External Cluster Validation - Categorical Data

[AC3112]

Dear All,

I've recently been attempting to evaluate output from k-modes (a cluster label), relative to a so-called True cluster label (labelled 'class' below).

In other words: I've been attempting to external validate the clustering output. However, when I tried external validation measures from the 'fpc' package, I was unsuccessful (error term posted below script).

I've attached my code for the mushroom dataset. I would appreciate if anyone could show me how to successful execute these external validation measures in the context of categorical data.

Any help appreciated.

# LIBRARIES 

install.packages('klaR')
install.packages('fpc')

library(klaR)
library(fpc)

#MUSHROOM DATA

mushrooms <- read.csv(file = "https://raw.githubusercontent.com/miachen410/Mushrooms/master/mushrooms.csv", header = FALSE)

names(mushrooms) <- c("edibility", "cap-shape", "cap-surface", "cap-color", 
                      "bruises", "odor", "gill-attachment", "gill-spacing", 
                      "gill-size", "gill-color", "stalk-shape", "stalk-root",
                      "stalk-surface-above-ring", "stalk-surface-below-ring", 
                      "stalk-color-above-ring", "stalk-color-below-ring", "veil-type", 
                      "veil-color", "ring-number", "ring-type", "spore-print-color", 
                      "population", "habitat")

names(mushrooms)[names(mushrooms)=="edibility"] <- "class"

indexes <- apply(mushrooms, 2, function(x) any(is.na(x) | is.infinite(x)))

colnames(mushrooms)[indexes]
table(mushrooms$class)
str(mushrooms)

#REMOVING CLASS VARIABLE

mushroom.df <- subset(mushrooms, select = -c(class))

#KMODES ANALYSIS

result.kmode <- kmodes(mushroom.df, 2, iter.max = 50, weighted = FALSE)

#EXTERNAL VALIDATION ATTEMPT


class <- as.numeric(mushroom$class)
clust_stats <- cluster.stats(d = dist(mushroom.df), 
                             class, result.kmode$cluster)

#ERROR TERM 

Error in silhouette.default(clustering, dmatrix = dmat) : 
  NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning message:
In dist(mushroom.df) : NAs introduced by coercion

[technocrat]

@AC3112

class <- as.numeric(mushroom$class)

Using a reprex (see the FAQ) helps catch errors such as this one— should be mushrooms$class. With that correction

class <- as.numeric(mushrooms$class) 
#> Warning: NAs introduced by coercion
which(isTRUE(class))
#> integer(0)

In other words, the class argument is empty and dist() has nothing to work with.