Re: Ordination dimensions and stress
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Thanks Michelle and Ross for a useful discussion. I have sat on my thoughts for a few weeks about this issue.
There is truth in all that has been said. I have certainly had situations where the 4th dimension in an ordination provided evidence for a genuine process that was generating variation in the data. Ross is right however in that caution is well justified. It is often too easy to interpret patterns that may be suspect, particularly in higher dimensions.
I have put the request for more than 3d on the ‘TO DO’ list, but not as priorty-1 (eg, I’d like to add a nearest-neighbour list function first as a number have requested it). I figure additional dimensions in SSH need not be selected, but can be there if desired.
Ross, on stress I do tend to use ~0.15 as a cut-off myself. If stress is higher than 0.15, I seek ways to reduce it closer to 0.1. I look back at the coding, transformations and standardisations, eliminate outlier objects and noisy variables. I’d would like to add an ability of determining which objects were the most difficult to fit in SSH. Another wishlist item!