Explain.bartMachine: Approximate Shapley Values Computed from a BART Model Fitted...

In bartXViz: Visualization of BART and BARP using SHAP

Approximate Shapley Values Computed from a BART Model Fitted using bartMachine

Description

This function is used to calculate the contribution of each variable in the Bayesian Additive Regression Trees (BART) model using permutation. It is used to compute the Shapley values of models estimated using the bartMachine function from the bartMachine.

Usage

## S3 method for class 'bartMachine'
Explain(
  object,
  feature_names = NULL,
  X = NULL,
  nsim = 1,
  pred_wrapper = NULL,
  newdata = NULL,
  parallel = FALSE,
  ...
)

Arguments

object	A BART model (Bayesian Additive Regression Tree) estimated using the bartMachine function from the bartMachine.
feature_names	The name of the variable for which you want to check the contribution. The default value is set to NULL, which means the contribution of all variables in X will be calculated.
X	The dataset containing all independent variables used as input when estimating the BART model. Categorical or character variables must not contain an underscore ("_") in their values or labels.
nsim	The number of Monte Carlo repetitions used for estimating each Shapley value is set to 1 by default for the BART model.
pred_wrapper	A function used to estimate the predicted values of the model.
newdata	New data containing the variables included in the model. This is used when checking the contribution of newly input data using the model. The default value is set to NULL, meaning that the input X data, i.e., the data used for model estimation, will be used by default.
parallel	The default value is set to FALSE, but it can be changed to TRUE for parallel computation.
...	Additional arguments to be passed

Value

An object of class ExplainbartMachine with the following components :

phis	A list containing the Shapley values for each variable.
newdata	The data used to check the contribution of variables. If a variable has categories, categorical variables are one-hot encoded.
fnull	The expected value of the model's predictions.
fx	The prediction value for each observation.
factor_names	The name of the categorical variable. If the data contains only continuous or dummy variables, it is set to NULL.

Examples

## Friedman data
set.seed(2025)
n <- 200
p <- 5
X <- data.frame(matrix(runif(n * p), ncol = p))
y <- 10 * sin(pi* X[ ,1] * X[,2]) +20 * (X[,3] -.5)^2 + 10 * X[ ,4] + 5 * X[,5] + rnorm(n)

##  Using the bartMachine 
model <- bartMachine::bartMachine(X, y, seed = 2025, num_iterations_after_burn_in =200 )

## prediction wrapper function
pfun <- function (object, newdata) {
  bartMachine::bart_machine_get_posterior(object,newdata) $ y_hat_posterior_samples
  }
  
## Calculate shapley values
model_exp <-  Explain  ( model, X = X,  pred_wrapper =  pfun )

bartXViz documentation built on Aug. 8, 2025, 6:23 p.m.