options(ggplot2.discrete.colour = palette_okabe_ito())
options(width = 10000)
```

`tidymodels`

`marginaleffects`

also supports the `tidymodels`

machine learning framework. When the underlying engine used by `tidymodels`

to train the model is itself supported as a standalone package by `marginaleffects`

, we can obtain both estimates and their standard errors:

```
library(tidymodels)
penguins <- modeldata::penguins |>
na.omit() |>
select(sex, island, species, bill_length_mm)
mod <- linear_reg(mode = "regression") |>
set_engine("lm") |>
fit(bill_length_mm ~ ., data = penguins)
avg_comparisons(mod, type = "numeric", newdata = penguins)
```

```
Term Contrast Estimate Std. Error z Pr(>|z|) S 2.5 % 97.5 %
island Dream - Biscoe -0.489 0.470 -1.04 0.299 1.7 -1.410 0.433
island Torgersen - Biscoe 0.103 0.488 0.21 0.833 0.3 -0.853 1.059
sex male - female 3.697 0.255 14.51 <0.001 156.0 3.198 4.197
species Chinstrap - Adelie 10.347 0.422 24.54 <0.001 439.4 9.521 11.174
species Gentoo - Adelie 8.546 0.410 20.83 <0.001 317.8 7.742 9.350
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high
Type: numeric
```

`avg_predictions(mod, type = "numeric", newdata = penguins, by = "island")`

```
island Estimate Std. Error z Pr(>|z|) S 2.5 % 97.5 %
Torgersen 39.0 0.339 115 <0.001 Inf 38.4 39.7
Biscoe 45.2 0.182 248 <0.001 Inf 44.9 45.6
Dream 44.2 0.210 211 <0.001 Inf 43.8 44.6
Columns: island, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high
Type: numeric
```

When the underlying engine that `tidymodels`

uses to fit the model is not supported by `marginaleffects`

as a standalone model, we can also obtain correct results, but no uncertainy estimates. Here is a random forest model:

```
library(modelsummary)
# pre-processing
pre <- penguins |>
recipe(sex ~ ., data = _) |>
step_ns(bill_length_mm, deg_free = 4) |>
step_dummy(all_nominal_predictors())
# modelling strategies
models <- list(
"Logit" = logistic_reg(mode = "classification", engine = "glm"),
"Random Forest" = rand_forest(mode = "classification", engine = "ranger"),
"XGBoost" = boost_tree(mode = "classification", engine = "xgboost")
)
# fit to data
fits <- lapply(models, \(x) {
pre |>
workflow(spec = x) |>
fit(penguins)
})
# marginaleffects
cmp <- lapply(fits, avg_comparisons, newdata = penguins, type = "prob")
# summary table
modelsummary(
cmp,
shape = term + contrast + group ~ model,
coef_omit = "sex",
coef_rename = coef_rename)
```

Logit | Random Forest | XGBoost | |||
---|---|---|---|---|---|

Bill Length Mm | +1 | female | -0.101 | -0.080 | -0.098 |

(0.004) | |||||

male | 0.101 | 0.080 | 0.098 | ||

(0.004) | |||||

Island | Dream - Biscoe | female | -0.044 | 0.002 | -0.004 |

(0.069) | |||||

male | 0.044 | -0.002 | 0.004 | ||

(0.069) | |||||

Torgersen - Biscoe | female | 0.015 | -0.057 | 0.008 | |

(0.074) | |||||

male | -0.015 | 0.057 | -0.008 | ||

(0.074) | |||||

Species | Chinstrap - Adelie | female | 0.562 | 0.170 | 0.441 |

(0.036) | |||||

male | -0.562 | -0.170 | -0.441 | ||

(0.036) | |||||

Gentoo - Adelie | female | 0.453 | 0.118 | 0.361 | |

(0.025) | |||||

male | -0.453 | -0.118 | -0.361 | ||

(0.025) | |||||

Num.Obs. | 333 | ||||

AIC | 302.2 | ||||

BIC | 336.4 | ||||

Log.Lik. | -142.082 |

`mlr3`

`mlr3`

is a machine learning framework for `R`

. It makes it possible for users to train a wide range of models, including linear models, random forests, gradient boosting machines, and neural networks.

In this example, we use the `bikes`

dataset supplied by the `fmeffects`

package to train a random forest model predicting the number of bikes rented per hour. We then use `marginaleffects`

to interpret the results of the model.

