Plotting variable importance from ensemble of models with for loop - r

Question

I keep running into an error while attempting to plot variable importance from ensemble of models.
I have ensemble of models I've fitted and now I am trying to create multiple variable importance plots for each algorithm I've fitted. I am using varImp() function from caret to extract variable importance, then plot() it. To fit ensemble of models, I am using caretEnsemble package.
Thank you for any help, please see the example of code below.
# Caret ensemble is needed to produce list of models
library(caret)
library(caretEnsemble)
# Set algorithms I wish to fit
my_algorithms <- c("glmnet", "svmRadial", "rf", "nnet", "knn", "rpart")
# Define controls
my_controls <- trainControl(
method = "cv",
savePredictions = "final",
number = 3
)
# Run the models all at once with caretEnsemble
my_list_of_models <- caretEnsemble::caretList(Species ~ .,
data = iris,
trControl = my_controls,
methodList = my_algorithms)
# Subset models
list_of_algorithms <- my_list_of_models[my_algorithms]
# Create first for loop to extract variable importance via caret::varImp()
importance <- list()
for (algo in seq_along(list_of_algorithms)) {
importance[[algo]] <- varImp(list_of_algorithms[[algo]])
}
# Create second loop to go over extracted importance and plot it using plot()
importance_plots <- list()
for (imp in seq_along(importance)) {
importance_plots[[imp]] <- plot(importance[[imp]])
}
# Error occurs during the second for loop:
Error in data.frame(values = unlist(unname(x)), ind, stringsAsFactors = FALSE):arguments imply differing number of rows: 16,

Answer 1

I've come up with the solution to the problem above and decided to post it as my own answer. I've written a small function to plot variable importance without relying on caret helper functions to create plots. I used dotplot and levelplot because caret returns data.frame that differs based on provided algorithm. It may not work on different algorithms and models that didn't fit.
# Libraries ---------------------------------------------------------------
library(caret) # To train ML algorithms
library(dplyr) # Required for %>% operators in custom function below
library(caretEnsemble) # To train multiple caret models
library(lattice) # Required for plotting, should be loaded alongside caret
library(gridExtra) # Required for plotting multiple plots
# Custom function ---------------------------------------------------------
# The function requires list of models as input and is used in for loop
plot_importance <- function(importance_list, imp, algo_names) {
importance <- importance_list[[imp]]$importance
model_title <- algo_names[[imp]]
if (ncol(importance) < 2) { # Plot dotplot if dim is ncol < 2
importance %>%
as.matrix() %>%
dotplot(main = model_title)
} else { # Plot heatmap if ncol > 2
importance %>%
as.matrix() %>%
levelplot(xlab = NULL, ylab = NULL, main = model_title, scales = list(x = list(rot = 45)))
}
}
# Tuning parameters -------------------------------------------------------
# Set algorithms I wish to fit
# Rather than using methodList as provided above, I've switched to tuneList because I need to control tuning parameters of random forest algorithm.
my_algorithms <- list(
glmnet = caretModelSpec(method = "glmnet"),
rpart = caretModelSpec(method = "rpart"),
svmRadial = caretModelSpec(method = "svmRadial"),
rf = caretModelSpec(method = "rf", importance = TRUE), # Importance is not computed for "rf" by default
nnet = caretModelSpec(method = "nnet"),
knn = caretModelSpec(method = "knn")
)
# Define controls
my_controls <- trainControl(
method = "cv",
savePredictions = "final",
number = 3
)
# Run the models all at once with caretEnsemble
my_list_of_models <- caretList(Species ~ .,
data = iris,
tuneList = my_algorithms,
trControl = my_controls
)
# Extract variable importance ---------------------------------------------
importance <- lapply(my_list_of_models, varImp)
# Plotting variable immportance -------------------------------------------
# Create second loop to go over extracted importance and plot it using plot()
importance_plots <- list()
for (imp in seq_along(importance)) {
# importance_plots[[imp]] <- plot(importance[[imp]])
importance_plots[[imp]] <- plot_importance(importance_list = importance, imp = imp, algo_names = names(my_list_of_models))
}
# Multiple plots at once
do.call("grid.arrange", c(importance_plots))