mapclust_cut_tree {SPARTAAS}

Function to cut the dendrogram for a new height (distance limit) or a new number of clusters and map the new partition

Description

The function returns the new map, one dendrogram with the cut line, the silhouette width and the new vector cluster. You must call mapclust beforehand to get a mapclust_cl object that can be used by mapclust_cut_tree.

Usage

mapclust_cut_tree(classification, nb_grp = NA, dlim = NA)

Arguments

classification

The object return by mapclust Class: mapclust_cl

nb_grp

The number of groups you want to have on the partition. Must be an integer. (don't use dlim in this case)

dlim

The value of dlim at which you wish to cut the dendrogram. You can enter any value (numerical) and the function will select the nearest lower dlim with the same partition. (do not use nb_grp in this case).

Value

the function returns a list.

Plot:

dendrogram

The global dendrogram (hclust object)

dendrogram_ggplot

The global dendrogram (ggplot2 object)

cuttree

The cut dendrogram

map

The map of the selected partition

AveSilPlot

The average silhouette width plot (for each partition)

WSSPlot

The Within Sum of Square plot (for each partition)

silhouette

The silhouette plot of the selected partition

Value:

X

The x-coordinate data you have used

Y

The y-coordinate data you have used

var

The regionalised variable data you have used

label

The label vector you have used

density

The estimated density based on var. Equal to var if you used a unidimensional density variable

cluster

The cluster vector of the selected partition

Plabel

Logical parameter to activate or not the printing of labels on the dendrogram

fullhist

The compositional cluster for each observation

hist

The compositional cluster without duplicates (corresponds to the split on the dendogram)

dlim

The vector of the different limit distances

cutdlim

The select dlim for the cut of the current partition

DiMatrix

The weighted euclidean distance matrix

silhouetteData

The silhouette data of the selected partition

AveSilData

The average silhouette value for each partition

Moran

The Moran index for each group for each partition

lonlat

Logical parameter, whether your coordinates are in latitude-longitude format or not

Author(s)

A. COULON L. BELLANGER P. HUSI

Examples

## loading data
library(SPARTAAS)
data(datarcheo)

##First you need to run the mapclust function.
#This function allow you to obtain one partition
# object <- mapclust( coord = ..., var = ..., label = ...)
OldClassif <- mapclust(datarcheo$coord, datarcheo$var, datarcheo$label, n = 4)

##In order to cut the dendrogram for another dlim
NewCut <- mapclust_cut_tree(classification = OldClassif, dlim = 0.37)
##In order to cut the dendrogram for another number of cluster
NewCut2 <- mapclust_cut_tree(classification = OldClassif, nb_grp = 4)

#See evaluation using Silhouette width by running:
NewCut$silhouette
#If the plot is empty try to increase the height of the window (full screen).

#See summary of the data by running:
summary(NewCut$silhouetteData)