The R Package HCV for Hierarchical Clustering from Vertex-links

TL;DR

The HCV R package offers a novel hierarchical clustering method that incorporates spatial contiguity by considering geographical locations as vertices, ensuring clusters are both feature-homogeneous and geographically contiguous.

Contribution

It introduces a modified hierarchical clustering algorithm that enforces spatial contiguity using vertex-link constraints, enhancing spatial data analysis.

Findings

Successfully enforces spatial contiguity in clustering results

Provides methods for optimal cluster number determination

Automatically reports cluster members with spatial constraints

Abstract

The HCV package implements the hierarchical clustering for spatial data. It requires clustering results not only homogeneous in non-geographical features among samples but also geographically close to each other within a cluster. We modified typically used hierarchical agglomerative clustering algorithms to introduce the spatial homogeneity, by considering geographical locations as vertices and converting spatial adjacency into whether a shared edge exists between a pair of vertices. The main function HCV obeying constraints of the vertex links automatically enforces the spatial contiguity property at each step of iterations. In addition, two methods to find an appropriate number of clusters and to report cluster members are also provided.