[MORPHMET] Replicating the scores and Mahalanobis distance
To those who sent me messages for helping me in my paper, thank you very much. Hopefully I could still ask for more help from you with my following concerns: 1. I have the five canonical variates (CV) score and per row are the CV loadings of each shape configurations. There are, let's say 15 scores belonging to group 1, 20 to group 2, 18 to group 3, and 24 to group 4. How will I replicate (through an R code) these scores such that it will replicate into 1000 per group, so that per CV score, there are 4000 loadings, 1000 each? 2. In relation to 1, how will I get the Mahalanobis distance of each group? I will use the Mahalanobis distance for the minimum spanning tree and dendogram to compare the minimum spanning tree and dendogram of the original sample size? Thank you very much. -- 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.
[MORPHMET] An R code for full Procrustes mean shape by GPA
Hello! I would like to ask for help as I use the book of Dryden and Mardia, "Statistical Shape Analysis with Application in R"? I cannot find where in the book (or maybe I just overlooked), how did he plot the mean shapes in Figure 8.4. Thank you very much. -- 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.
[MORPHMET] Integrated Morphometrics Package Installer
Hello! As I do morphometrics study, I am looking for the Integrated Morphometrics Package software. However, I searched the very website but it is not working anymore and I do not know where to find. Hopefully I may request for anybody for a copy of this software. Your help is very much appreciated. Thank you very much. -- 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.
[MORPHMET] morphmet - 1000 subscribers!
I note that we recently have achieved 1000 subscribers to morphmet! Caveat 1: Over the years, some have removed themselves from the list or asked me to remove them. So, there have actually been more than 1000 people subscribing, but we have never had 1000 subscribers on the list at the same time. Caveat 2: We have about 50 addresses that are either bouncing or disabled indicating members who have probably moved on from their subscribed addresses. In the future, I will remove those with persistent bouncing dropping the list (temporarily, no doubt) below 1000. -the moderator -- 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.
Re: [MORPHMET] morphmet - list problems
Yeah! This msg came through. Let's see/hope if/that the list continues to function. -the moderator On 5/19/19 3:56 AM, morphmet_moderator wrote: There seem to be some problems with the mailing list that have come to my attention over the past several days, e.g., it thinks every post is spam, but doesn't give me the chance to moderate such posts. Even I, the moderator, am only able to post via the website intermittently. There is a notice that the server-side software will be changed this month, so I suspect this is part of the problem, but I don't know. I am in contact with support to try to see what is going on. For now, I have no idea if your individual posts to the list (including this one - fourth attempt) will appear. In the meantime, please be patient. -the moderator -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- 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.
[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)
[Final, summary post.] I thought I should post some notes about the responses to Andrea’s recent postings. Several people seem to have extrapolated beyond what Andrea said. After a few months of the Cardini, O’Higgins, Rohlf, and Bookstein collaboration (Polly was CC:ed on the very early emails but I do not remember him engaging), I suggested to Andrea that there should be two publications not one. I could see that while writing about the same flaws in the same method the approaches Fred and I were taking would be difficult to combine in the same paper. Andrea and Paul agreed and Andrea then suggested to Fred that he write a paper separate from ours. Thus, Fred did not unilaterally jump ahead and just write his own paper as some seem to have assumed. The understanding was that we expected the two papers to be published together as “companion papers” in some journal yet to be determined. I know that Fred was concerned about the ethics of waiting a long time to warn people that they were using a severely flawed (I would say strongly biased) method. The usage of BG-PCA seems to have increased lately and it did not seem fair to let people continue to write papers and dissertations based on this method once we knew how bad it was. His biorxiv upload and his announcement of it on morphmet were not a surprise to us. There were emails exchanged about the need to warn users. At the time, Fred told me that he needed to go ahead with the biorxiv upload as it was unclear how long it would take our ms. to be completed due to other demands on our time. Reading Fred’s papers can take time but if one just looks at his Fig. 1 (Google "biorxiv 627448" if you lost the link that Fred posted) you will see the magnitude of the problem. It is not subtle! Incidentally, the Cardini et al. draft also has a more extensive Figure illustrating the same problem as a function of n but the rest of the paper is very different. In fact, I found it interesting how two papers about the same defect in the same method and reaching the same conclusion could have so little overlap. Thus, Fred’s paper does not infringe on the content of the Cardini et al. manuscript or interfere with its publication – in fact I think it makes it more important as it will show the problem does not require an understanding of an abstract theorem. I believe the Cardini et al. paper will show that the defects in the method are very easy to understand and obvious once you think about it in the right way. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University -- 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.
[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)
Dear MorphMetters, Yesterday David Polly reminded us of the existence of a 3.5-page draft fragment emailed by Andrea Cardini on September 5, 2018 and headed as by "Cardini, O'Higgins, Polly, Rohlf, Bookstein." So, yes, David Polly was indeed present at the creation. It begins with paragraphs of an introduction acknowledged to be "largely borrowed" from me and continues with a summary of some of Cardini's simulation results, which are consistent with mine but reported using mostly different simulations and quantifications, together with a sketch of a discussion quite different from mine. This fragment, particularly its style of simulating and reporting, may have served later as the basis of the second of the two papers as I referred to it both in my Monday morphmet posting and in my biorxiv preprint. (I say "may have" because I have not seen any more recent state of that second manuscript.) So my Monday note to morphmet pointing to my biorxiv preprint should have mentioned the September document as part of the history of our project before it split into two. I apologize to David for not realizing the role he played in this early history, and apologize to Andrea for overlooking this early draft of the less algebraic half of our joint project. I hope the authors of this second paper will post it to biorxiv as urgently as mine was posted once theirs, too, is in final draft. FB On Tuesday, May 14, 2019 at 1:32:24 PM UTC-4, MORPHMET wrote: > > Dear MorphMetters, > > Some of you may have been in the auditorium in the Department of Botany, > University of Vienna, back in March when Philipp Mitteroecker and I were > the two scheduled discussants for the conference "GMAustria19" on > applications of geometric morphometrics. Several of the papers delivered > there used between-group principal components analysis (bgPCA), and after > each of those papers I mentioned in the course of my commentary that bgPCA > was fatally flawed in applications to most GMM data sets and should NEVER > be used here. In my keynote address, which closed the meeting, I had one > cryptic slide about this assertion, with an example that flashed on the > screen but was immediately replaced by the next slide. > > The typical response to both my own talk and my criticism of the talks of > others, as far as bgPCA was concerned, was along the lines of "Hunh?" or > sometimes "What are you blathering about this time? Isn't bgPCA in the > standard toolkit?" I answered that the Bookstein paper they should read was > just then being written, as one of a pair jointly arising from > conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following > an original hunch of Cardini's, and that my argument would be pretty > convincing once it was actually written down. The claim isn't that people > are using bgPCA incorrectly. They're using it according to the published > formulas, yes, but the method itself yields biological nonsense much too > often. > > That was March. In April, two different articles in Nature (one by > Detroit et al., one by Chen et al.) buttressed claims about sister species > of Homo sapiens using the bgPCA method, and so suddenly it became clear > that we authors had to do something quickly lest this become an epidemic of > bad biometrics. So we accelerated our writing. My paper was the first to be > finished, probably because it is a single-authored item by an emeritus with > no other obligations, and it seemed like a good idea to upload the final > draft to https://www.biorxiv.org even before submitting the paper, so > that any letter to the editors of Nature could include a link to the > argument as to exactly WHY bgPCA is nearly always unsound and its > inferences invalid for applications in contemporary GMM. > > That is the draft that has just appeared as > > https://www.biorxiv.org/content/10.1101/627448v1 > > For those of you who were at the March meeting, this is the argument > (complete with formulas) defending my stern condemnation there. I won't try > to summarize it in this morphmet note -- if you're interested, just read > the abstract on page 1 of the link. For those of you who have already > published bgPCA analyses, you know who you are -- my paper argues strongly > that you need to go back and revisit the inferences of those papers in a > mood of much more intense multivariate skepticism. For the rest of you, > please consider this draft manuscript to be a wake-up call. A technique > that has appeared in dozens of papers and that was, alas, specifically > praised by Mitteroecker and Bookstein personally (back in 2011) could > nevertheless, when examined closely (for the first time!), turn out to be >
[MORPHMET] PREPRINT: between-group principal components analysis (bgPCA)
Dear MorphMetters, Some of you may have been in the auditorium in the Department of Botany, University of Vienna, back in March when Philipp Mitteroecker and I were the two scheduled discussants for the conference "GMAustria19" on applications of geometric morphometrics. Several of the papers delivered there used between-group principal components analysis (bgPCA), and after each of those papers I mentioned in the course of my commentary that bgPCA was fatally flawed in applications to most GMM data sets and should NEVER be used here. In my keynote address, which closed the meeting, I had one cryptic slide about this assertion, with an example that flashed on the screen but was immediately replaced by the next slide. The typical response to both my own talk and my criticism of the talks of others, as far as bgPCA was concerned, was along the lines of "Hunh?" or sometimes "What are you blathering about this time? Isn't bgPCA in the standard toolkit?" I answered that the Bookstein paper they should read was just then being written, as one of a pair jointly arising from conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following an original hunch of Cardini's, and that my argument would be pretty convincing once it was actually written down. The claim isn't that people are using bgPCA incorrectly. They're using it according to the published formulas, yes, but the method itself yields biological nonsense much too often. That was March. In April, two different articles in Nature (one by Detroit et al., one by Chen et al.) buttressed claims about sister species of Homo sapiens using the bgPCA method, and so suddenly it became clear that we authors had to do something quickly lest this become an epidemic of bad biometrics. So we accelerated our writing. My paper was the first to be finished, probably because it is a single-authored item by an emeritus with no other obligations, and it seemed like a good idea to upload the final draft to https://www.biorxiv.org even before submitting the paper, so that any letter to the editors of Nature could include a link to the argument as to exactly WHY bgPCA is nearly always unsound and its inferences invalid for applications in contemporary GMM. That is the draft that has just appeared as https://www.biorxiv.org/content/10.1101/627448v1 For those of you who were at the March meeting, this is the argument (complete with formulas) defending my stern condemnation there. I won't try to summarize it in this morphmet note -- if you're interested, just read the abstract on page 1 of the link. For those of you who have already published bgPCA analyses, you know who you are -- my paper argues strongly that you need to go back and revisit the inferences of those papers in a mood of much more intense multivariate skepticism. For the rest of you, please consider this draft manuscript to be a wake-up call. A technique that has appeared in dozens of papers and that was, alas, specifically praised by Mitteroecker and Bookstein personally (back in 2011) could nevertheless, when examined closely (for the first time!), turn out to be algebraic garbage when applied to data sets where there are far more shape coordinates than specimens. But isn't that the usual situation in GMM these days? As always, I welcome all responses, both positive and negative. The biorxiv posting is permanent, but there is plenty of time for me to make changes before the paper is published (at present it has not yet even been submitted anywhere), so feel free to try to find the flaws in my argument. But I hope you will want to try some of these simulations on your own before you argue against mine. You will also want to study the companion piece by Cardini, O'Higgins, and Rohlf that should likewise be available for download before too long. Fred Bookstein -- 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.
Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe
474.6507 85.1190 135.9783473.3503 79.3694 122.8234477.4590 78.4327 115.8613477.4715 84.2949 108.1328485.4598 97.2760 93.4345 481.8105 89.2901 111.8870483.4924 90.0784 117.8522490.4405 91.4313 106.3994494.9362 79.4173 144.0817472.9395 88.3825 141.0176474.3985 90.9274 140.2106477.6371 85.2512 140.7932478.2403 I would apreciate if somebody could help me. Please don't hesitate to ask me for more details. King regards Azadeh -- 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.
[MORPHMET] Re: New Article: Reflections on a Biometrics of Organismal Form
For some reason, the link to the article I rec'd was excessively long. After some research, I figured out how to edit the original post, but elected not to since many receive messages as email. I am not sure they would get/see the edit. Hence, I provide a shorter link here: https://link-springer-com.proxy.lib.fsu.edu/journal/13752 -ds [the MORPHMET moderator] On Tuesday, April 30, 2019 at 11:01:15 AM UTC-4, MORPHMET wrote: > > [Posted on behalf of Dr. Bookstein] > > Dear MorphMetters, > > I'm happy to announce that my paper "Reflections on a Biometrics of > Organismal Form" has just been posted for open access by the Springer > journal Biological Theory. You can get a free copy by pointing your browser > at > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752=DwIBAg=HPMtquzZjKY31rtkyGRFnQ=T8Sxf-U51iRHIXQayyjGAA=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E= > > > and clicking on what is, for now, the top entry in the Latest Articles > table on the home page. > > This article is a sequel to my 2015 article in Benedikt Hallgrimsson's > journal Evolutionary Biology that introduced the BE-PwV plot as the best > tool for studying integration in GMM data sets. I trace the basic idea here > back nearly a hundred years, not to D'Arcy Thompson but to a > hitherto-untranslated critique of his ideas by the Vivarium group under > Hans Przibram in Vienna arguing that the only valid way that a biologist > should study organismal form is by direct experimental observation of > transformation grids: "Thompson's holistic deformations can be made > comprehensible if we can visualize a space lattice upon the living form, so > as to assess how each little piece changes its shape under conditions that > vary by species. Here lies open a rich, nearly undeveloped field that > invites a mathematization, one whose erection we hope will begin very > soon." But the timing seems to have slipped a bit, namely, by 97 years. The > new paper argues that BE-PwV is exactly the "mathematization" they were > envisioning, which could not be made empirical until the development of > geometric morphometrics, and further that it is the only morphometric > method consistent with the most fundamental fact in all of biology, "the > repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as > Walter Elsasser put it in 1987, "the transfer of information over finite > intervals of time without an intermediate message." For instance, the new > article demonstrates how to recognize a growth-gradient explicitly even in > the presence of unstructured residual variability. I close with a plea that > others help me build the bridge that we need so urgently between the > arithmetic of today's burgeoning image-based data resources and the > rhetoric of biological explanations of organismal form both over evolution > and over development. > > As always I welcome all comments on these ideas, enthusiastic or > otherwise. > > Fred Bookstein > -- 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.
