optpart (version 3.0-3)

archi: Archipelago Analysis

Description

Archipelago analysis finds connected clusters in a dissimilarity matrix. Samples in the same cluster are at most alpha dissimilar to at least one other sample in the cluster, and are more than alpha dissimilar to all samples in all other clusters. The solution is equivalent to slicing a nearest neighbor cluster analysis at alpha, but does not require (or produce) a hierarchical structure.

Usage

archi(dist,alpha)

Arguments

dist

an object of class ‘dist’ from dist, vegdist, or dsvdis

alpha

the dissimilarity threshold to establish the relationship

Value

produces an object of class ‘clustering’, a list with a vector ‘clustering’ of cluster memberships

Details

Archipelago analysis is a topological, as opposed to metric space, cluster routine that returns connected clusters. Every sample in a cluster is connected by a path with step lengths of at most alpha dissimilarity to every other sample in the cluster, and is more than alpha dissimilar to all other samples in all other clusters.

Examples

# NOT RUN {
data(shoshveg) # produces a vegetation dataframe
dis.bc <- dsvdis(shoshveg,'bray/curtis') 
               # produces a Bray/Curtis dissimilarity matrix
arc.50 <- archi(dis.bc,0.5) # clusters at 0.5 dissimilarity 
table(arc.50$clustering)
# }