Introduction to metaforest

Tuning parameters

MetaForest has several “tuning parameters”, whose optimal values must be determined empirically: 1) the number of candidate variables considered at each split of each tree; 2) the minimum number of cases that must remain in a post-split group within each tree; 3) the type of weights (uniform, fixed-, or random-effects). The optimal values for these tuning parameters are commonly determined using cross-validation, with the well-known machine learning R-package caret.

Next, we tune the model using the R-package caret. The function ModelInfo_mf tells caret how to tune a MetaForest analysis. As tuning parameters, we consider all three types of weights (uniform, fixed-, and random-effects), number of candidate variables at each split from 2-6, and a minimum node size from 2-6. We select the model with smallest prediction error (RMSE) as final model, based on 10-fold clustered cross-validation.

# Load the caret library
library(caret)
# Set up 10-fold grouped (=clustered) CV
grouped_cv <- trainControl(method = "cv", 
                           index = groupKFold(data$id_exp, k = 10))

# Set up a tuning grid for the three tuning parameters of MetaForest
tuning_grid <- expand.grid(whichweights = c("random", "fixed", "unif"),
                       mtry = 2:6,
                       min.node.size = 2:6)

# X should contain only retained moderators, clustering variable, and vi
X <- data[, c("id_exp", "vi", retain_mods)]

# Train the model
mf_cv <- train(y = data$yi,
               x = X,
               study = "id_exp", # Name of the clustering variable
               method = ModelInfo_mf(), 
               trControl = grouped_cv,
               tuneGrid = tuning_grid,
               num.trees = 5000)
# Examine optimal tuning parameters
mf_cv$results[which.min(mf_cv$results$RMSE), ]

The object returned by train already contains the final model, estimated with the best combination of tuning parameters. Consequently, we can proceed directly to reporting the results. First, we examine convergence again . Then, we examine the R_oob².

Inspecting the results

# For convenience, extract final model
final <- mf_cv$finalModel
# Extract R^2_{oob} from the final model
r2_oob <- final$forest$r.squared
# Plot convergence
plot(final)

We can conclude that the model has converged, and has a positive estimate of explained variance in new data. Now, we proceed to interpreting the model findings. We will plot the variable importance, and partial dependence plots.

# Plot variable importance
VarImpPlot(final)
# Sort the variable names by importance, so that the
# partial dependence plots will be ranked by importance
ordered_vars <- names(final$forest$variable.importance)[
  order(final$forest$variable.importance, decreasing = TRUE)]
# Plot partial dependence
PartialDependence(final, vars = ordered_vars,
                  rawdata = TRUE, pi = .95)

Because this is an exploratory, non-parametric analysis, we cannot conclude whether any of these findings are “significant”. However, the PartialDependence function has two settings that help visualize the “importance” of a finding: rawdata, which plots the weighted raw data (studies with larger weights are plotted with a larger point size), thereby visualizing the variance around the mean prediction, and pi, which plots a (e.g., 95%) percentile interval of the predictions of individual trees in the model. This is not the same as a confidence interval, but it does show how variable or stable the model predictions are. This exploratory moderator analysis could be followed with a linear regression model, focusing only on relevant moderators identified by MetaForest.