I am trying to use the NbClust method in R to determine the best number of clusters in a cluster analysis following the approach in the book from Manning. However, I get an error message saying:
Error in hclust(md, method = "average"): must have n >= 2 objects to cluster.
Even though the hclust method appears to work. Therefore, I assume that the problem is (which is also stated by the error message), that NbClust tries to create groups with only one object inside.
Here is my code:
mydata = read.table("PLR_2016_WM_55_5_Familienstand_aufbereitet.csv", skip = 0, sep = ";", header = TRUE)
mydata <- mydata[-1] # Without first line (int)
data.transformed <- t(mydata) # Transformation of matrix
data.scale <- scale(data.transformed) # Scaling of table
data.dist <- dist(data.scale) # Calculates distances between points
fit.average <- hclust(data.dist, method = "average")
plot(fit.average, hang = -1, cex = .8, main = "Average Linkage Clustering")
library(NbClust)
nc <- NbClust(data.scale, distance="euclidean",
min.nc=2, max.nc=15, method="average")
I found a similar problem here, but I was not able to adapt the code.
There are some problems in your dataset.
The last 4 rows do not contain data and must be deleted.
mydata <- read.table("PLR_2016_WM_55_5_Familienstand_aufbereitet.csv", skip = 0, sep = ";", header = TRUE)
mydata <- mydata[1:(nrow(mydata)-4),]
mydata[,1] <- as.numeric(mydata[,1])
Now rescale the dataset:
data.transformed <- t(mydata) # Transformation of matrix
data.scale <- scale(data.transformed) # Scaling of table
For some reason data.scale
is not a full rank matrix:
dim(data.scale)
# [1] 72 447
qr(data.scale)$rank
# [1] 71
Hence, we delete a row from data.scale
and transpose it:
data.scale <- t(data.scale[-72,])
Now the dataset is ready for NbClust
.
library(NbClust)
nc <- NbClust(data=data.scale, distance="euclidean",
min.nc=2, max.nc=15, method="average")
The output is
[1] "Frey index : No clustering structure in this data set"
*** : The Hubert index is a graphical method of determining the number of clusters.
In the plot of Hubert index, we seek a significant knee that corresponds to a
significant increase of the value of the measure i.e the significant peak in Hubert
index second differences plot.
*** : The D index is a graphical method of determining the number of clusters.
In the plot of D index, we seek a significant knee (the significant peak in Dindex
second differences plot) that corresponds to a significant increase of the value of
the measure.
*******************************************************************
* Among all indices:
* 8 proposed 2 as the best number of clusters
* 4 proposed 3 as the best number of clusters
* 8 proposed 4 as the best number of clusters
* 1 proposed 5 as the best number of clusters
* 1 proposed 8 as the best number of clusters
* 1 proposed 11 as the best number of clusters
***** Conclusion *****
* According to the majority rule, the best number of clusters is 2
*******************************************************************