nbr_pres: Neighborhood Preservation Between Distance Matrices

In jlmelville/sneer: Stochastic Neighbor Embedding Experiments in R

Neighborhood Preservation Between Distance Matrices

Description

Calculates the neighborhood preservation for each observation in a dataset, represented by two distance matrices. The first matrix is the "ground truth", the second being the estimation or approximation. The neighborhood preservation is calculated for each row where each element d[i, j] is taken to be the distance between observation i and j.

Usage

nbr_pres(din, dout, k)

Arguments

din	Distance matrix. The "ground truth" or reference distances.
dout	Distance matrix. A set of distances to compare to the reference distances.
k	The size of the neighborhood, where k is the number of neighbors to include in the neighborhood.

Details

The neighborhood preservation can vary between 0 (no neighbors in common) and 1 (perfect preservation). However, random performance gives an approximate value of k / n, where k is the size of the neighborhood and is the number of observations or items in the dataset.

Value

Vector of preservation values, one for each row of the distance matrix.

Note

This is not a very efficient way to calculate the preservation if you want to calculate the value for multiple values of k. For more global measures of preservation, see rnx_auc_embed.

jlmelville/sneer documentation built on Nov. 15, 2022, 8:13 a.m.