proximityMatrix function

proximityMatrix

Creates a matrix of proximity values.

proximityMatrix(trees, nRows, normalize = TRUE, reorder = TRUE, iter = NULL)

Arguments

• trees: A list of tree attributes created by extractTreeData function.
• nRows: Number of rows to consider.
• normalize: Default is TRUE. Divide the total number of pairs of observations by the number of trees.
• reorder: Default is TRUE. Whether to sort the matrix so high values are pushed to top left.
• iter: Which iteration to use, if NULL the proximity matrix is calculated over all iterations.

Returns

A matrix containing proximity values.

Examples

if(requireNamespace("dbarts", quietly = TRUE)){
 # Load the dbarts package to access the bart function
 library(dbarts)
 # Get Data
 df <- na.omit(airquality)
 # Create Simple dbarts Model For Regression:
 set.seed(1701)
 dbartModel <- bart(df[2:6], df[, 1], ntree = 5, keeptrees = TRUE, nskip = 10, ndpost = 10)

 # Tree Data
 trees_data <- extractTreeData(model = dbartModel, data = df)
 # Create Proximity Matrix
 mProx <- proximityMatrix(trees = trees_data, reorder = TRUE, normalize = TRUE, iter = 1)
}