Sorry for the splitted message; Also...in the cited paper all metrics can be now performed in both 2D and 3D; in the 3D case the two sub-cases of "surface/shell" computation or "fully 3D volume" computation are faced and differently approached (TPS first and second derivatives in 3D cannot be used to interpret what happens along the surface). Distinguishing between the two 3D cases could lead to very different interpretations. See fig. 14 for example. We also propose a simple method to export, **tentatively**, the same triangulation between source and target (or whatever) that could be thinked as "continuously homologous" despite the elusive meaning of "homology" when speaking about it in the context of Geometric Morphometrics. All the best Paolo
Il giorno ven 4 set 2020 alle ore 16:00 'David Houle' via Morphmet < [email protected]> ha scritto: > Dear Igor, > > Thanks for your interest in using Lory. Lory is purely a visualization > program, and does not do any statistical testing. It only performs the > operations necessary to produce visualizations of the relationships between > pairs of forms, using whatever configurations of landmarks are furnished to > the program as input. The program and documentation is available at > https://www.bio.fsu.edu/~dhoule/software.html. > > More important though, is how to do similar analyses to those in the > Márquez et al. (2012) paper: > > On the example data with *Drosophila* species authors have computed > sample mean wing shape deformations for the two Drosophila species (Fig. 4). > > Fig. 4 in Márquez et al. (2012) is based on simulated deformations using > the Drosophila wing mean shape as the origin. > > o How did they do that? Did they computed the group means in other > programs or R packages and then imported them in Lory or there is a way to > get them in Lory because I haven’t found an option to do that. One of the > ways, as I see it, is to compute the mean shapes in geomorph and them > import those means shapes in Lory to visualise those means shapes. > > Yes, you are correct. Forms that are functions of other forms must be > calculated outside of Lory, then furnished to Lory. > > After one iteration of the Delaunay algorithm, without any selection of > evaluation nodes, Lory found 74 nodes for evaluation. Based on that map of > interspecific differences in local wing shape (Fig.5), on the extracted > Jacobian determinants (74) ANOVA with Bonferroni correction for multiple > comparison was performed which resulted with significant (stars) and > non-significant (crosses) differences. > > o How did they computed that one shape with displayed interspecific > differences? > > I believe that Fig. 5 was produced in Lory, by furnishing each > subcompartment's data to Lory separately. > > o Did they extracted Jacobians determinants from Lory and then performed > ANOVA in some other program? > > Lory does not output the Jacobian determinants directly. We first > calculated the determinants in Matlab, then analyzed the differences in > SAS. > > o How did they know which node was significant or not? I suppose that > you have to extract the coordinates that reflect their position on the map > of interspecific differences or did I get it wrong? > > Yes, you do local analyses on the sets of determinants that interest you. > > How did they computed the mean representation of intraspecific variance > in Drosophila species? In Lory or in other program? > > Again, this is based on simulated data using the Drosophila mean wing > shape. Means were calculated in another program, then furnished to Lory. > > Figures 7. and 8. represent interspecific correlations and interspecific > differences and intraspecific variances. I suppose that these figures were > computed in Coriandis software** on Jacobian determinants? I tried to > import the data in Coriandis to explore if I could compute and get those > figures but I am having problems with assigning group info and names to the > imported non landmark data such as Jacobian determinants – no way I could > manage to do that even when I tried to follow the footsteps in the manual > that authors provided. > > The left plots in Fig. 7 were produced in Lory, the right side plots were > not. Since the bubble plots do not represent shape directly, they are not > part of Lory. Eladio Márquez made the bubble plots, and Fig. 8. > > > > Eladio Márquez wrote Lory, and performed most of the analyses in the > Márquez et al. (2012) paper. He would probably have more insight into > precisely how some of the Figures you mentioned were produced. > Unfortunately, this paper was published before journals started to force us > to furnish all the code necessary to produce the data. I probably have all > the programs archived, but these are not clearly documented. As noted in > the paper, analyses were performed in SAS, Matlab, Java, C++, and Python > software. I can dig them out and send them on if you wish. > > > > * Márquez, EJ., Cabeen, R., Woods, RP., Houle, D. 2012. The Measurement of > Local Variation in Shape. Evol Biol, 39: 419 – 439. > > ** Márquez, EJ. & Knowles LL. 2007. Correlated evolution of multivariate > traits: detecting codivergence across multiple dimensions. J. Evol. Biol., > 20: 2334 - 2348. > > > -- > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/morphmet2/7c4bfdf0-79a4-50d4-a9a9-20b0b0d77041%40bio.fsu.edu > <https://groups.google.com/d/msgid/morphmet2/7c4bfdf0-79a4-50d4-a9a9-20b0b0d77041%40bio.fsu.edu?utm_medium=email&utm_source=footer> > . > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CAAdPgfMpOP5K3-%2Bw8QO1HuGE_e1zPdUjhYstduSD4vYzaXfjiw%40mail.gmail.com.
