Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread alcardini
Yes, but doesn't that also add more covariance that wasn't there in the first place? Neither least squares nor minimum bending energy, that we minimize for sliding, are biological models: they will reduce variance but will do it in ways that are totally biologically arbitrary. In the examples I

RE: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread F. James Rohlf
I agree with Philipp but I would like to add that the way I think about the justification for the sliding of semilandmarks is that if one were smart enough to know exactly where the most meaningful locations are along some curve then one should just place the points along the curve and

RE: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread F. James Rohlf
Perhaps, but Procrustes superimposition already adds lots of covariances also. It is a bit tricky (meaning that I do not know of a good solution) to preserve the "real" covariances and distinguish them from artifacts of fitting. GM works well for testing differences among means of groups but

Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread Mike Collyer
Andrea, I am intrigued by your initial comment about adding covariance that was apparently absent. I tend to think of the problem from the other perspective of not accounting for covariance that should be present. As a thought experiment (that could probably be simulated, and maybe I am not

Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread alcardini
Indeed one of my favourite examples where semilandmarks are really useful is a paper by Hublin, Gunz et al. (with apologies for the inaccurate ref. and mixed up order of authors) where they manage to classify as Neanderthal a piece of cranial vault found (I believe) in Belgium and possibly in the

Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread mitte...@univie.ac.at
Yes, it was always well known that sliding adds covariance but this is irrelevant for most studies, especially for group mean comparisons and shape regressions: the kind of studies for which GMM is most efficient, as Jim noted. If you consider the change of variance-covariance structure due to

[MORPHMET] Re: Are more semi landmarks better??

2018-11-06 Thread Diego Ardón
Thanks to everyone who have replied, I sure have a lot of reading to do, but overall I feel more comfortable about my data. I might end up playing around with removing some semi-landmarks, figuring that it shouldn't affect in much the outcome. I'll get back in case I find any other doubts.

Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread N. MacLeod
Agreed. In addition, I think it’s important to note that, in the original implementations of the sliding algorithm, semilandmarks were slid not along the curve itself, but along tangents to the curve (= off the boundary outline). How much distortion this induces is, of course, a function of how

[MORPHMET] Re: Are more semi landmarks better??

2018-11-06 Thread mitte...@univie.ac.at
I'd like to respond to your question because it comes up so often. As noted by Carmelo in the other posting, a large number of variables relative to the number of cases can lead to statistical problems. But often it does not. In all analyses that treat each variable separately - including the

Re: [MORPHMET] A question regarding "target shape"

2018-11-06 Thread Carmelo Fruciano
On 05/11/2018 18:50, Diego Ardón wrote: Captura de pantalla 2018-11-05 a la(s) 11.40.26.png Thank you Mr. Fruciano. I had already made the DFA, but wasn't aware the graphical output represented both groups (it certainly makes sense). I have a couple of other questions regarding

Re: [MORPHMET] Re: Are more semi landmarks better??

2018-11-06 Thread Mike Collyer
Philipp’s message below felt a little like a déjà vu moment. I checked the Morphmet archives and sure enough, we had a similar thread back in late May/Early June, 2017. Diego, you might want to check that thread, as a lot of what was discussed is relevant to your current questions. Cheers!

[MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread mitte...@univie.ac.at
I agree only in part. Whether or not semilandmarks "really are needed" may be hard to say beforehand. If the signal is known well enough before the study, even a single linear distance or distance ratio may suffice. In fact, most geometric morphometric studies are characterized by an