Igor and David and Paolo, Eladio sent me all of the matlab code for those programs,and I have them on dropbox. I was originally planning on porting it to R, but then Paulo and I chatted a few months back, and I figured he would make an R package that among other things included the approach implemented in LORY (among others) so I figure it would be better for me to be patient for a fully implemented R library. Not sure if that is in the cards, Paolo?
In any case, if this is ok with David and Eladio, I can provide a link to the matlab code for LORY if that is relevant. What I don't have is the specific scripts for the examples in the paper itself. Ian On Fri, 4 Sep 2020 at 10:00, 'David Houle' via Morphmet < [email protected]> wrote: > 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> > . > -- Ian Dworkin Department of Biology McMaster University Office phone 905 525 9140 ext. 21775 Lab phone 905 525 9140 ext. 20076 [email protected] dworkinlab.github.io -- 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]. 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