Package: Proximum 1.1.0

Proximum: Statistical Analysis of Ensemble Proximity Matrices

Treats the proximity matrices produced by tree ensembles as first-class statistical objects rather than as model by-products. Provides a unified extractor across ensemble engines, in-bag and out-of-bag definitions, transformations to dissimilarities with metric diagnostics, corrections that make an indefinite proximity usable as a kernel, and permutation inference for comparing two proximity matrices or partitioning one across the terms of a design. Also provides a Nystrom approximation, a thresholded sparse representation and a streaming form that never allocates the matrix at all, for samples too large to hold it, measures how far the proximity moves between replicates of the ensemble, and draws each object through 'ggplot2': the seriated matrix, the configuration it implies, and the thresholded graph with its communities.

Authors:Agostino Gnasso [aut, cre, cph]