Dear Ian, Paolo and David,
Thank you so much for your efforts regarding my inquiry. I would like to say that anything that is related to the replicating the analysis that I previously posted would be great since I plan to implement them in my research, and hopefully, in my PhD thesis. Paolo, I will take some time to do more in-depth studying of your paper and to see if I can implement those methods on my sample dataset, with the R scripts that you have provided. Thank you for your given time and consideration. Sincerely, Igor Dana petak, 4. rujna 2020. u 16:31:31 UTC+2 korisnik [email protected] napisao je: > I Ian and David, > yes, maybe an ad hoc R package would be great but for reasons not > depending on my merits (or de-merits) I'm not (virtually and hoping for > some miracles that could bring me again in the research field) on the field > of scientific research anymore. So.....only if Antonio Profico and Pasquale > Raia will take the commitment to compile the package it will born. > Anyway...I can assure all audience here that the functions and the scripts > are not difficult to use at all. > As we wrote on the supp info all "supplementary material contains > necessary R functions and R scripts to reproduce all figures presented in > the main text that imply specific analyses. The file "Piras et al Frontiers > ancillary functions.r" must be loaded as source. It checks if required > packages are installed and loaded and, if not, it calls the corresponding > installing and/or loading commands. Any script is intended to work "stand > alone" and all landmarks necessary for analyses are defined within the > scripts so that no workspace loading is necessary. The ad hoc built > functions will be present in a future package that is under development. > Some basic functions are wrappers or hacking of functions present in > existing packages; others, mainly regarding speed optimization, are > inspired by some Stackoverflow comments. Also, function names are not in a > "CRAN style" and may change in future." > All the best > Paolo > > > > > Il giorno ven 4 set 2020 alle ore 16:22 Ian Dworkin <[email protected]> > ha scritto: > >> 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 <(905)%20525-9140> >> Lab phone 905 525 9140 ext. 20076 <(905)%20525-9140> >> [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]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/morphmet2/CAGudrjnvkRdBoZePpbASnAvGo4YTY1FMymJEP%2BuxhOGMCtxiDA%40mail.gmail.com >> >> <https://groups.google.com/d/msgid/morphmet2/CAGudrjnvkRdBoZePpbASnAvGo4YTY1FMymJEP%2BuxhOGMCtxiDA%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. 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