[MORPHMET] New Article: Reflections on a Biometrics of Organismal Form
[Posted on behalf of Dr. Bookstein] Dear MorphMetters, I'm happy to announce that my paper "Reflections on a Biometrics of Organismal Form" has just been posted for open access by the Springer journal Biological Theory. You can get a free copy by pointing your browser at https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752=DwIBAg=HPMtquzZjKY31rtkyGRFnQ=T8Sxf-U51iRHIXQayyjGAA=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E= and clicking on what is, for now, the top entry in the Latest Articles table on the home page. This article is a sequel to my 2015 article in Benedikt Hallgrimsson's journal Evolutionary Biology that introduced the BE-PwV plot as the best tool for studying integration in GMM data sets. I trace the basic idea here back nearly a hundred years, not to D'Arcy Thompson but to a hitherto-untranslated critique of his ideas by the Vivarium group under Hans Przibram in Vienna arguing that the only valid way that a biologist should study organismal form is by direct experimental observation of transformation grids: "Thompson's holistic deformations can be made comprehensible if we can visualize a space lattice upon the living form, so as to assess how each little piece changes its shape under conditions that vary by species. Here lies open a rich, nearly undeveloped field that invites a mathematization, one whose erection we hope will begin very soon." But the timing seems to have slipped a bit, namely, by 97 years. The new paper argues that BE-PwV is exactly the "mathematization" they were envisioning, which could not be made empirical until the development of geometric morphometrics, and further that it is the only morphometric method consistent with the most fundamental fact in all of biology, "the repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as Walter Elsasser put it in 1987, "the transfer of information over finite intervals of time without an intermediate message." For instance, the new article demonstrates how to recognize a growth-gradient explicitly even in the presence of unstructured residual variability. I close with a plea that others help me build the bridge that we need so urgently between the arithmetic of today's burgeoning image-based data resources and the rhetoric of biological explanations of organismal form both over evolution and over development. As always I welcome all comments on these ideas, enthusiastic or otherwise. Fred Bookstein -- 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.
[MORPHMET] 2019 CALL FOR NOMINATIONS: The Rohlf Medal for Excellence in Morphometrics
2019 CALL FOR NOMINATIONS The Rohlf Medal for Excellence in Morphometrics (http://life.bio.sunysb.edu/ee/rohlf_medal/) The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the Department of Anthropology. Recipients of the Rohlf Medal will be recognized for excellence in their body of work on the development of new morphometric methods or for their applications in the biomedical or biological sciences, including evolutionary biology, population biology, physical anthropology, developmental biology, neurobiology, computer sciences, and medicine. The term "morphometrics" is intended to include high-dimensional pattern analyses of biological shape, especially those that analyze shape in a comprehensive way, or of covariation of shape with other variables. The award can recognize advances in the mathematical or statistical theory underlying morphometric methods, new software that implements or visualizes new methods, or specific new biological findings that rely crucially on contemporary morphometric methods and represent major advances. Candidates for the Rohlf Medal may be self-nominated or nominated by others. They must possess a Ph.D. degree or the equivalent. The winning candidate must agree to attend the award ceremony in person in order to accept the Rohlf Medal and then deliver the award lecture. Nomination packages should include, (1) a description of the body of work (not to exceed two pages) on which the candidacy is based, (2) reprints of no more than three relevant papers and/or software products, (3) a curriculum vitae, and (4) three letters of support. Nominating packages should be uploaded to the Rohlf Medal website (http://life.bio.sunysb.edu/ee/rohlf_medal/apply.html) and received by 5 pm, EST, 15 July 2019 to be assured of full consideration. The successful candidate will receive the Rohlf Medal and a cash prize at Stony Brook University, planned for Thursday October 24th, 2019. She or he will deliver a lecture that is appropriate for a broad audience, ranging from the exact sciences to the humanities, concerning the morphometric methodology, software, or findings for which the Rohlf Medal was awarded. -- 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.
Re: [MORPHMET] MorphoJ: problem with reading the tps files
Your system is set up to us commas (',') to mark the decimal instead of
the period ('.'). I think there is an option as to which to use within
the tps programs. Some morphometrics programs assume the use of the
period. -ds
On 12/31/18 2:55 PM, Ewa Krzeminska wrote:
When trying to create a dataset from a tps file I got a response: Invalid
number format in the file. The file was created in TpsDig, and the text in a
notepad is:
LM=18
943,0 1455,0
902,0 1097,0
947,0 981,0
954,0 866,0
945,0 632,0
954,0 397,0
817,0 1313,0
664,0 1335,0
797,0 1429,0
559,0 1477,0
679,0 1503,0
391,0 1217,0
485,0 1093,0
533,0 914,0
880,0 809,0
849,0 715,0
707,0 802,0
496,0 632,0
IMAGE=3572.jpg
ID=0
The option "tps" was chosen. What can be wrong?
--
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[MORPHMET] Geometric morphometrics of nested symmetries unravels hierarchical inter- and...[published version]
Dear colleagues, Here is the published version of the manuscript previously deposited at BioRxiv, now entitled "Geometric morphometrics of nested symmetries unravels hierarchical inter- and intra-individual variation in biological shapes". Y. Savriama & S. Gerber. 2018. “Geometric morphometrics of nested symmetries unravels hierarchical inter- and intra-individual variation in biological shapes,” Sci. Rep., 8, no. 18055. DOI:10.1038/s41598-018-36147-z https://rdcu.be/bd7BP Best wishes, Yoland Savriama, PhD Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND -- 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.
[MORPHMET] Bracketing phenogenotypic limits of mammalian hybridization [Published Version]
Dear colleagues, Here is the published version of the manuscript previously deposited at BioRxiv, now entitled "Bracketing phenogenotypic limits of mammalian hybridization". This is the first study combining seals' genome data, 3D geometric morphometrics of crania, and computational modeling of teeth to examine the potential for mammalian hybridization between phenotypically disparate taxa. Savriama, Y., Valtonen, M., Kammonen, J. I., Rastas, P., Smolander, O.-P., Lyyski, A., Häkkinen,T.J.,Corfe, I.J., Gerber, S.,Salazar-Ciudad, I.,Paulin, L.,Holm, L., Löytynoja, A.,Auvinen, P., Jernvall, J. (2018). Bracketing phenogenotypic limits of mammalian hybridization. *Royal Society Open Science*,*5*(11). http://rsos.royalsocietypublishing.org/content/5/11/180903 Best wishes, Yoland Savriama, PhD Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND -- 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.
[MORPHMET] Human Skull Evolution Video?
Hello! Has anyone ever used 3D data to make a video showing the shape changes in human skull evolution? For example warping from a chimpanzee to modern human? I think it would be great to have a movie like this to use when teaching human evolution. Thanks! Abby -- 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.
[MORPHMET] Re: Morphometrics in Solanaceas
Hi Christian, I just released a step-by-step guide for geometric morphometrics of flowers. This could be of interest. SAVRIAMA, Y. (2018). A Step-by-Step Guide For Geometric Morphometrics Of Floral Symmetry. *Frontiers in Plant Science*, *9*, 1433. https://doi.org/10.3389/fpls.2018.01433 Best wishes, Yoland On Thursday, October 25, 2018 at 6:21:09 PM UTC+3, Christian Borja Tacuri wrote: > > Hi everyone. > > I'm here looking for some help. I've been assigned to create a small > project where I have to compare morphometric characteristics among the > flowers of 10 species of Solanaceas in my country, Ecuador. So, I'd like > some help because I need to locate the landmarks and semilandmarks and I'm > not sure in which parts of the flower I should put the marks for the > comparison. Also, I need to look for differences between the flowers, based > on the abiotic factors of the places the plants live in. > > I'll be so thankful for any guide that you can provide me. > -- 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.
[MORPHMET] New Book Announcement: A Course in Morphometrics for Biologists (Cambridge, University Press, 2018)
Posted on behalf of Dr. Bookstein... Dear Morphmetters, I'm delighted to announce the publication of my latest book, A Course in Morphometrics for Biologists (Cambridge University Press, 2018). There are very nice comments on the back cover from several of our colleagues, including Morphmet's own Dennis Slice. Here's the blurb, from the first inside page: "This book builds a much-needed bridge between biostatistics and organismal biology by linking the arithmetic of statistical studies of organismal form to the biological inferences that may follow from it. It incorporates a cascade of new explanations of regression, correlation, covariance analysis, and principal components analysis, before applying these techniques to an increasingly common data resource: the description of organismal forms by sets of landmark point configurations. For each data set, multiple analyses are interpreted and compared for insight into the relation between the arithmetic of the measurements and the rhetoric of the subsequent biological explanations. The text includes examples that range broadly over growth, evolution, and disease. For graduate students and researchers alike, this book offers a unique consideration of the scientific context surrounding the analysis of form in today's biosciences." For those of you who have been intrigued by any of my recent papers -- on integration and the BE-PwV plot, on the serious problems with Procrustes analysis, on the many pathologies of principal components in GMM, or on the possible resolution of these problems via a new version of factor analysis -- all of these topics are touched on here, and many, many others as well. Fred Bookstein -- 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.
[MORPHMET] A Step-by-Step Guide For Geometric Morphometrics Of Floral Symmetry
Dear colleagues, I would like to attract your attention on this newly published paper. SAVRIAMA, Y. (2018). A Step-by-Step Guide For Geometric Morphometrics Of Floral Symmetry. *Frontiers in Plant Science*, *9*, 1433. https://doi.org/10.3389/fpls.2018.01433 A detailed guide for shape analysis of flowers with any type of symmetry using tpsdig2 (or equivalent) for data acquisition, R for data formatting and MorphoJ for visualisations. This is a practical translation of the theoretical and mathematical framework contained in Savriama & Klingenberg (2011). Savriama, Y., & Klingenberg, C. P. (2011). Beyond bilateral symmetry: geometric morphometric methods for any type of symmetry. *BMC evolutionary biology*, *11*(1), 280. Best wishes! -- 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.
[MORPHMET] Bracketing phenotypic limits of mammalian hybridization
Dear colleagues, I would like to attract your attention on another manuscript we deposited to bioRxiv. Our study combines 3D geometric morphometrics, computational modeling with genomics to investigate the phenotypic limits of mammalian hybridization. Yoland Savriama, Mia Valtonen, Juhana Kammonen, Pasi Rastas, Olli-Pekka Smolander, Annina Lyyski, Teemu J Hakkinen, Ian J Corfe, Sylvain Gerber, Isaac Salazar-Ciudad, Lars Paulin, Liisa Holm, Ari Loytynoja, Petri Auvinen, Jukka Jernvall 2018. Bracketing phenotypic limits of mammalian hybridization. bioRxiv 310789; doi: https://doi.org/10.1101/310789 Best wishes, Yoland Savriama -- 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.
[MORPHMET] Geometric Morphometrics of Nested Symmetries
Dear colleagues, I would like to attract your attention on this manuscript we just deposited to bioRxiv. Savriama, Y. & Gerber, S. 2018. Geometric morphometrics of nested symmetries: Hierarchical inter- and intra-individual variation in biological shapes. *bioRxiv*. bioRxiv 306712; doi: https://doi.org/10.1101/306712 Best wishes, Yoland Savriama -- 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.
[MORPHMET] digitizing very variable leaves
Thank you all for sharing experiences and ideas. For the moment we decided to stick to methods based on landmarks but analyze simple leaves and leaves with exactly three lobes separately. In addition, leaves from simple oval to heavily lobed will be analyzed jointly with outline methods as most of you suggested. Hopefully all works out well. Kind regards from Slovenia, Tina [cid:image002.jpg@01D3BF71.6B169C90] doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160, 2000 Maribor, Slovenija T: +386 41 808 366 E: tina.klenov...@um.si<mailto:ime.prii...@um.si>, www.fnm.um.si<http://www.fnm.uni-mb.si> -- 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.
