Using clValid in R getting Error in cutree.default(clusterObj, nc) : Function cutree is only available for hclust/dendrogram/phylo objects only

Question

Using the default data set from Brock et al., 2008

install.packages("clValid", dependencies = TRUE)
library(clValid)
data("mouse")
express <- mouse[, c("M1", "M2", "M3", "NC1", "NC2", "NC3")]
rownames(express) <- mouse$ID
intern <- clValid(express, 2:6, clMethods = c("hierarchical", "kmeans", "diana", "fanny", 
"som", "pam", "sota", "clara", "model"), validation = "internal")

and getting the following:

Error in cutree.default(clusterObj, nc) :
Function cutree is only available for hclust/dendrogram/phylo objects only.

Answer 1

The problem seems to come from the fact that stats::cutree is masked by dendextend::cutree once the package dendextend is loaded and that dendextend::cutree does not work for objects generated with some functions of the cluster package like diana and agnes (while stats::cutree works fine).

EDIT : this problem was observed with dendextend 1.9.0 but has been very quickly fixed by the package author after bug report . The new version 1.10.0 works perfectly fine with cluster and the clValid version from the CRAN. It can be installed via : devtools::install_github("talgalili/dendextend")

This is the best solution now. I let here the rest of my initial answer below for the archives only.

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Some code to test that (everything works fine without dendextend but loading dendextend triggers the error message :

# detach(package:dendextend)
# library(dendextend)
# 
library(cluster)
d <- iris[,-5]
cl <- diana(dist(d))
cutree(cl, 3)
cl <- agnes(dist(d))
cutree(cl, 3)

library(clValid)
intern <- clValid(d, 2:10,
                  clMethods = c("hierarchical", "kmeans", "diana", "fanny",
                                "model", "pam", "agnes"),
                  method = "ward", validation = "internal")

Sadly clValid seems to be orphaned so it is not possible to ask the developer to change the code (or am I wrong ?).

Solutions :

• do not use dendextend and clValid at the same time
• do not use agnes and diana in the clMethods argument of clValid
• I have forked the clValid github repository (from CRAN) and made the small changes necessary in the code. You can install this version with devtools::install_github("GillesSanMartin/clValid") . It works for me also when dendextend is loaded.