Dear all, Apologies in advance for the total beginner's question. I would like to perform a simple ordination on a dataset of species traits, contaning both continous and categorical variables, as well as a cluster analysis on the same dataset. My aim is to identify, species niche-breadth using the ordination and identify any clusters of similar species, with the cluster analysis. I would possibly like to overlay the results of the cluster analysis results onto an ordination plot.
I have seen from previous discussions on this mailing list that it is possible to apply hierchical clustering to a distance matrix, created with the function daisy from the cluster package. This function can be set to use the Gower dissimilarity coefficient (1971), to create a distance matrix, from a dataset that contains both continous and categorical variables. Is the best option available? As for the ordination, I am not entirely sure about which ordination method which I should use. Is Correspondence Analysis suitable or would it be better to use Principal coordinates analysis? Any suggestions/help would be greatly appreciated! Gower, J. C. (1971) A general coefficient of similarity and some of its properties, Biometrics 27, 857–874. Cheers Mario -- Padova Italy _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