RE: [MORPHMET] digitizing very variable leaves
Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf, my dilemma occurred because some botanists (I work with mammal skulls) have asked me to help them evaluate leaf variability of two tree species from different localities. So, variability within and among individual trees and species. In which user friendly program (like MorphoJ ☺) can I analyse outline data and visualize variability? Thank you again, Tina From: Joanna Lenarczyk [mailto:j.kowal...@botany.pl] Sent: Thursday, March 15, 2018 10:21 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves Hello Tina, You can try a program which does not need landmarks: http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html I hope it will help you :) I have not tried it yet by myself, but it can be useful when you cannot or do not want use landmarks :) Best, Joanna 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>>: One could do that computationally but I would worry about the homology it might imply for such variable leaf shapes. You might try it and then check to see if, for example, a lobe on one leaf might be 20% of the linear distance around the outline but in another it might be 30% of the way around. In such a case the lobe on one leaf would effectively be treated as homologous to a location between lobes on another leaf. If so, does that make biological sense for your study? If simple leaves were also included the implied homology of a point along its outline to that of one of the lobed leaves might be pretty arbitrary. Would be better if one knew something about the development of these leaves (which I do not!) and used that knowledge. An alternative would be to use outline methods to group shapes for the purpose of say identification with little implication that groups need be biologically meaningful. Sorry to be rather negative but I find highly variable leaf shapes difficult to put in a simple standard framework. Perhaps others will have better suggestions. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Tina Klenovšek <tina.klenov...@um.si<mailto:tina.klenov...@um.si>> Sent: Wednesday, March 14, 2018 12:28 AM To: f.james.rohlf <f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>> Cc: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org> Subject: RE: [MORPHMET] digitizing very variable leaves Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Wednesday, March 14, 2018 3:59 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University ---- Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org<mailto:morphmet@morphometrics.org>> Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org> Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. Any experience? 2.)Is it possible/sensible to put objects that are so differently shaped (photos attached) into the same group or is it better to analyse simple and lobed leaves separately? I apologize if similar questions have been already answered... Kind regards, Tina Napaka! Ime datoteke ni navedeno. doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160<https://maps.google.com/
RE: [MORPHMET] digitizing very variable leaves
Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Wednesday, March 14, 2018 3:59 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org> Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. Any experience? 2.)Is it possible/sensible to put objects that are so differently shaped (photos attached) into the same group or is it better to analyse simple and lobed leaves separately? I apologize if similar questions have been already answered... Kind regards, Tina [cid:image002.jpg@01D3BA4C.D9433EA0] doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160, 2000 Maribor, Slovenija T: +386 41 808 366 E: tina.klenov...@um.si<mailto:ime.prii...@um.si>, www.fnm.um.si<http://www.fnm.uni-mb.si> -- 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.
[MORPHMET] The ecological origins of snakes as revealed by skull evolution [New Publication]
Dear colleagues, I would like to attract your attention on this newly published paper. Da Silva, F. O., A.-C. Fabre, Y. Savriama, J. Ollonen, K. Mahlow, A. Herrel, J. Müller, and N. Di-Poï. 2018. The ecological origins of snakes as revealed by skull evolution. Nature communications 9:376. doi:10.1038/s41467-017-02788-3 Best wishes, Yoland Savriama -- 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.
[MORPHMET] Re: Dino-lite/digital microscope
I love my dino-lite, but I use it to take pictures of human teeth, not rodents! I generally work at 100x and have used my microscope in a variety of different situations. I find it easy to use and love the portability. I just would wonder if the levels of magnification it works best at, under 150x, would work for you. Best of luck! -- 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.
[MORPHMET] New Publication on Geometric Morphometrics and Genetics of Floral Symmetry
Dear colleagues, I would like to attract your attention on this newly published paper. Berger, BA, Ricigliano, VA, Savriama, Y., Lim, A., Thompson, V. & Howarth DG. 2017. Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of *CYCLOIDEA* and *ANTHOCYANIDIN SYNTHASE*.* BMC Plant Biology*. 17:205. https://doi.org/10.1186/s12870-017-1152-x The very first study coupling geometric morphometrics and Virus Induced Gene Silencing (VIGS) to quantify the phenotypic effects of knocking down a single CYC2 paralog, FgCYC2A, as well as the reporter gene, FgANS in symmetry of flowers. Best wishes! Yoland Savriama -- 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.
[MORPHMET] Post-doc in morphometric analysis in phenotypic evolution and embryonic development:
conclusions and its underlying motivation. -Application should be sent to Isaac Salazar-Ciudad by email: isaac.sala...@helsinki.fi No official documents are required for the application first stage but these may be required latter on. 6. Deadline: There is no specific deadline, the position will be filled as soon as a suitable candidate is found. 7. Examples of recent publications by Isaac Salazar-Ciudad group. -Salazar-Ciudad I, Marín-Riera M. Adaptive dynamics under development-based genotype-phenotype maps. Nature. 2013 May 16;497(7449):361-4. -Salazar-Ciudad I, Jernvall J. A computational model of teeth and the developmental origins of morphological variation. Nature. 2010 Mar 25;464(7288):583-6. 8. Interested candidates should check our group webpage: http://www.biocenter.helsinki.fi/salazar/index.html The center of Excellence webpage: http://www.biocenter.helsinki.fi/bi/evodevo/ECDev.html -- 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.
[MORPHMET] New Bookstein GMM papers: PCA and Factor Analysis...
roster of variables.
But contemporary applications of PCA in organismal systems biology,
particularly in geometric morphometrics (GMM), generally involve much
greater counts of variables. The way one might expect pure noise to
degrade the biometric signal in this more contemporary context is
described by a different mathematical literature concerned with the
situation where the count of variables itself increases while remaining
proportional to the count of specimens. The founders of this literature
established a result of startling simplicity.
Consider steadily larger and larger data sets consisting of completely
uncorrelated standardized Gaussians (mean zero, variance 1) such that
the ratio of variables to cases (the so-called p/n ratio) is fixed at a
value y. Then the largest eigenvalue of their covariance matrix tends
to (1+\sqrt{y})^2, the smallest tends to (1-\sqrt{y})^2, and their ratio
tends to the limiting value ((1+\sqrt{y})/(1-\sqrt{y}))^2, whereas in
the uncorrelated model both of these eigenvalues and also their ratio
should be just 1.0. For y=1/4, not an atypical value for GMM data sets,
this ratio is 9; for y=1/2, which is still not atypical, it is 34.
These extrema and ratios, easily confirmed in simulations of realistic
size and consistent with real GMM findings in typical applied settings,
bear severe negative implications for any technique that involves
inverting a covariance structure on shape coordinates, including
multiple regression on shape, discriminant analysis by shape, canonical
variates analysis of shape, covariance distance analysis from shape, and
maximum-likelihood estimation of shape distributions that are not
constrained by strong prior models. The theorem also suggests that we
should use extreme caution whenever considering a biological
interpretation of any Partial Least Squares analysis involving large
numbers of landmarks or semilandmarks. I illuminate these concerns with
the aid of one simulation, two explicit reanalyses of previously
published data, and several little sermons.
For the second one:
Currently the most common reporting style for a geometric morphometric
(GMM) analysis of anthropological data begins with the principal
components of the shape coordinates to which the original landmark data
have been converted. But this focus often frustrates the organismal
biologist, mainly because principal component analysis (PCA) is not
aimed at scientific interpretability of the loading patterns actually
uncovered. The difficulty of making biological sense of a PCA is
heightened by aspects of the shape coordinate setting that further
diverge from our intuitive expectations of how morphometric measurements
ought to combine. More than fifty years ago one of our sister
disciplines, psychometrics, managed to build an algorithmic route from
principal component analysis to scientific understanding via the toolkit
generally known as factor analysis. This article introduces a
modification of one standard factor-analysis approach, Henry Kaiser's
varimax rotation of 1958, that accommodates two of the major differences
between the GMM context and the psychometric context for these
approaches: the coexistence of "general" and "special" factors of form
as adumbrated by Sewall Wright, and the typical loglinearity of partial
warp variance as a function of bending energy. I briefly explain the
history of principal components in biometrics and the contrast with
factor analysis, introduce the modified varimax algorithm I am
recommending, and work three examples that are reanalyses of previously
published cranial data sets. A closing discussion emphasizes the
desirability of superseding PCA by algorithms aimed at anthropological
understanding rather than classification or ordination.
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Re: [MORPHMET] geiger rescale error
Hi Andrea,
The code you provided works for me and I am using R 3.2.2, geiger 2.0.6
and ape_4.0.
However, ensure that the gegier is loaded in the R environment or ensure
that other packages with the same function name do not possibly
interfere with geiger (see this post:
http://stackoverflow.com/questions/5564564/r-2-functions-with-the-same-name-in-2-different-packages).
What might happen here is that when you called rescale function, R used
rescale function from some other (loaded) packages (from different
namespaces...). Try to run the new R session and load just geiger (with
dependencies) using library (geiger) command, check the rescale function
by getAnywhere("rescale") command and if rescale is called from the
geiger () you will likely get an expected
output (without error).
There is a shorter way as well. Load geiger and just type
geiger::rescale().
Marko
On 2016-12-06 10:19, andrea cardini wrote:
Dear All,
I've just tried the rescale function in geiger on my data and got an
error message. As I have no experience with it, I tried the first
example for this function in the help: same error message (see below).
Has anyone had similar issues? Probably I made some silly mistake.
Thanks in advance for your feedback.
Cheers
Andrea
geo <- get(data(geospiza))
ltrns <- rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")
Error message:
Error in rescale(as.numeric(x, range = range, domain = domain, ...)) :
(list) object cannot be coerced to type 'double'
--
Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università
di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472
Adjunct Associate Professor, School of Anatomy, Physiology and Human
Biology, The University of Western Australia, 35 Stirling Highway,
Crawley WA 6009, Australia
E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main
FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
ESTIMATE YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
--
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Re: [MORPHMET] problems opening ply files
Two possibilities... 1) Make sure you are using the latest version and running the program via a .bat, .sh, or .app. There could be memory problems if you try to run the .java file directly. The scripts provide for more memory. but more likely... 2) Some programs create .ply files that are somehow indigestible by Morpheus. Open the file in Meshlab and (re)save it (binary or ascii doesn't matter). That might clear up any problems. -ds On 10/28/16 1:37 PM, Gabriel Wrobel wrote: Hi all. I am new to this sort of analysis, so apologize in advance for the rudimentary nature of my question. I am attempting to open ply files of 3D cranial models built with Agisoft Photoscan on Morpheus and am not having any luck at all. Morpheus reads the file, but does not open it. It seems to be fine with ply files created from laser scans. Is this an issue anyone is familiar with? Thanks! gabe wrobel -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- 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.
Re: [MORPHMET] Trying to trace a quote
According to wikiquote it was John von Neumann: https://en.wikiquote.org/wiki/John_von_Neumann except they have it as: "With four parameters I can fit an elephant, and with five I can make him wiggle his trunk." Abby *Abby Grace Drake, PhDDepartment of Ecology and Evolutionary BiologyCornell UniversityPhone: 508.981.2783Skype: abby.drake* On Wed, Oct 19, 2016 at 1:10 PM, Bill Sellers <w...@mac.com> wrote: > Dear All, > > I wonder if anyone can help me. I'm trying to trace a quotation that a now > long retired colleague of mine used to use. He doesn't remember where he > got it from but it is very apt, and since it relates to animal shape I'm > hoping someone on this mailing list will recognise it (particularly since > I'm probably not remembering it quite properly and google is being > unhelpful). The quote as best I remember it is: > > "Give me 4 parameters and I can build you an elephant. Give me 5 and I can > make it wag its tail." > > I've always imagined it was something that a 1930s developmental biologist > or mathematician would have said when discussing the utility of > developmental models at the time. > > Can anyone help? > > Cheers > Bill > -- > Bill Sellers, Tel: 01612751719, Mobile: 07857655786, > http://www.animalsimulation.org > University of Manchester, D1239 Michael Smith Building, Manchester, M13 > 9PT. > > -- > 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. > > -- 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.
[MORPHMET] New publication on patterns of skull modularity and integration over postnatal ontogeny
Dear Morphometricians, we wish to inform you about a publication on skull modularity and integration across ontogenetic stages in a long-lived vole with well-defined age stages conducted on wild and laboratory bred specimens from two phylogenetic groups: Modularity and cranial integration across ontogenetic stages in Martino's vole, Dinaromys bogdanovi Link: http://www.ctoz.nl/vol85/nr03/a02 Abstract: We explored modularity and morphological integration of the ventral cranium during postnatal ontogeny in Martino's vole (Dinaromys bogdanovi). Two closely related phylogenetic groups, originating from the Central and Southeastern part of the species range in the western Balkans, were considered. As expected, both phylogroups had similar patterns of ontogenetic changes in cranial size and shape variation, modularity and integration. At the level of within individual variation, the hypothesis that the viscerocranial and neurocranial regions are separate modules was rejected, indicating that the hypothesized modules are not developmental, but rather functional. At the level of among individual variation, the viscerocranium and the neurocranium could not be recognized as separate modules at the juvenile stage. The strength of association between the hypothesized modules becomes lower with age which finally results in a clear 2-module organization of the ventral cranium at the adult stage. On the other hand, patterns of morphological integration for the cranium as a whole, the viscerocranium and the neurocranium stay consistent across ontogenetic stages. The developmental mechanism producing integration of the cranium as a whole, as well as integration of the neurocranium, varies throughout postnatal ontogeny. In contrast, we detected the ontogenetic stability of the mechanism responsible for covariation of viscerocranial traits which could provide ongoing flexibility of the viscerocranial covariance structure for high functional demands during lifetime. Findings from our study most likely support the idea of the 'palimpsest-like' model of covariance structure. Moreover, similarity or dissimilarity in the patterns of within and among individual variation in different sets of analyzed traits and comparisons across ontogenetic stages demonstrate how studies on small mammals other than mice can give new insights into postnatal cranial development. Kind regards, Tina Klenovšek and Vida Jojić [cid:image002.jpg@01CDF575.0D631B30] doc. dr. Tina Klenovšek Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160, 2000 Maribor, Slovenija T: (00 386) 041 808 366 E: tina.klenov...@um.si<mailto:tina.klenov...@um.si>, www.fnm.um.si<http://www.fnm.uni-mb.si/> -- 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.
