Object of class `dist` as an input to `fviz_nbclust`

[Nowosad]

Hi!

I've tried to use fviz_nbclust function. Based on the help page, it should takes an object x (matrixor data.frame). However, it's also possible to put there dist object and to get different results:

library('cluster')
library('factoextra')
options(scipen=9)

df <- USArrests
dist_df <- dist(USArrests)

fviz_nbclust(x=df, FUNcluster=pam, method='wss')
fviz_nbclust(x=dist_df, FUNcluster=pam, method='wss')

I've checked the source code and found out that inside the function fviz_nbclust every x object is transformed to dist object. Maybe the better way is to transform only matrixand data.frameobject and not transforming dist. Alternatively (but probably not so good) is to forbid dist object as an input.

What do you think?

[kassambara]

Hi @Nowosad ,

Thank you very much for reporting that.

yes, every x is transformed to dist for computing 'wss' but we need also the original matrix value to compute FUNcluster, for example "pam".

I think that the best option is to accept only the original matrix value as an input. I changed the function accordingly.

Best regards,
A.

[Nowosad]

Hi @kassambara,
thanks for the answer. Yes, you probably right about the best option.

Best regards,
J.

PS Correct me if I'm wrong - pam accept dist object also (without having an original matrix). On the other hand clara needs to have an original matrix...