hclustgeo: Ward clustering with soft contiguity contraints
In chavent/ClustGeo: Hierarchical Clustering with Spatial Constraints

Description Usage Arguments Details Value References See Also Examples

View source: R/hclustgeo.R

Implements a Ward-like hierarchical clustering algorithm including soft contiguity constraints. The algorithm takes as input two dissimilarity matrices D0 and D1 and a mixing parameter alpha between 0 an 1. The dissimilarities can be non euclidean and the weights of the observations can be non uniform. The first matrix gives the dissimilarities in the "feature space". The second matrix gives the dissimilarities in the "constraint" space. For instance, D1 can be a matrix of geographical distances or a matrix build from a contiguity matrix. The mixing parameter alpha sets the importance of the constraint in the clustering process.

1	hclustgeo(D0, D1 = NULL, alpha = 0, scale = TRUE, wt = NULL)

`D0`	an object of class `dist` with the dissimilarities between the n observations. The function `as.dist` can be used to transform an object of class `matrix` to object of class `dist`.
`D1`	an object of class "dist" with other dissimilarities between the same n observations.
`alpha`	a real value between 0 and 1. This mixing parameter gives the relative importance of `D0` compared to `D1`. By default, this parameter is equal to 0 and `D0` is used alone in the clustering process.
`scale`	if TRUE the two dissimilarity matric `D0` and `D1` are scaled i.e. divided by their max. If `D1`=NULL, this parameter is no used and D0 is not scaled.
`wt`	vector with the weights of the observations. By default, wt=NULL corresponds to the case where all observations are weighted by 1/n.

The criterion minimized at each stage is a convex combination of the homogeneity criterion calculated with D0 and the homogeneity criterion calculated with D1. The parameter alpha (the weight of this convex combination) controls the importance of the constraint in the quality of the solutions. When alpha increases, the homogeneity calculated with D0 decreases whereas the homogeneity calculated with D1 increases.

Returns an object of class hclust.

M. Chavent, V. Kuentz-Simonet, A. Labenne, J. Saracco. ClustGeo: an R package for hierarchical clustering with spatial constraints. Comput Stat (2018) 33: 1799-1822.

choicealpha

data(estuary)
# with one dissimilarity matrix
w <- estuary$map@data$POPULATION # non uniform weights 
D <- dist(estuary$dat)
tree <- hclustgeo(D,wt=w)
sum(tree$height)
inertdiss(D,wt=w)
inert(estuary$dat,w=w)
plot(tree,labels=FALSE)
part <- cutree(tree,k=5)
sp::plot(estuary$map, border = "grey", col = part)

# with two dissimilarity matrix
D0 <- dist(estuary$dat) # the socio-demographic distances
D1 <- as.dist(estuary$D.geo) # the geographical distances
alpha <- 0.2 # the mixing parameter
tree <- hclustgeo(D0,D1,alpha=alpha,wt=w)
plot(tree,labels=FALSE)
part <- cutree(tree,k=5)
sp::plot(estuary$map, border = "grey", col = part)