Hi Igor, let me know if you have some problems in running the scripts; I'm confident you should be able to achieve this easily... contact me for any (theorical or computational) clarification I will try to answer according to my new tasks... all the best Paolo
Il giorno dom 6 set 2020 alle ore 22:16 Igor Talijančić < [email protected]> ha scritto: > 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. > 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/morphmet2/1d27f92a-5416-4a72-a772-c15ff120d7f8n%40googlegroups.com > <https://groups.google.com/d/msgid/morphmet2/1d27f92a-5416-4a72-a772-c15ff120d7f8n%40googlegroups.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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