On Sun, Nov 25, 2012 at 6:32 PM, Charles Jones <cnjo...@vt.edu> wrote: > Professor Oksanen: > > Thanks for the reply and sorry for the confusion! (I'm still trying to wrap > my head around the multivariate lingo.) > > > 1.) The scores from my NMDS analysis are non-normal (tested using the > multivariate Shapiro-Wilks test.) > 2 and 3) I am using these scores as input for the Cluster Analysis (Ward's > Method) to define several different groups. One of the underlying > assumptions associated with Wards algorithm is that the input is normal. > > So, the question is, is it okay to "ignore" that assumption (normality of > input data) to define the groups? Since I used the MMRP test > (nonparametric) to show there is a difference between the groups, it seems > like this is reasonable. However, I wasn't quite sure. > > Thanks Again! > Nate Jones
Nate, IIRC Ward's method assumes multivariate normality of each cluster formed by multivariate observations (as it treats cluster analysis as an ANOVA problem and so it is sensitive to outliers), but as this method tends to create rather small clusters I would suggest you to try some of the other algorithms available in R to test the stability of the clustering obtained by Ward's linkage. However, I wonder why do you need to get trough the NMDS step -- can't you directly cluster the cases in your dataset? Something like: distances <- dist(USArrests, method = "euclidean") # we need Euclidean distances here fit <- hclust(distances, method="ward") # Ward's method plot(fit) # plot dendrogram grps <- cutree(fit, k=5) # suppose you can interpret 5 clusters rect.hclust(fit, k=5, border="red") # add red boxes around the 5 clusters in dendogram Then, you could experiment with mmrp() and different grouping indexes (obtained from different cuts trough the dendrogram), but I am not sure if this wouldn't be regarded as circular reasoning. Cheers, Ivailo -- UBUNTU: a person is a person through other persons. _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology