[R] how to calculate the consistency of different clusterings

Mao Jianfeng jianfeng.mao at gmail.com
Thu Jan 13 16:36:20 CET 2011

Dear R-listers,

I do clustering on tens of individuals by thousands of traits. I have
known the assignment of each individual. I want to classify the
individuals by randomly resampling different subsets of the traits,
for example, randomly resampling 100 traits for 100 times, then 200
traits for 100 times, then 300 traits for 100 times, ,,,,,,. By each
subset of traits, I do clustering of the same individuals.

In the end, I want to get the consistency (in percentage) of each of
these clusterings (as examples, here "cluster.1", "cluster.2" and
"cluster.3" in the dummy data) with the assignment which is already
known ("populations" in the dummy data). I want to know how such work
can be implemented, maybe by using R.

#dummy data,

clus.data <- data.frame(individual = paste("ind", 1:12, sep = ""),
populations = c(rep("popA", 5), rep("popB", 7)), cluster.1 = c(rep(1,
5), rep(2, 7)), cluster.2 = c(rep(2, 4), rep(1, 8)), cluster.3 =
c(rep(4, 7), rep(5, 5)))



Jian-Feng, Mao

the Institute of Botany,
Chinese Academy of Botany,

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