Thank you very much! Indeed, I compared results column by column, that was a mistake. I took PCs from both datasets and they correlate! ))
On Tuesday, October 31, 2017 at 6:35:46 PM UTC+3, dcadams wrote: > > Andrey, > > > > To repeat: there is no reason to expect the numbers to match identically > across software packages, particularly column by column (if that is what > you are examining). Even if two packages perform things identically in > terms of the algebra (e.g,. GPA using TpsRelw and geomorph), the numbers > may differ slightly for other reasons (post-rotation of the alignment to > the principal axes of the consensus, etc.). > > > > What is important for downstream statistical analyses is not the > individual columns of numbers found from the GPA alignment, but rather the > relationships of specimens in the resultant shape space. That is, how > different are shapes from one another? In the case I mentioned above, if > you took the aligned specimens from TpsRelw and obtained the Procrustes > (Euclidean) distance matrix from them, and did the same with the aligned > specimens from geomorph, and then performed a matrix correlation, the > correlation would be precisely 1.0. This means the information is > identical in the two superimpositions, even if they differ slightly in how > the entire set is oriented relative to the X-Y axis. Incidentally, in the > above case one would also find a perfect correlation between distances from > the GPA-aligned specimens, those shapes rotated to their principal axes, or > differences in shape found from the thin-plate spline and uniform shape > components taken together. For an early discussion of these issues see > Rohlf 1999. > > > However, performing the procedure above where one set of GPA-aligned > coordinates is from MorphoJ will not produce a perfect correlation of 1.0, > as MorphoJ uses Full Procrustes superimposition. That means the perceived > relationships between shapes is not being represented in the same manner: > which of course is a known difference between full and partial Procrustes > fitting. How much of a difference one finds between a full and partial > Procrustes alignment is dataset dependent. > > > Dean > > > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