[MORPHMET] 2-year post-doc in artefact morphometrics
Dear all, I am advertising a 2-year post-doctorial fellowship focused on artefact morphometrics (lithics). Those interested, please have a look here http://www.au.dk/om/stillinger/videnskabelige-stillinger/stillinger/Vacancy/show/852090/5285/; feel free to share. Yours, Felix -- 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.
[MORPHMET] Please send links to online morphometrics resources...
I would like to freshen up the online resource links on the www.morphometrics.org page. If you have any relevant active links, please post them so I can add them to the website (if I can remember how). Thanks, the MORPHMET Management -- 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.
[MORPHMET] Append tps Curve to Landmarks
Hi, I have a similar problem like a girl who wrote asked a question on this site in 2012. I coppied her Email because my written english isn't the best. "I just started to use the tps suite and I'm having problems with sliding 2D semilandmarks. I have digitised curves in tpsDig with the curve tool and then resampled them to get an equal number of points for each individual." I then removed the control lines 'Ponints=' and 'Curves='. "As I understand it, I then need to turn the points into landmarks (appending) and then create a slider file to slide them in tpsUtil. The bit I'm stuck with is'appending tps curve to landmarks' in tpsUtil. I enter the file name in 'input' and chose a file name for 'output', but when I press 'create', I just get the error message:" This is my error massege: '435.0' is not a valid floating point value Bad decimal character in coordinates?.' I get the same error for tps files with and without removed control lines. I hope someone has an idea why this Problem shows up and can help me. Thanks Jan -- 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.
[MORPHMET] New paper by Bookstein: The inappropriate symmetries of multivariate statistical analysis in GM
Dear MorphMetters, As I did last year, I'd like to grab your attention for a moment to advertise a long essay of mine, "The inappropriate symmetries of multivariate statistical analysis in geometric morphometrics," just posted by the Springer journal Evolutionary Biology. The article is free for download via http://link.springer.com/article/10.1007/s11692-016-9382-7/fulltext.html or from the journal's own website. The paper runs to 37 double-column pages, but a summary can be brief. I am claiming that the ways we use GMM in most of today's organismal biological applications, whether of growth, evolution, or disease, don't actually make much biological sense. I go on to offer a small assortment of better alternatives, including but not limited to the idea of deflated Procrustes analysis that I published in the same journal last year. The article incorporates two appendices that might merit your closer attention. Appendix 1 is a principled criticism of the RV coefficient some people are recommending nowadays for use in connection with PLS analyses; my conclusion is that it serves no valid scientific purpose and should never be used. Appendix 2 shows what covariances of Procrustes shape coordinates actually look like and why it follows that principal components of these covariance matrices are usually less useful than we hoped they were. Feel free to go get your own copy of this publication and either learn from it or send me your objections. Yours from Vienna with best wishes, Fred Bookstein -- 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.
Re: [MORPHMET] Information on 3d portable scanner
Replying to the list... Hi, Anna! No, I am not familiar with that. For the grant that secured the HDI, we also included the purchase of the similar Artec hand scanner (http://landing.artec3d.com/?keyword=artec%20scanner=CNHLk8TL3skCFUQ2gQod2YQMTQ) for archaeological field work, but did not get enough money for both. For our lab, the table-top seemed the best choice. I have used (well, minions, you know...) the Artec hand scanner some years ago and it was a bit flaky, but worked. I understand now that folks are using it quite successfully. I wish we had one. I might can refer you to someone if no one on the list has info. -ds On 12/15/15 2:12 PM, Anna Loy wrote: Thank you Dennis! Do you have any info regarding the portables CREAFORM? Best Anna Anna Loy Dip. Bioscienze e Territorio Università del Molise Contrada Fonte Lappone I-86090 Pesche (IS), Italy Tel. 0874 404100 Cell. 3316265137 mail: a@unimol.it <mailto:a@unimol.it> Il giorno 15/dic/2015, alle ore 19:31, Dennis E. Slice <dsl...@morphometrics.org <mailto:dsl...@morphometrics.org>> ha scritto: We have the HDI 109 scanner with automatic turntable. My minions tell me it is quite easy to use with ridiculous resolution (I no longer get to play with the toys. This is probably for the best.). Part of the proposal for this was to digitize mouse skulls, so we opted for higher resolution without color. We were recently asked to scan a human skull at full resolution. The resulting file was 10s of gigabytes. I believe bear skulls would be a challenge because of both physical and digital size. I suspect resolution is controllable. One student is currently looking at morphometrics-appropriate decimation algorithms. Attached are pics of a macaque we scanned rendering only the vertices. The skull is about 100cm. Morpheus can't handle the full-res scan. Rendering done in Meshlab. full resolution: 3.4 million vertices (only vertices shown)6.8 million faces Morpheus Pic 1) 500k vertices, 1000k faces Pic 2) 50k vertices, 100k faces -ds On 12/13/15 2:54 PM, ANNA LOY wrote: Hello everyone Do any of you have experience with portable 3d scanner (no structured light) like *CREAFORM HANDY SCAN700 AMETEK *http://www.creaform3d.com/en/metrology-solutions/portable-3d-scanner-handyscan-3d *GOSCAN 3D CREAFORM*video demo https://www.youtube.com/watch?v=4IY1IN8swEc 2pounds no structured light (no laser) molto veloce, res fino a 0.1 mm. They seems very fast and easy to use Also which are differences with portable structured light 3d scanners like *HDI 120 Blue-Light Scanner <http://www.3d-microscribe.com/HDI%20Blitz%20Scanner%20Page.htm>*? I should scan mammal skulls, from otters to bears, in various museum collections Any advice or suggestions would be appreciated Thanks Anna ___ Anna Loy Dip. Bioscienze e Territorio Università del Molise Contrada Fonte Lappone 86090 Pesche (IS), Italy e-mail istituzionale: a@unimol.it <mailto:a@unimol.it> <mailto:a@unimol.it> e-mail: anna.lo...@gmail.com <mailto:anna.lo...@gmail.com> <mailto:anna.lo...@gmail.com> Tel: +39 0874404140 Fax: +39 087440123 skype:anna.loy56 http://scholar.google.com/citations?hl=it=_dVgP6YJ Project 'It is never too Darwin': Project therio.it <http://therio.it> : https://dibt.unimol.it/therio/ Assistan Editor Italian Journal of Zoology http://www.tandfonline.com/toc/tizo20/current#.Uuv5YfjANf9 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- If a response is important to you, keep trying -> I receive 50-100 msgs/day -- 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 <mailto:morphmet+unsubscr...@morphometrics.org>. <500k_vertices_1000k_faces.png><50k_vertices_100k_faces.png><3400k_vertices_6800k_faces.png> -- 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.
Re: [MORPHMET] Information on 3d portable scanner
Sorry, that should have been 10cm for the skull length, and that is just a guess - it's less than fist size, IIRC. -ds On 12/15/15 1:31 PM, Dennis E. Slice wrote: We have the HDI 109 scanner with automatic turntable. My minions tell me it is quite easy to use with ridiculous resolution (I no longer get to play with the toys. This is probably for the best.). Part of the proposal for this was to digitize mouse skulls, so we opted for higher resolution without color. We were recently asked to scan a human skull at full resolution. The resulting file was 10s of gigabytes. I believe bear skulls would be a challenge because of both physical and digital size. I suspect resolution is controllable. One student is currently looking at morphometrics-appropriate decimation algorithms. Attached are pics of a macaque we scanned rendering only the vertices. The skull is about 100cm. Morpheus can't handle the full-res scan. Rendering done in Meshlab. full resolution: 3.4 million vertices (only vertices shown)6.8 million faces Morpheus Pic 1) 500k vertices, 1000k faces Pic 2) 50k vertices, 100k faces -ds On 12/13/15 2:54 PM, ANNA LOY wrote: Hello everyone Do any of you have experience with portable 3d scanner (no structured light) like *CREAFORM HANDY SCAN700 AMETEK *http://www.creaform3d.com/en/metrology-solutions/portable-3d-scanner-handyscan-3d *GOSCAN 3D CREAFORM*video demo https://www.youtube.com/watch?v=4IY1IN8swEc 2pounds no structured light (no laser) molto veloce, res fino a 0.1 mm. They seems very fast and easy to use Also which are differences with portable structured light 3d scanners like *HDI 120 Blue-Light Scanner <http://www.3d-microscribe.com/HDI%20Blitz%20Scanner%20Page.htm>*? I should scan mammal skulls, from otters to bears, in various museum collections Any advice or suggestions would be appreciated Thanks Anna ___ Anna Loy Dip. Bioscienze e Territorio Università del Molise Contrada Fonte Lappone 86090 Pesche (IS), Italy e-mail istituzionale: a@unimol.it <mailto:a@unimol.it> e-mail: anna.lo...@gmail.com <mailto:anna.lo...@gmail.com> Tel: +39 0874404140 Fax: +39 087440123 skype:anna.loy56 http://scholar.google.com/citations?hl=it=_dVgP6YJ Project 'It is never too Darwin': Project therio.it <http://therio.it> : https://dibt.unimol.it/therio/ Assistan Editor Italian Journal of Zoology http://www.tandfonline.com/toc/tizo20/current#.Uuv5YfjANf9 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- 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.
[MORPHMET] 750 subscribers to morphmet...
Sitting in the Atlanta airport on my way back from the third Rohlf Medal award ceremony, and I just approved the 750th subscriber to the list. Congratulations to HS in Alaska who wins a free subscription to MORPHMET. :) -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Post-hoc calculation of PC and CV scores
I have a vague recollection from some years ago of lda() having a small bug/feature. Something like division by n instead of (n-1) or vice-versa. As always, best to check code and results against other, independent programs and resolve the reason for any differences. -ds On 8/19/15 7:08 PM, Fábio Machado wrote: I would consider using the lda() function from MASS package. The function allows for the use of a training dataset (the extant data, in your case) and the associated predict function gives you the score of all specimens (extant and fossil). In my experience, the ordination of specimens on the discriminant functions of lda and on the canonical variate axis of cva from Morpho are identical, except for arbitrary inversion of the sign of some axis, usually the first. Additionally, predict.lda already give you group membership probabilities. As for PCA, I think that princomp and prcomp functions have a predict option that would produce scores for specimens not included in the original analysis. Best, Fabio Andrade Machado Laboratório de Evolução de Mamíferos Departamento de Genética e Biologia Evolutiva- USP f.mach...@usp.br mailto:f.mach...@usp.br ; macfa...@gmail.com mailto:macfa...@gmail.com +55 11 982631029 skype: fabio_a_machado Lattes: http://lattes.cnpq.br/3673327633303737 Google Scholar: http://scholar.google.com/citations?hl=enuser=2l6-VrQJ Em 19/08/2015, à(s) 18:40, Blake Dickson bdick...@g.harvard.edu mailto:bdick...@g.harvard.edu escreveu: Hey Morphmetricians, So I have a question regarding calculating PC scores and CV scores post-hoc: I have a GMM dataset of extant and fossil species which I want to plot using PCA and CVA. I want to calculate the extant species first, then use the eigenvectors from this the plot the scores for the fossil taxa. I have done this successfully for the PCA in R by centering the whole dataset, then calculating the covariance matrix and eigenvectors for the extant species only. I then calculate the PC scores for the fossil taxa using these eigenvalues. I am not certain whether the same tactic for the CVA is valid. I have tried it: performing the CVA (using the Morpho package) on the extant dataset with associated groupings, then correcting the fossil coordinates by the mean of this CVA and calculating the CV scores for the fossil taxa using the canonical variates (CV) matrix. This gives me a result, with plot-able CV scores for the fossil taxa, but I want to be certain the method is valid. In addition, assuming that what I have done with the CVA is correct; how would I best go about testing the likelihood of group membership for these fossil taxa? Cheers all, Blake Dickson -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org http://www.morphometrics.org/ To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org mailto:morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: The Rohlf Medal: 2015 Call for Nominations
The deadline approaches: July 15, 2015! Time to get your applications in. On Monday, March 9, 2015 at 8:24:10 AM UTC-4, MORPHMET wrote: *2015 CALL FOR NOMINATIONS* *The Rohlf Medal* The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the Department of Anthropology. Recipients of the Rohlf Medal will be recognized for excellence in their body of work on the development of new morphometric methods or for their applications in the biomedical sciences, including evolutionary biology, population biology, physical anthropology, and medicine. The term ‘morphometrics’ is intended to include high-dimensional pattern analyses of biological shape, especially those that analyze shape in a comprehensive way, or of covariation of shape with other variables. The award can recognize advances in the mathematical or statistical theory underlying morphometric methods, new software that implements or visualizes new methods, or specific new biological findings that rely crucially on contemporary morphometric methods and represent major advances. Candidates for the Rohlf Medal may be self-nominated or nominated by others. They must possess a Ph.D. degree or the equivalent. The winning candidate must agree to attend the award ceremony in person in order to accept the Rohlf Medal and then deliver the award lecture. Nomination packages should include, (1) a description of the body of work (not to exceed two pages) on which the candidacy is based, (2) reprints of no more than three relevant papers and/or software products, (3) a curriculum vitae, and (4) the names and addresses of three referees. Nominating packages should be uploaded to the Rohlf Medal website ( http://life.bio.sunysb.edu/ee/rohlf_medal/apply.html) and received by 5 pm, EST, 15 July 2015 to be assured of full consideration. The successful candidate will receive the Rohlf Medal and a cash prize at Stony Brook University, planned for October 26th, 2015. She or he will deliver a lecture that is appropriate for a broad audience, ranging from the exact sciences to the humanities, concerning the morphometric methodology, software, or findings for which the Rohlf Medal was awarded -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] image names tps series
Dear Patrick, If you convert the tps into a NTS file (you can do that using tpsutil), and then open the nts file in MorphoJ, you should get the names of the images. Best, Elis Damasceno PhD CandidateMichael Smith BuildingFaculty of Life SciencesUniversity of Manchester Em Quarta-feira, 10 de Junho de 2015 10:25, Patrick Arnold patrick.arn...@uni-jena.de escreveu: Dear all, I am having a tiny problem when combining tps series and MorphoJ. I created tps file with tpsutil, digitized landmarks with tpsdig2 and import the dataset into MorphoJ. Unfortunately, image names are not included in MorphoJ and thus I am not able to extract classifiers from ID. I thought image names are automatically included when creating tps file and I cannot find to option to do this manually. How to solve this? Thanks in advance. Patrick -- Patrick Arnold, M.Sc. Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Friedrich-Schiller-Universität Jena Germany This message was sent through https://webmail.uni-jena.de -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: The Rohlf Medal: 2015 Call for Nominations
A friendly reminder to start getting your nominations packages together. On Monday, March 9, 2015 at 1:24:10 PM UTC+1, MORPHMET wrote: *2015 CALL FOR NOMINATIONS* *The Rohlf Medal* The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the Department of Anthropology. Recipients of the Rohlf Medal will be recognized for excellence in their body of work on the development of new morphometric methods or for their applications in the biomedical sciences, including evolutionary biology, population biology, physical anthropology, and medicine. The term ‘morphometrics’ is intended to include high-dimensional pattern analyses of biological shape, especially those that analyze shape in a comprehensive way, or of covariation of shape with other variables. The award can recognize advances in the mathematical or statistical theory underlying morphometric methods, new software that implements or visualizes new methods, or specific new biological findings that rely crucially on contemporary morphometric methods and represent major advances. Candidates for the Rohlf Medal may be self-nominated or nominated by others. They must possess a Ph.D. degree or the equivalent. The winning candidate must agree to attend the award ceremony in person in order to accept the Rohlf Medal and then deliver the award lecture. Nomination packages should include, (1) a description of the body of work (not to exceed two pages) on which the candidacy is based, (2) reprints of no more than three relevant papers and/or software products, (3) a curriculum vitae, and (4) the names and addresses of three referees. Nominating packages should be uploaded to the Rohlf Medal website ( http://life.bio.sunysb.edu/ee/rohlf_medal/apply.html) and received by 5 pm, EST, 15 July 2015 to be assured of full consideration. The successful candidate will receive the Rohlf Medal and a cash prize at Stony Brook University, planned for October 26th, 2015. She or he will deliver a lecture that is appropriate for a broad audience, ranging from the exact sciences to the humanities, concerning the morphometric methodology, software, or findings for which the Rohlf Medal was awarded -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Why exported raw coordinates differ from the imported in MorphoJ?
