bioregion (version 1.1.1)

hclu_diana: Divisive hierarchical clustering based on dissimilarity or beta-diversity

Description

This function computes a divisive hierarchical clustering from a dissimilarity (beta-diversity) data.frame, calculates the cophenetic correlation coefficient, and can get clusters from the tree if requested by the user. The function implements randomization of the dissimilarity matrix to generate the tree, with a selection method based on the optimal cophenetic correlation coefficient. Typically, the dissimilarity data.frame is a bioregion.pairwise.metric object obtained by running similarity or similarity and then similarity_to_dissimilarity.

Usage

hclu_diana(
  dissimilarity,
  index = names(dissimilarity)[3],
  n_clust = NULL,
  cut_height = NULL,
  find_h = TRUE,
  h_max = 1,
  h_min = 0
)

Value

A list of class bioregion.clusters with five slots:

1. name: character containing the name of the algorithm

2. args: list of input arguments as provided by the user

3. inputs: list of characteristics of the clustering process

4. algorithm: list of all objects associated with the clustering procedure, such as original cluster objects

5. clusters: data.frame containing the clustering results

Arguments

dissimilarity

the output object from dissimilarity() or similarity_to_dissimilarity(), or a dist object. If a data.frame is used, the first two columns represent pairs of sites (or any pair of nodes), and the next column(s) are the dissimilarity indices.

index

name or number of the dissimilarity column to use. By default, the third column name of dissimilarity is used.

n_clust

an integer or an integer vector indicating the number of clusters to be obtained from the hierarchical tree, or the output from partition_metrics. Should not be used at the same time as cut_height.

cut_height

a numeric vector indicating the height(s) at which the tree should be cut. Should not be used at the same time as n_clust.

find_h

a boolean indicating if the height of cut should be found for the requested n_clust.

h_max

a numeric indicating the maximum possible tree height for the chosen index.

h_min

a numeric indicating the minimum possible height in the tree for the chosen index.

Author

Pierre Denelle (), Boris Leroy () and Maxime Lenormand ()

Details

The function is based on diana. Chapter 6 of Kaufman and Rousseeuw (1990) fully details the functioning of the diana algorithm.

To find an optimal number of clusters, see partition_metrics()

References

Kaufman2009bioregion

See Also

cut_tree

Examples

comat <- matrix(sample(0:1000, size = 500, replace = TRUE, prob = 1/1:1001),
20, 25)
rownames(comat) <- paste0("Site",1:20)
colnames(comat) <- paste0("Species",1:25)

dissim <- dissimilarity(comat, metric = "all")

data("fishmat")
fishdissim <- dissimilarity(fishmat)
fish_diana <- hclu_diana(fishdissim, index = "Simpson")