```
library(mlr3verse)
data("bikes", package = "fmeffects")
task <- as_task_regr(x = bikes, id = "bikes", target = "count")
forest <- lrn("regr.ranger")$train(task)
```

As described in other vignettes, we can use the `avg_comparisons()`

function to compute the average change in predicted outcome that is associated with a change in each feature:

`avg_comparisons(forest, newdata = bikes)`

```
Term Contrast Estimate
count +1 0.0000
holiday False - True 12.3721
humidity +1 -20.3053
month +1 4.1072
season spring - fall -30.3891
season summer - fall -7.9020
season winter - fall 2.9935
temp +1 2.4185
weather misty - clear -8.3007
weather rain - clear -61.1444
weekday Fri - Sun 76.2615
weekday Mon - Sun 84.4357
weekday Sat - Sun 25.9174
weekday Thu - Sun 91.4191
weekday Tue - Sun 90.2726
weekday Wed - Sun 92.5078
windspeed +1 -0.0132
workingday False - True -187.3379
year 1 - 0 98.3355
Columns: term, contrast, estimate
Type: response
```

These results are easy to interpret: An increase of 1 degree Celsius in the temperature is associated with an increase of 2.418 bikes rented per hour.

We could obtain the same result manually as follows:

## Simultaneous changes

With `marginaleffects::avg_comparisons()`

, we can also compute the average effect of a simultaneous change in multiple predictors, using the `variables`

and `cross`

arguments. In this example, we see what happens (on average) to the predicted outcome when the `temp`

, `season`

, and `weather`

predictors all change together:

```
avg_comparisons(
forest,
variables = c("temp", "season", "weather"),
cross = TRUE,
newdata = bikes)
```

```
Estimate C: season C: temp C: weather
-36.44 spring - fall +1 misty - clear
-80.43 spring - fall +1 rain - clear
-14.34 summer - fall +1 misty - clear
-64.89 summer - fall +1 rain - clear
-4.03 winter - fall +1 misty - clear
-58.78 winter - fall +1 rain - clear
Columns: term, contrast_season, contrast_temp, contrast_weather, estimate
Type: response
```

## Partial Dependence Plots

```
# https://stackoverflow.com/questions/67634344/r-partial-dependence-plots-from-workflow
library("tidymodels")
library("marginaleffects")
data(ames, package = "modeldata")
dat <- transform(ames,
Sale_Price = log10(Sale_Price),
Gr_Liv_Area = as.numeric(Gr_Liv_Area))
m <- dat |>
recipe(Sale_Price ~ Gr_Liv_Area + Year_Built + Bldg_Type, data = _) |>
workflow(spec = rand_forest(mode = "regression", trees = 1000, engine = "ranger")) |>
fit(data = dat)
# Percentiles of the x-axis variable
pctiles <- quantile(dat$Gr_Liv_Area, probs = seq(0, 1, length.out = 101))
# Select 1000 profiles at random, otherwise this is very memory-intensive
profiles <- dat[sample(nrow(dat), 1000), ]
# Use a counterfactual grid to replicate the full dataset 101 times. Each time, we
# replace the value of `Gr_Liv_Area` by one of the percentiles, but keep the
# other profile features as observed.
nd <- datagrid(
Gr_Liv_Area = pctiles, newdata = profiles,
grid_type = "counterfactual")
# Partial dependence plot
plot_predictions(m,
newdata = nd,
by = c("Gr_Liv_Area", "Bldg_Type")) +
labs(x = "Living Area", y = "Predicted log10(Sale Price)", color = "Building Type")
```

We can replicate this plot using the `DALEXtra`

package:

```
library("DALEXtra")
pdp_rf <- explain_tidymodels(
m,
data = dplyr::select(dat, -Sale_Price),
y = dat$Sale_Price,
label = "random forest",
verbose = FALSE)
pdp_rf <- model_profile(pdp_rf,
N = 1000,
variables = "Gr_Liv_Area",
groups = "Bldg_Type")
plot(pdp_rf)
```

Note that `marginaleffects`

and `DALEXtra`

plots are not exactly identical because the randomly sampled profiles are not the same. You can try the same procedure without sampling — or equivalently with `N=2930`

— to see a perfect equivalence.

## Other Plots

We can plot the results using the standard `marginaleffects`

helpers. For example, to plot predictions, we can do:

```
library(mlr3verse)
data("bikes", package = "fmeffects")
task <- as_task_regr(x = bikes, id = "bikes", target = "count")
forest <- lrn("regr.ranger")$train(task)
plot_predictions(forest, condition = "temp", newdata = bikes)
```

As documented in `?plot_predictions`

, using `condition="temp"`

is equivalent to creating an equally-spaced grid of `temp`

values, and holding all other predictors at their means or modes. In other words, it is equivalent to:

Alternatively, we could plot “marginal” predictions, where replicate the full dataset once for every value of `temp`

, and then average the predicted values over each value of the x-axis:

`plot_predictions(forest, by = "temp", newdata = bikes)`

Of course, we can customize the plot using all the standard `ggplot2`

functions:

```
plot_predictions(forest, by = "temp", newdata = d) +
geom_point(data = bikes, aes(x = temp, y = count), alpha = 0.1) +
geom_smooth(data = bikes, aes(x = temp, y = count), se = FALSE, color = "orange") +
labs(x = "Temperature (Celsius)", y = "Predicted number of bikes rented per hour",
title = "Black: random forest predictions. Orange: LOESS smoother.") +
theme_bw()
```

``geom_smooth()` using method = 'loess' and formula = 'y ~ x'`