On 25.5.2015 5:52, lv xiao wrote: Dear all, I am using morphoJ to do geometric morphometric analysis. I imported the TPS file with three specimens into MorphoJ.*Without doing any further analysis, I exported the raw coordinates from MorphoJ.* To my surprise, I found that *the exported coordinates differ from the imported one, except for the first specimen.* * * May I know why does this happen? Will this affect subsequent analyses? Your kind reply is highly appreciated! Best regards, Patrick -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org mailto:morphmet+unsubscr...@morphometrics.org. Hi Patric, MorphoJ provided you with appropriate output. Note that you have set a SCALE argument in the tps file for last two specimens (line 85 and 128), but not for the first one. Therefore, coordinates for the last two specimens were rescaled. That is each coordinate were multiplied by respective value of SCALE argument (e.g. raw x1 for second specimen is 1144.0; x1 from MorphoJ will be 1144.0*0.146663 = 167.782472). Maybe you forgot to set the SCALE value for the first specimen during digitization procedure. Hope this helps, Marko -- Marko Djurakic, Teaching assistant, Faculty of Sciences Department of Biology and Ecology University of Novi Sad Trg Dositeja Obradovića 2 21 000 Novi Sad Serbia PhD student at Faculty of Biology, University of Belgrade Studentski trg 16 11000 Belgrade Serbia e-mail: marko.djura...@dbe.uns.ac.rs -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] New paper by Bookstein: Integration, Disintegration, and Self-Similarity
Vienna, April 22, 2015 Dear MorphMetters, As some of you may know already, for years I've been working on a methodology that replaces the Procrustes method with an alternative where, intuively speaking, the closer together two landmarks lie, the more their shifts of position with respect to the rest are correlated (which of course is the actual situation in just about every organismal data set we ever encounter). If you happened to be in St. Louis last month for the AAPA national conference you might have seen my poster on the new method, but a topic this mathematical isn't really suited to a poster format. Today, at last, my first fundamental article on this stuff has been published online by the Springer journal Evolutionary Biology. This is an open-access article, which means you can just go grab your own copy of the 32 double-column pages and 22 diagrams without having to involve your university library. Just point your browser to link.springer.com/journal/11692 and click on the button reading View Open Access Articles. As of this morning, anyway, my piece Integration, Disintegration, and Self-Similarity is the first item that comes up on offer. The title is what it is because there is an immediate application to integration studies in GMM whereby the Procrustes model must be replaced by something different as the null model for such studies. With best wishes, Fred Bookstein -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Analysis of semilandmark data
On a technical point, one does not transform landmarks into semilandmarks. They either are landmarks or semilandmarks. The fact that they are semilandmarks is sometimes ignored, and they are treated as landmarks if the ambiguity in positioning on one direction is deemed sufficiently small or they can be allowed to slide to take out variability in that direction. So, semilandmarks are semilandmarks, but they can be transformed into sliding landmarks. -ds On 5/6/15 7:29 AM, Nico Posnien wrote: Dear all, I have a question concerning the analysis of landmark and semilandmark data in fly heads. So far I placed landmarks on 2D images. Some of these actually represent semilandmarks. I used tps Util (Make Sliders File; see attched picture) to generate a sliders file. In the attached picture, 1 and 8 are landmarks and 2-7 in between them are supposed to be semilandmarks. My first question is: Is this the right way to transform landmarks into semilandmarks? My second question is: What is the best (most accepted, straight-forward) way to further analyze this data? I am mainly interested in shape differences between different groups (2 species + hybrids, males and females). Which programs should be used? I saw that geomorph can handle this kind of data. Any UI software? Are there any suggestions for good tutorials? Thanks a lot for any recommendation and help! Cheers, Nico -- Nico Posnien Georg-August-University Göttingen Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Department of Developmental Biology Ernst-Caspari-Haus (GZMB) Justus-von-Liebig-Weg 11 37077 Göttingen Germany Phone: +49 (0) 55139 20817 E-mail: npos...@gwdg.de web: http://www.evolution.uni-goettingen.de/posnienlab/index.html web: http://www.uni-goettingen.de/en/44993.html -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] The Rohlf Medal: 2015 Call for Nominations
*2015 CALL FOR NOMINATIONS* *The Rohlf Medal* The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the Department of Anthropology. Recipients of the Rohlf Medal will be recognized for excellence in their body of work on the development of new morphometric methods or for their applications in the biomedical sciences, including evolutionary biology, population biology, physical anthropology, and medicine. The term ‘morphometrics’ is intended to include high-dimensional pattern analyses of biological shape, especially those that analyze shape in a comprehensive way, or of covariation of shape with other variables. The award can recognize advances in the mathematical or statistical theory underlying morphometric methods, new software that implements or visualizes new methods, or specific new biological findings that rely crucially on contemporary morphometric methods and represent major advances. Candidates for the Rohlf Medal may be self-nominated or nominated by others. They must possess a Ph.D. degree or the equivalent. The winning candidate must agree to attend the award ceremony in person in order to accept the Rohlf Medal and then deliver the award lecture. Nomination packages should include, (1) a description of the body of work (not to exceed two pages) on which the candidacy is based, (2) reprints of no more than three relevant papers and/or software products, (3) a curriculum vitae, and (4) the names and addresses of three referees. Nominating packages should be uploaded to the Rohlf Medal website ( http://life.bio.sunysb.edu/ee/rohlf_medal/apply.html) and received by 5 pm, EST, 15 July 2015 to be assured of full consideration. The successful candidate will receive the Rohlf Medal and a cash prize at Stony Brook University, planned for October 26th, 2015. She or he will deliver a lecture that is appropriate for a broad audience, ranging from the exact sciences to the humanities, concerning the morphometric methodology, software, or findings for which the Rohlf Medal was awarded -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Testing Group Mean Differences, Nonparametric Framework
On 6.2.2015 22:54, Eugenia Leone Gold wrote: Hi everyone, I am trying to run a non-parametric test for group mean differences using PC scores and I can’t seem to find a function to do that. I am using PC scores instead of Procrustes Coordinates so as to have fewer variables than specimens. Does anyone know of a function that can do this? I came across the function adonis in Vegan, but that seems to use distances so I don’t think it’s applicable to this situation. Thanks for any help! Best, Eugenia Hi Eugenia, If you want (just) to make a statistical inference regarding difference between two shape means, you can use permutation test. You can do it in MorphoJ, geomorph, PAST...All of them are distance based. If you want to perform hypothesis testing that describe patterns of shape variation and covariation in regard to some factor(s), solution is to perform appropriate linear model. However, regardless whether dependent variables are original procrustes residuals or PC scores of them, small sample size may be a problem in traditional (parametric) approaches. There is recent paper by Collyer and Adams published in Heredity (http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy201475a.html) which demonstrated efficacy of non-parametric approach that is not constrained by low sample size compared to number of variables. That approach can evaluate effect size of factors in the model even if sample size is small relative to number of variables. Procedure is described and justified in the paper and you can perform it in the geomorph package (procD.lm function). Regarding non-parametric tests, as far as I know, most of them use distance based methods. E.g. see here: http://www.entsoc.org/PDF/MUVE/6_NewMethod_MANOVA1_2.pdf Hope this help. All the best. -- Marko Djurakic, Teaching assistant, Faculty of Sciences Department of Biology and Ecology University of Novi Sad Trg Dositeja Obradovića 2 21 000 Novi Sad Serbia PhD student at Faculty of Biology, University of Belgrade Studentski trg 16 11000 Belgrade Serbia e-mail: marko.djura...@dbe.uns.ac.rs -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: Migration update
I have just sent out the final re-re-...invitations to addresses on the old MORPHMET mailing list. When these expire, they addresses will be deleted, and anyone wanting to join will have to do so using the standard procedure. At this writing, we have 640 subscribers, which is pretty impressive in my estimation. -The Management -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] POSTDOCTORAL POSITION: Max Planck CIAA, IEA, Leipzig, Germany
POSTDOCTORAL POSITION - DOMESTICATION EFFECTS ON BITING PERFORMANCE IN RATS Max Planck Weizmann Center for Integrative Archaeology and Anthropology, Leipzig, Germany The Max Planck Weizmann Center for Integrative Archaeology and Anthropology at the Max Planck Institute for Evolutionary Anthropology, Leipzig (Germany) invites applications for a post-doctoral position to work on a collaborative project to study the effect of domestication on bite force performance and skull and muscle anatomy in rats. We are seeking a highly qualified and motivated candidate with experience in in vivo bite force measurements, anatomical dissection, muscle physiology, microscopy, histology, immunohistochemistry, CT imaging and/or geometric morphometrics. This position is set to begin as soon as 1 November 2014, and applications will be considered until the position is filled. The initial length of the appointment will be one year, with an option for extension. The selected candidate should have a Ph.D. (or be close to completion) in a relevant area and a significant track record of research. The Max Planck Society is committed to employing more physically impaired individuals and to increasing the share of women in areas where they are underrepresented, and therefore expressly encourages applications from such qualified individuals. Applications including cover letter, curriculum vitae, reprints of selected publications, a short statement of research interests and the names of at least two referees should be sent as a single PDF document to Dr Kornelius Kupczik (kupczik (AT) eva (DOT) mpg (DOT) de). For further information about the Max Planck Weizmann Center see http://www.eva.mpg.de/mpwc. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] 3D stuff
Chapter 6: More Complex Examples in the User's Guide for the latest version of Morpheus et al. (http://morphlab.sc.fsu.edu/index.html) shows how to do this via batch processing. More common landmarks are much better, but this worked for croc skulls with only three. Actually, this surprised me since when I tried this years ago with three landmarks, the computations collapsed the data into the three-landmark plane. -ds On 9/18/14 6:08 AM, Gaëtan Bourgeois wrote: Hello everybody, I did acquisition of 3D landmarks (about skulls) with a Microscribe in 2 views (superior and inferior) and I have to put together these series now. I know I need to do multiregression but I don't know how exactly I have to proceed. Is anyone can help me to do this? Other question: what is the best freeware for 3D landmarks treatment in your opinion? Thank you, have a nice day! -- Gaëtan Bourgeois -- PhD Student Université de Perpignan Via Domitia, ED 544, UR MEDI-TERRA Centre Européen de Recherche Préhistorique de Tautavel, UMR CNRS 7194 -- EPCC - CERPT Avenue Léon-Jean Grégory 66720 Tautavel -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Recent site outage
Yesterday, the website and MORPHMET went down. The reason was that I asked to cancel account with the original (more expensive) service provider. When they did this, it wiped out something called the Zone File. I spent a significant part of today getting that restored. I think it works, now, but I cannot be certain about access to non-owners - I am, of course, the owner and it works perfectly for me. I think, but am not certain, that it should now be accessible to all as before: http://www.morphometrics.org. -The Management -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: Migration update
Delight has been achieved! I am delighted to report that membership in the new MORPHMET has surpassed the 600 subscriber mark - 603 as of this writing. Also, www.morphometrics.org has rec'd nearly 400 unique (by IP) visits from computers in 45 countries (see embedded map on the website). We began with subscribed email addresses to the old MORPHMET mailing list. These had accumulated over a decade, and my personal goal was that we achieve near or above a 50% response to the new list. I still have about 500 pending invitations that expire approximately weekly. I will continue to reissue these (a tedious process) periodically through September, then purge the list. Thank you for your continued interest and support, The Management On Saturday, August 16, 2014 10:34:42 AM UTC-4, MORPHMET wrote: Hi, Folks. This is just an update on the ongoing migration to the new system. First, I am pleased to note that we currently have 456 subscribed members. These are real, interested parties who have either initiated their own subscription or responded to my invitations. The old subscriber list included over 1100 addresses. If we get 500+ active subscribers I will be satisfied. 600+ and I will be delighted. After more than a decade of subscription accumulation, getting 50% response will be pretty good, I think. And, I know many are currently on vacation. Second, I have over the past two days reissued subscription invitations to over 600 addresses. The subscriptions expire after a week, and I must reissue them...ten at a time, typing in those illegible security codes. I plan to continue to reissue unanswered subscriptions periodically through September. I appreciate your patience in this should you get multiple subscription invitations you don't want. Please ignore them, but if they are too annoying, write me and I will manually remove you from the invitation list. I can also make manual adjustments to the subscribed address. But note,... To use the web interface, you must be logged in via a Google account. If you do not have one (and are subscribed), you may post to the list by sending an email to morphmet@morphometrics.org or replying (to the list) to postings appearing in your email account. Users are initially set up to receive real-time email of individual list posts, but you can change that to no email, or a digest format including multiple postings. I am not sure how one responds to the latter, but I suspect some sort of obvious reply would work. Also, you can adjust your own email subscription by either subscribing to the list by sending an email message from your desired subscription address to morphmet+subscr...@morphometrics.org and you can unsubscribe by sending an email from the address to be unsubscribed to: morphmet+unsubscr...@morphometrics.org As always, earlier posts to the list (new or old) can be found at mail-archive.com Best, ds -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: Migration update
