Clustering Using SOM Codebook
I've recently been using the aweSOM R package for cluster visualisation, https://cran.r-project.org/web/packages/aweSOM/vignettes/aweSOM.html.
In particular, the aweSOM package entails using partitioning around medoids (pam) on the SOM codebook, as demonstrated below.
However, one limitation of the aweSOM package is that it only allows for two cluster validation measures: silhouette and elbow.
Therefore, I wondered if someone was aware of how to generate other validation statistics (Dunn, Davies-Bouldin etc) using the output of pam clustering on the codebook?
I've currently tried packages 'fpc' and 'clvalid' but ran into some problems using the codebook.
I would appreciate if anyone had suitable code to handle this problem.
Thanks
library(aweSOM)
library(kohonen)
library(RColorBrewer)
library(cluster)
full.data - iris
train.data - full.data[, c(Sepal.Length, Sepal.Width, Petal.Length, Petal.Width)]
train.data - scale(train.data)
set.seed(1465)
init - somInit(train.data, 4, 4)
iris.som - kohonen::som(train.data, grid = kohonen::somgrid(4, 4, hexagonal),
rlen = 100, alpha = c(0.05, 0.01), radius =
c(2.65,-2.65),
dist.fcts = sumofsquares, init = init)
#####
#PAM CLUSTERING
#####
superclust_pam - cluster::pam(iris.som$codes[[1]], 3)
superclasses_pam - superclust_pam$clustering
#####
#VALIDATION METHODS
#####
aweSOMscreeplot(som = iris.som, method = pam, nclass = 3)
aweSOMsilhouette(iris.som, superclasses_pam)
```
Topic r clustering
Category Data Science