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Since that post I have made ‘quantum’ leaps on this topic. I even bravely ventured into the non-heirachial clustering analysis, imported the row group stats (medians) and then ran a heirachical with ordination. Neat.

I still haven’t quite understood the ‘weaknesses’ of doing what I did above. The advantage was that all quadrats and species were included (minus a couple of obvious outliers as identified in a prelim heirachial analysis). This increases the robustness of the analysis.

However, choosing the right number of groups is a bit tricky – it matters!

What weaknesses are there in comparision to the hierachial clustering?

Also, I have researched CANOCO a bit. It seems PATN and CANOCO do similar things but in different ways. i.e. CANOCO can directly evaluate environmental gradients along with the variables whereas PATN cannot (what I mean is that PATN can only infer the environmental gradients from the variables – species in my case). Is this correct?

I know extrinsics can represent your environmetnal variables, such as aspect etc, thus analysed in PATN, but this seems less robust when compared to CANOCO. Is this correct or am I missing something?

Can I do everything I need to do in PATN or does CANOCO offer me more in other areas?