Satisfaction obtained - currently at exactly 500 subscribers. Now, anticipating delight...600 The Management On Saturday, August 16, 2014 10:34:42 AM UTC-4, MORPHMET wrote: Hi, Folks. This is just an update on the ongoing migration to the new system. First, I am pleased to note that we currently have 456 subscribed members. These are real, interested parties who have either initiated their own subscription or responded to my invitations. The old subscriber list included over 1100 addresses. If we get 500+ active subscribers I will be satisfied. 600+ and I will be delighted. After more than a decade of subscription accumulation, getting 50% response will be pretty good, I think. And, I know many are currently on vacation. Second, I have over the past two days reissued subscription invitations to over 600 addresses. The subscriptions expire after a week, and I must reissue them...ten at a time, typing in those illegible security codes. I plan to continue to reissue unanswered subscriptions periodically through September. I appreciate your patience in this should you get multiple subscription invitations you don't want. Please ignore them, but if they are too annoying, write me and I will manually remove you from the invitation list. I can also make manual adjustments to the subscribed address. But note,... To use the web interface, you must be logged in via a Google account. If you do not have one (and are subscribed), you may post to the list by sending an email to morphmet@morphometrics.org or replying (to the list) to postings appearing in your email account. Users are initially set up to receive real-time email of individual list posts, but you can change that to no email, or a digest format including multiple postings. I am not sure how one responds to the latter, but I suspect some sort of obvious reply would work. Also, you can adjust your own email subscription by either subscribing to the list by sending an email message from your desired subscription address to morphmet+subscr...@morphometrics.org and you can unsubscribe by sending an email from the address to be unsubscribed to: morphmet+unsubscr...@morphometrics.org As always, earlier posts to the list (new or old) can be found at mail-archive.com Best, ds -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Joining - you don't need a gmail account.
Please be aware that you DO NOT have to have a gmail account to subscribe to the list. That is only necessary if you want to use the web interface. You can request to join the list from any email address (as far as I know) by sending a message to: morphmet+subscr...@morphometrics.org The google account (with requisite gmail address) is only required for using the web interface. Note, you can join from whatever address you want AND create a google account to use the web interface. Your preferred email address will receive and be able to send messages as always. Only posts made via the web interface (I am guessing a bit, here) will appear to come from your gmail account. In such a configuration, you might want to turn off email notifications of postings for your google account to prevent them from going, unseen, to your gmail account. The Management -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Migration update
Hi, Folks. This is just an update on the ongoing migration to the new system. First, I am pleased to note that we currently have 456 subscribed members. These are real, interested parties who have either initiated their own subscription or responded to my invitations. The old subscriber list included over 1100 addresses. If we get 500+ active subscribers I will be satisfied. 600+ and I will be delighted. After more than a decade of subscription accumulation, getting 50% response will be pretty good, I think. And, I know many are currently on vacation. Second, I have over the past two days reissued subscription invitations to over 600 addresses. The subscriptions expire after a week, and I must reissue them...ten at a time, typing in those illegible security codes. I plan to continue to reissue unanswered subscriptions periodically through September. I appreciate your patience in this should you get multiple subscription invitations you don't want. Please ignore them, but if they are too annoying, write me and I will manually remove you from the invitation list. I can also make manual adjustments to the subscribed address. But note,... To use the web interface, you must be logged in via a Google account. If you do not have one (and are subscribed), you may post to the list by sending an email to morphmet@morphometrics.org or replying (to the list) to postings appearing in your email account. Users are initially set up to receive real-time email of individual list posts, but you can change that to no email, or a digest format including multiple postings. I am not sure how one responds to the latter, but I suspect some sort of obvious reply would work. Also, you can adjust your own email subscription by either subscribing to the list by sending an email message from your desired subscription address to morphmet+subscr...@morphometrics.org and you can unsubscribe by sending an email from the address to be unsubscribed to: morphmet+unsubscr...@morphometrics.org As always, earlier posts to the list (new or old) can be found at mail-archive.com Best, ds -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] The new MORPHMET is now open for business.
I am pleased to announce that the new MORPHMET is open for business. Usage notes follow. 1) Anyone can view the list's content, but only subscribers can post. 2) moderation - Initial posts from all users will be moderated. When your first post is approved, moderation will be turned off. All subsequent posts from your address will go directly to the entire list. Posts can be deleted, but not recalled. Be careful with the Send button if you are prone to rash commentary. 3) archive - Posts will continue to be archived at www.mail-archive.com. With the new system, however, all posts will remain available at the list website. 4) email - If you prefer, you may continue to use MORPHMET as before. To post, simply send your content via email to morphmet@morphometrics.org or use the Reply to list option for replying the posts of others. To subscribe or unsubscribe from the list, send an email to either morphmet+subscr...@morphometrics.org or morphmet+unsubscr...@morphometrics.org, as appropriate. 5) web - In addition to the classic email interface, you can view and post messages through the MORPHMET webpage at http://www.morphometrics.org site or access it directly at http://www.morphometrics.org/home/morphmet . Anyone can view the posts, but to add or reply to a post or request to subscribe via the web, you must be logged in to a Google account. You must be logged in to a subscribed account to post. There is a sign-in item at the bottom of the page. A basic account that will allow you to post or request a subscription is free and can be created at http://accounts.google.com (because I have multiple accounts, I cannot see what a user without an account would see here, but you can directly go to the site to create an account at https://accounts.google.com/signup?service=mail ). Enjoy! -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
MORPHMET - progress, but not there, yet.
I have been making progress preparing the migration to the new system, but not quite there, yet. I hope to have this done by or over the weekend. I am writing this to let you know that when MORPHMET does come back up, you will receive an invitation to join the new list (actually just the old list in a new environment). You need to reply to this message when you receive it to continue to be a subscriber to the new (=old) MORPHMET. -dslice
Re: Slicer question
Original Message Subject:Re: Slicer question Date: Mon, 28 Jul 2014 21:16:07 -0400 From: m...@uw.edu To: morphmet@morphometrics.org morphmet@morphometrics.org Hi Donna, We use it daily, what would you like to know? *From:* morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org *Sent:* Monday, July 28, 2014 4:33 PM *To:* morphmet@morphometrics.org mailto:morphmet@morphometrics.org - Forwarded message from Jones, Donna donna.jon...@cchmc.org - Date: Sat, 26 Jul 2014 12:01:24 -0400 From: Jones, Donna donna.jon...@cchmc.org Reply-To: Jones, Donna donna.jon...@cchmc.org Subject: Slicer question To: morphmet@morphometrics.org morphmet@morphometrics.org Dear Morphmet, Does anyone have experience working with 3D Slicer and dicom slices from microCT? If yes, I’d be interested in asking you some direct questions about functionality. Cheers, Donna * Donna C. Jones, Ph.D. Research Assistant Professor Division of Plastic Surgery Division of Biostatistics and Epidemiology Cincinnati Children's Hospital Medical Center Burnett Ave. ML 2020 Cincinnati, OH 45229 phone: 513-803-0383 donna.jon...@cchmc.org - End forwarded message -
MORPHMET - going down for upgrades
It is my intention to take morphmet down shortly (today?). I believe I have cleared all pending postings and subscription requests. If all goes well, it should be down for a few hours or a couple of days. Most likely the latter to give me a chance to test the new system. If all goes well, when it comes back online, users may see no difference whatsoever (other than improved performance) if they do not wish to, i.e., same mailing list as before. Others will be able to avail themselves of new features. Any messages posted during the downtime may be lost. On the other hand, if all does not go well, I suppose you may never hear from me again. =8O -dslice
Fwd: Re: Image rotation data loss
Original Message Subject: Re: Image rotation data loss Date: Sun, 29 Jun 2014 03:38:32 -0400 From: Dennis E. Slice dsl...@morphometrics.org To: morphmet@morphometrics.org First guess would be your landmarks are out of order on one or more specimens. You can check this by creating a set of links in tpsUtil and plotting the data showing the links. And/or, in tps, plot the data showing points and vectors. -ds On 6/29/14, 12:27 AM, morphmet_modera...@morphometrics.org wrote: Hello all, I'm trying to digitize photos in tpsDig for a geometric morphometrics study on Notropis fishes. In order to test for digitization error I've copied the first fish photo I took 10 times and digitized each one onto the same TPS file (made in tpsUtil). I then performed a relative warps analysis in tpsRelw and performed a Procruste's superimposition in R (package geomorph) to glance and see if any landmarks varied significantly. My results show very drastic variation in landmark placement, with dots all over the place in the GPA plot. I know my landmark placement isn't that bad, so I think it might have something to do with data loss. When I photographed the specimen the fish was flipped, so I had to rotate and flip it to turn it rightside up before digitization. Is it possible that rotating the photo resulted in data loss and therefore digitization error? The TPS file had the landmark coordinates for each specimen pretty close together (about normal landmark placement error), but the GPA and relative warps plots showed drastic variance. I've attached the GPA plot to show what I mean. The landmarks are supposed to go around the entire fish. Also let me know if you have any other ideas for why there might be crazy variance. Best, Connor connorfre...@utexas.edu mailto:connorfre...@utexas.edu - End forwarded message - - End forwarded message - - End forwarded message -
ANNOUNCEMENT: morphometrics.org to go down for upgrades
Sorry for jumping the queue, but... Over time, we have had a number of problems with message distribution on MORPHMET. The fundamental issue is that when multiple messages are distributed the host sometimes shuts down the list thinking it is spam. We believe the problem ultimately arises from the list exceeding the 1000-subscriber limit of the host system. Anyway, we have taken to approving a limit of five messages per day to try to avoid this. This is unacceptable. So,... In the very near future, the morphometrics.org domain will go down for major changes. If successful and despite the magnitude of the changes, subscribers may be insulated from noticing any difference at all besides the downtime if they so desire. Otherwise, we hope to have some major enhancements to MORPHMET for those who wish to avail themselves of them. Of immediate relevance to me is that this will also mean that my mail address at morphometrics.org will be inoperable for a while. This might be a couple of hours, a couple of days, or you might never hear from me again. Hopefully it will be something closer to the former than the latter. During this period, if you really need to contact me, please do so through my university (fsu.edu) address. I have come very close to pushing the button for this at least twice in the past, but hesitated about bringing the whole domain down. This time, I promise to push that button. I am currently (re)familiarizing myself with the necessary steps and software. I wanted to do it today, but we have events at the university that demand my attention Friday and early next week. So, I am thinking it will happen around the middle-to-end of next week. I would like an entire free day to deal with the transition and any associated problems. I will advise the membership immediately before the domain goes down. Thank you, Dennis E. Slice
RE: bilat.symmetry output in geomorph
Original Message Subject:RE: bilat.symmetry output in geomorph Date: Sun, 14 Jul 2013 18:30:13 -0400 From: Adams, Dean [EEOBS] dcad...@iastate.edu To: morphmet@morphometrics.org morphmet@morphometrics.org CC: Dean Adams (dcad...@iastate.edu) dcad...@iastate.edu Milos, At present, bilat.symmetry() does not return the symmetric components for each specimen. That is something we could add in the next version. As for FA, one can assess this for a population using bilat.symmetry() (see the help file for instructions). -- Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University Ames, Iowa 50011 www.public.iastate.edu/~dcadams/ http://www.public.iastate.edu/~dcadams/ phone: 515-294-3834 *From:*morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org] *Sent:* Saturday, July 13, 2013 10:16 PM *To:* morphmet@morphometrics.org *Subject:* bilat.symmetry output in geomorph - Forwarded message from Milos Blagojevic spearsata...@hotmail.com mailto:spearsata...@hotmail.com - Date: Sat, 13 Jul 2013 08:29:45 -0400 From: Milos Blagojevic spearsata...@hotmail.com mailto:spearsata...@hotmail.com Reply-To: Milos Blagojevic spearsata...@hotmail.com mailto:spearsata...@hotmail.com Subject: bilat.symmetry output in geomorph To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org morphmet@morphometrics.org mailto:morphmet@morphometrics.org Hi to all morphometricians, I was wondering how to use bilat.symmetry function from geomorph package in order to extract symmetric and asymmetric components of shape variation in the case of object symmetry. By looking at the function code it can be observed that DA.mns and FA.mns arrays are used for plotting shape changes associated with directional and fluctuating asymmetry, but they only represent extreme configurations. Is it possible to return landmark coordinate arrays for every individual so that they can be used as the gpagen$coords output, but separately for symmetric and asymmetric component of shape variation (individual scores on symmetric and asymmetric component and their coordinates)? Also I am wondering is there a way to quantify FA per populations (or any groups) using this package? Best regards, Milos Blagojevic, PhD student University of Kragujevac, Serbia - End forwarded message -
possible duplicate posts
Dear Morphmeters, I may sent out some duplicate messages from the past few days - some seemed familiar, though not in my personal archive. If so, I apologize. -the morphmet mod (dslice)
Re: Morpheus: java versions
Thought I would post an update. On one system running Apple OS X 10.8.4, I uninstalled Apple Java 1.6(1) and installed Oracle Java 1.7(2). Morpheus runs just fine in this environment, and there is no need to run the mac_os_x_prepare script. jEdit(3) is still partially broken, but looking into that. -ds (1) Deleted Java directory from /System/Library, requires admin-level access, e.g., sudo rm -rf ./Java (2) Requires installation of Java Development Kit (jdk) from here: http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html The Java Runtime Environment (jre) only installs web-related files. You need the jdk to run local, standalone applications like Morpheus et al. (3) jEdit is an excellent text editor that easily handles huge files and, especially, supports block/column-mode operations - great for moving around, editing, etc. columns of data in a text file. See. http://www.jedit.org/ -ds On 6/28/13 12:32 PM, Dennis E. Slice wrote: Some background and current status of Morpheus et al., Java Edition. The software was developed and tested on Mac OS X with the Apple-default Java version 1.6. The resulting distribution was tested on various Windows and Linux platforms available to me (mostly installations running on virtual machines). In those cases, the general structure worked, but Morpheus would not run because the default environments (in the VMs) did not have sufficient openGL capabilities. On an old MacBookPro, I installed Windows 7 and Linux. I upgraded the Windows 7 drivers and it worked fine. I was not successful upgrading the Ubuntu drivers for the MacBookPro given the limited time I spent trying. My students have reported it to run on various proper Windows and Linux systems, though some problems are reported on older, less contemporary systems probably due to openGL drivers. This is relevant because java 1.6 was provided and maintained by Apple, but Apple has suspended this effort as of 1.6 and has turned future development over to the general java development community. Apple's 1.6, in fact, is the source of the outdated (java3D) files require the execution of the mac_os_x_prepare script - they must be hidden from view. However, 1.6 is still, for now, the default installation when java programs are detected. A few days ago, I had to install Java 1.7 to run some lab code that requires that version. This broke two of my favorite programs, jEdit and Morpheus. Installing 1.6 alongside 1.7 allowed jEdit to run, but Morpheus still did not. There are two issues at play - the shift from Apple 1.6 to community-provided 1.7 and the difference between Oracle and the openJDK products. We are currently looking into this, and I have some leads that should address one or more of these issues. Also, I have information that some of these problems will be addressed in a new release of java due out this summer. I would generally prefer to avoid commenting on future developments, but I will a bit since it provides context for the current situation. The current 3D graphics in Morpheus use java3d running on top of jogl 2.0. We are currently developing a new graphics engine that will be built directly on top of jogl 2.0 and using OpenGL shader language. This is a significant and fundamental change, but better in the long term. This is also the reason I am reluctant to develop new graphics windows and options until we see what adjustments are necessary to the existing graphics objects to work with our new graphics engine. I will keep you posted. -ds
RE: tps format problem reading in R
Original Message Subject: RE: tps format problem reading in R Date: Wed, 3 Jul 2013 11:32:55 -0400 From: Adams, Dean [EEOBS] dcad...@iastate.edu To: morphmet@morphometrics.org morphmet@morphometrics.org Hi John, There were two issues here, and both of which have easy fixes. First, there is only 1 specimen in your tps file, and the current version of readland.tps() was written for datasets with more than one specimen (we didn't envision folks reading in a single specimen for a morphometric analysis). This is easily fixed by changing the 3rd to last line of the function as below. Next, your file had a non-numeric ID for the specimen. To catch this, change the 4th to last line of the function as below. These two lines should now read: ID -sub(ID=, , tpsfile[grep(ID, tpsfile)]) #delete the 'as.numeric' dimnames(coords)[[3]] - as.list(imageID) # add 'as.list' The updated function code is attached, and will be in the next update of geomorph. Thanks for catching these; this makes the function more general. Best, Dean -- Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University Ames, Iowa 50011 www.public.iastate.edu/~dcadams/ phone: 515-294-3834 -Original Message- From: morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org] Sent: Wednesday, July 03, 2013 1:31 AM To: morphmet@morphometrics.org Subject: tps format problem reading in R - Forwarded message from John Denton jden...@amnh.org - Date: Tue, 2 Jul 2013 23:04:22 -0400 From: John Denton jden...@amnh.org Reply-To: John Denton jden...@amnh.org Subject: tps format problem reading in R To: morphmet@morphometrics.org morphmet@morphometrics.org Hi folks, I'm trying to read a tps file in the geomorph v1.1-1 R package using readland.tps(file), but every time I try the above, I get the error Error in dimnames(coords)[[3]] - imageID : 'dimnames' must be a list In addition: Warning message: In readland.tps(Lter_mean.TPS) : NAs introduced by coercion I do not get the error when I read in some of my other tps files (all of which were produced using append files in tpsUtil). The file I'm trying to read in is the side-averaged Procrustes coordinates, generated in MorphoJ. I've checked the hidden formatting, the line breaks, the number of decimal places, and the file extension, but I can't seem to figure it out. The file is attached. ~John John S. S. Denton Ph.D. Candidate Department of Ichthyology and Richard Gilder Graduate School American Museum of Natural History www.johnssdenton.com - End forwarded message - readland.tps Description: Binary data
Remembrances of Robert Sokal
[Added to the Announcements page at www.morphometrics.org -the morphmet moderator (dslice)] Remembrances of Robert Sokal Save the date: Sunday November 18, 2-4 P.M., Wang Center Chapel at Stony Brook University Robert Sokal passed away last April and his funeral and memorial service were completed quickly in accordance with his faith. Because of his great impact as a beloved friend, mentor, scholar, and university citizen we would like to give Bob’s family, friends, and colleagues an opportunity to remember him at a public memorial, open to all who wish to remember fondly his many contributions to our lives. We ask that you register at the link given below as soon as possible so we can get an idea of how many will attend. We ask especially that you indicate whether you would like to speak, send text for a brief remembrance, or even a brief video (less than one minute, please). We look forward to your response, Warmly, Jim Rohlf and Jeff Levinton http://life.bio.sunysb.edu/ee/memsokal/memorial.html
RE: multi-class ANOVA analogue for geometric morphometrics
Original Message Subject: RE: multi-class ANOVA analogue for geometric morphometrics Date: Mon, 4 Jun 2012 14:59:23 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu Organization: Stony Brook University To: morphmet@morphometrics.org Once you have projected your shapes into the tangent space (e.g., partial warp scores) then you have what can be treated as ordinary multivariate data. You can use any multivariate method that is appropriate for the questions you wish to ask. Note that you should not normally use Goodall's test as it makes many unrealistic assumptions and thus in practice has much higher Type I error rates than you would expect. -- F. James Rohlf, John S. Toll Professor, Stony Brook University The much revised 4th editions of Biometry and Statistical Tables are now available: http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf Please consider the environment before printing this email -Original Message- From: morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org] Sent: Monday, June 04, 2012 2:05 AM To: morphmet@morphometrics.org Subject: multi-class ANOVA analogue for geometric morphometrics - Forwarded message from Robert Richardson - Date: Fri, 1 Jun 2012 17:42:44 -0400 From: Robert Richardson Reply-To: Robert Richardson Subject: multi-class ANOVA analogue for geometric morphometrics To: morphmet-requ...@morphometrics.org Fellow morphers, I'm familiar with the need to account for the lower degrees of freedom, when testing for differences between groups, hence the use of Goodall's-F test. However, as with basic (M)ANOVA, that just tells you if there's at least one group that's statistically different but doesn't identify which one(s) when you have more than two categories. Are there multi-class (M)ANOVAs (e.g. Ryan-Einot-Gabrial-Welsch Q-test or Tukey's test) that are out there that will directly identify which categories are different when dealing with many categories (e.g. samples from seven geographical locations)? Maybe there's a way to load the data into an R-script and manually adjust the degrees of freedom for a regular multi-category (M)ANOVA? Thanks for the input! Robert- -- === === === === Robert Richardson, PhD candidate Department of Biology Portland State University 1719 SW 10th Ave; SB 2, #246 Portland, OR 97201 503.725.8004; r...@pdx.edu === === === === - End forwarded message -
RE: CV shape variation
Original Message Subject:RE: CV shape variation Date: Mon, 4 Jun 2012 15:05:53 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu Organization: Stony Brook University To: morphmet@morphometrics.org I am not sure of the question being asked. Perhaps what was meant was how to visualize the shape deformation implied by changes along each axis? I think the CVAGen6 software has an option for that. Basically, one regresses shape on the CVA scores. This can be done in the tpsRegr software. -- F. James Rohlf, John S. Toll Professor, Stony Brook University The much revised 4^th editions of Biometry and Statistical Tables are now available: http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf PPlease consider the environment before printing this email *From:*morphmet_modera...@morphometrics.org [mailto:morphmet_modera...@morphometrics.org] *Sent:* Monday, June 04, 2012 2:03 AM *To:* morphmet@morphometrics.org *Subject:* Re: CV shape variation - Forwarded message from Philipp Mitteröcker - Date: Fri, 1 Jun 2012 05:52:44 -0400 From: Philipp Mitteröcker Reply-To: Philipp Mitteröcker Subject: Re: CV shape variation To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org For a single canonical variate, you can compute the variance along this CV and divide it by the total variance (computed, e.g., as the sum of the variances of all variables). But in contrast to PCA, you cannot add up the variances for two or more CVs, because the CV axes are not orthogonal. You could compute the variance within the plane spanned by two CVs when orthogonalizing the two CV axes. However, explained variance among the individuals is not often reported for CVA, as it is not the quantity that is maximized. Best, Philipp Am 01.06.2012 um 06:27 schrieb morphmet_modera...@morphometrics.org http://mailto:morphmet_modera...@morphometrics.org: - Forwarded message from beatriz gamarra- Date: Wed, 30 May 2012 13:29:58 -0400 From: beatriz gamarra Reply-To: beatriz gamarra Subject: CV shape variation To:morphmet-requ...@morphometrics.org http://mailto:morphmet-requ...@morphometrics.org Hi, I amanalyzinga dataset with 12 landmarks and 12 groups. I have run CVA by using CVAGen6 from IMP and I want to obtain the shape variation associated with first CVs. How could I achieve? Thanks in advance. Beatriz Gamarra - End forwarded message - ___ Dr. Philipp Mitteroecker Department of Theoretical Biology University of Vienna Althanstrasse 14 A-1090 Vienna, Austria Tel: +43 1 4277 56705 Fax: +43 1 4277 9544 email: philipp.mitteroec...@univie.ac.at http://mailto:philipp.mitteroec...@univie.ac.at homepage: http://theoretical.univie.ac.at/people/mitteroecker - End forwarded message -
PhD in morphological evolution
Original Message Subject: PhD in morphological evolution Date: Wed, 23 May 2012 05:35:58 -0400 From: coue...@mnhn.fr To: morphmet@morphometrics.org Hello, You'll find below a PhD subject proposed to the Ecole Pratique des Hautes Etudes (France) The subject (and ONE applicant) will be proposed to the EPHE, examined and the applicant will be interviewed in order to get the fellowship. Interviws are planned on July 4th and 5th in Paris. For further informations, please go to the EPHE website: http://www.ephe.sorbonne.fr/recherche/contrat-doctoral-2012.html) Applicants must contact Pr.Sophie Montuire (sophie.montu...@u-bourgogne.fr) before june 20th 2012. - Ecole Pratique des Hautes Etudes PhD Section of Life and Earth sciences Title: Evolutionary novelties and emergence of dental phenotypes in Mammals. Host laboratory: EPHE Paléobiodiversité et évolution UMR 6282 Biogéosciences Laboratory address: UMR 6282 uB/CNRS Biogéosciences Phone / Fax 6 bd Gabriel, 2100 Dijon, FRANCE +333 80 39 63 47 / +333 80 39 63 87 PhD supervisors: Names: Montuire Sophie, Couette Sébastien, Navarro Nicolas Address: UMR 6282 uB/CNRS Biogéosciences, 6 bd Gabriel, 2100 Dijon, FRANCE Téléphone /Fax +333 80 39 63 47 / +333 80 39 63 87 Emails : sophie.montu...@u-bourgogne.fr, sebastien.coue...@u-bourgogne.fr, nicolas.nava...@u-bourgogne.fr Descriptions and objectives Background Mammals display a high dental diversity in terms of number and complexity of teeth. This diversity attests of the influence of several parameters including diet and suggests a mammalian morphospace on which shape changes are possible in every direction. However, morphological changes within lineages seem to be constrained. Developmental processes producing the phenotypic expression of genetic variation are under natural selection. Favouring or limiting some directions of change in the morphospace, these processes will modify the evolutionary capacity on the short and long time scales. These constraints can influence the diversity of a clade (at a macroevolutionay level), forcing the accumulation of new species in one peculiar direction of the morphospace. In the dental raw the eruption of teeth follows an iterative developmental model in which interactions between teeth are controlled and lead to a final dental phenotype. Within teeth themselves, interactions occur between cusps following the same iterations and defining tooth morphology (number, position and shape of cusps). Some recent works showed that small modifications of cusp interactions can imply large modifications at the tooth scale, and for instance the development of new cusps. Objectives This subject will focus on two different mammal groups (rodents and primates) at different scales (population, lineages, clades). Complementary approaches will be addressed by both groups. Rodents display a reduced variation of the dental formula but a high diversity of molar form. In primates, the major part of variation occurs on the number of teeth and number of cusps on each tooth rather than on their shape. The main goal of this project is to understand the cusp interactions and their consequences on dental formula and teeth complexity (gains or losses of cusps and teeth). These variations of complexity will be analysed in the historic and evolutionary frameworks of the groups, and of the biotic (size, diet ) and abiotic parameters. National and international context The « EPHE -Paléobiodiversité et évolution » and « UMR uB/CNRS 6282 Biogéosciences » laboratories have national and international recognition for their knowledge and skills in form analysis. The evolution of dental morphology in rodents and especially Arvicolinae is an historic and major topic of the EPHE laboratory since it establishment. These last years, people from the laboratory developed international collaborations on Evo-Devo themes on teeth. -- Sébastien Couette Maitre de Conférences Laboratoire EPHE d'Evolution des Primates Muséum national d'Histoire naturelle Département Histoire de la Terre Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P) UMR 7207 du CNRS/MNHN/UPMC 8, rue Buffon CP 38 F-75231 Paris cedex 05 Tel.: (+33) 1 40793061 PhD proposal.doc Description: MS-Word document
tpsUtil update
Original Message Subject:tpsUtil update Date: Wed, 23 May 2012 21:46:50 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu Organization: Stony Brook University To: morphmet@morphometrics.org I have just uploaded version 1.49 to the Stony Brook University server at http://life.bio.sunysb.edu/morph It improved on some error messages when invalid files were loaded. -- F. James Rohlf, John S. Toll Professor, Stony Brook University The much revised 4^th editions of Biometry and Statistical Tables are now available: http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf PPlease consider the environment before printing this email
Geometric Morphometrics courses
Original Message Subject: Geometric Morphometrics courses Date: Fri, 25 May 2012 05:06:01 -0400 From: Soledad Esteban soledad.este...@icp.cat To: morphmet@morphometrics.org Dear colleagues: This e-mail is to inform you of some courses on Geometric Morphometrics, which may would be of your interest. I would appreciate if you could distribute this information between your colleagues: Introduction to Geometric Morphometrics. June 12-15, 2012. Instructors: Dr. Chris Klingenberg (University of Manchester, UK) and Dr. Jesús Marugán-Lobón (Universidad Autónoma de Madrid). Just 5 places left. More information at: http://www.transmittingscience.org/introduction_to_gm.htm “3D Geometric Morphometrics”. July 17-20, 2012. Instructor: Dra Melissa Tallman (CUNY/AMNH, New York). Early registration until May 31. More information at: http://www.transmittingscience.org/3d_gm.htm “Geometric Morphometrics and Phylogeny”. September 4-7, 2012. Instructor: Dr. Chris Klingenberg (University of Manchester, UK). More information at: http://www.transmittingscience.org/gm_and_phylogeny.htm For any questions: cour...@transmittingscience.org. These courses will be held in the premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont (Barcelona, Spain). They are co-organized by Transmitting Science and el Institut Catalá de Paleontologia Miquel Crusafont. Best regards Soledad De Esteban Trivigno Area de Paleobiología Institut Català de Paleontologia Edifici ICP, Campus de la UAB 08193 Cerdanyola del Vallès Barcelona. Spain 00-34-935868334 www.icp.cat
Re: EVAN Toolbox lighting problem
Original Message Subject:Re: EVAN Toolbox lighting problem Date: Thu, 17 May 2012 06:58:11 -0400 From: Helgi Pétur Gunnarsson helgipe...@gmail.com To: morphmet@morphometrics.org Hello Stephanie, The lighting sometimes can get messed up if you do a GPA on the surface (pass it through the GPA node). There is no easy solution but there may be a workaround, but it requires you to change the network a little. You could try to export the procrustes fitted surface, import again, and use it without sending it through the GPA node. This is what you have to do: Export the surface - connect the surface output of the GPA node to an Export node. - run the network again - export the surface from the Export node Then Import the surface again. - select the newly exported surface file from the Import node Use the surface in your network without sending it through the GPA node. - delete the links that lead to and from the surface ports of the GPA node - connect the surface directly from the Import Node to the Warper node. - run the network again If that does not work, you could also try to save the surface in another format (for example *.ply). Hope this helps, Helgi Petur Gunnarsson Evan Society On 16 May 2012 23:10, morphmet morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org wrote: Original Message Subject:EVAN Toolbox lighting problem Date: Wed, 16 May 2012 16:21:40 -0400 From: Stephanie Kozakowski stephanie.kozakowski@__utoronto.ca mailto:stephanie.kozakow...@utoronto.ca To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org Hi all, I am using the EVAN Toolbox v.1.52 and am having trouble getting the light to shine on the appropriate area of the object during surface warping in the 3D viewer. For example, the light will be shining on the inferior and posterior portions of the skull I am warping. However I would prefer to show the warpings in sagittal view but am unable to since the surface is completely black. Can the lighting be controlled within the Toolbox? If not, is there a way I can change where the light shines in the .stl surface file before loading it into the Toolbox? Sincerely, Stephanie Kozakowski Ph.D Candidate Evolutionary Anthropology University of Toronto stephanie.kozakowsk@utoronto.__ca mailto:stephanie.kozako...@utoronto.ca mailto:stephanie.kozakowsk@__utoronto.ca mailto:stephanie.kozako...@utoronto.ca
RE: Soft tissue analyse
Original Message Subject: RE: Soft tissue analyse Date: Tue, 15 May 2012 01:03:26 -0400 From: Ivan Huber i...@randomtech.com To: morphmet@morphometrics.org morphmet@morphometrics.org Interesting problem,. What about either freezing the organ in a standard way or preserving it in an appropriate solution, possibly formaldehyde or Bouin's. Please let us know-- What organ and what animal? Best wishes, Ivan Huber -Original Message- From: morphmet [mailto:morphmet_modera...@morphometrics.org] Sent: Monday, May 14, 2012 12:33 AM To: morphmet Subject: Re: Soft tissue analyse Original Message Subject: Re: Soft tissue analyse Date: Sun, 13 May 2012 13:04:45 -0400 From: Carmelo Fruciano c.fruci...@unict.it To: morphmet@morphometrics.org Dear all, I would like to quantify the shape of an soft tissue organ. However I am not sure what would be the best method to use. Working with soft tissue organs, I am having two problems: one is the absent of landmarks, and the other is that sometimes the preparation of the specimens may cause some deformations on the shape. Is there any way to get around this situation? Dear Julia, I think that your question is a bit tricky as not everyone likes semilandmarks and the like. My idea is that if the organ you're interested in is so soft and flexible that you cannot realy imagine a standard situation, then it's a bit too tricky and studying shape variation might even be not particularly meaningful in itself. On the other hand, if there is some sort of normal status that you can imagine your organ in (and you can get your organ in this status), then you can use sliding semilandmark or other outline methods. About the deformation, apart the obvious of avoiding it, if it's somewhat predictable then maybe it can be modeled and removed from your data. Sorry if I sound too vague but your question is quite general... I hope that the answer is of some help, though... Best, Carmelo -- Carmelo Fruciano Post-doc - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ Universita' di Catania - A.P.Se.Ma. Servizio di Posta Elettronica
correcting for body size
Original Message Subject: correcting for body size Date: Tue, 15 May 2012 11:03:28 -0400 From: Saad Arif arifs...@gmail.com To: morphmet@morphometrics.org Hello all, I have linear measurements for eye area and body size in Drosophila. I want to get residuals for eye area by regressing it on body size. Both variables appear to have a straight-line relationship. my question is: do i need to square my body size measurement before i regress it to eye area even if they are both seemingly linearly related? Any response would be appreciated! Thanks in advance. Saad
Re: Soft tissue analyse
Original Message Subject: Re: Soft tissue analyse Date: Wed, 16 May 2012 08:26:16 -0400 From: Kim van der Linde k...@kimvdlinde.com To: morphmet@morphometrics.org CC: morphmet morphmet_modera...@morphometrics.org I would suggest looking into techniques that go beyond the techniques using landmarks. One article for which I have a reference handy is Parr, WCH, Ruto, A, Soligo, C and Chatterjee, HJ (2011) Allometric shape vector projection: A new method for the identification of allometric shape characters and trajectories applied to the human astragalus (talus), Journal of Theoretical Biology, 272, 64–71. Good luck... Kim On 5/13/2012 12:15 PM, morphmet wrote: Original Message Subject: Soft tissue analyse Date: Wed, 9 May 2012 12:55:57 -0400 From: Julia Klaczko jklac...@gmail.com To: morphmet@morphometrics.org Dear all, I would like to quantify the shape of an soft tissue organ. However I am not sure what would be the best method to use. Working with soft tissue organs, I am having two problems: one is the absent of landmarks, and the other is that sometimes the preparation of the specimens may cause some deformations on the shape. Is there any way to get around this situation? Thank you very much for your help, Julia -- http://www.kimvdlinde.com
Re: correcting for body size
Original Message Subject: Re: correcting for body size Date: Wed, 16 May 2012 08:30:33 -0400 From: Kim van der Linde k...@kimvdlinde.com To: morphmet@morphometrics.org CC: morphmet morphmet_modera...@morphometrics.org You effectively ask for an allometric regression. 1. take the square root of the eye area 2. log transform the measurements 3. use a type 2 regression (major axis, reduced major axis) 4. calculate the distance between the point and the regression line This should do it. Kim On 5/16/2012 2:59 AM, morphmet wrote: Original Message Subject: correcting for body size Date: Tue, 15 May 2012 11:03:28 -0400 From: Saad Arif arifs...@gmail.com To: morphmet@morphometrics.org Hello all, I have linear measurements for eye area and body size in Drosophila. I want to get residuals for eye area by regressing it on body size. Both variables appear to have a straight-line relationship. my question is: do i need to square my body size measurement before i regress it to eye area even if they are both seemingly linearly related? Any response would be appreciated! Thanks in advance. Saad -- http://www.kimvdlinde.com
EVAN Toolbox lighting problem
Original Message Subject:EVAN Toolbox lighting problem Date: Wed, 16 May 2012 16:21:40 -0400 From: Stephanie Kozakowski stephanie.kozakow...@utoronto.ca To: morphmet@morphometrics.org Hi all, I am using the EVAN Toolbox v.1.52 and am having trouble getting the light to shine on the appropriate area of the object during surface warping in the 3D viewer. For example, the light will be shining on the inferior and posterior portions of the skull I am warping. However I would prefer to show the warpings in sagittal view but am unable to since the surface is completely black. Can the lighting be controlled within the Toolbox? If not, is there a way I can change where the light shines in the .stl surface file before loading it into the Toolbox? Sincerely, Stephanie Kozakowski Ph.D Candidate Evolutionary Anthropology University of Toronto stephanie.kozako...@utoronto.ca mailto:stephanie.kozako...@utoronto.ca
Re: Soft tissue analyse
Original Message Subject: Re: Soft tissue analyse Date: Sun, 13 May 2012 13:04:45 -0400 From: Carmelo Fruciano c.fruci...@unict.it To: morphmet@morphometrics.org Dear all, I would like to quantify the shape of an soft tissue organ. However I am not sure what would be the best method to use. Working with soft tissue organs, I am having two problems: one is the absent of landmarks, and the other is that sometimes the preparation of the specimens may cause some deformations on the shape. Is there any way to get around this situation? Dear Julia, I think that your question is a bit tricky as not everyone likes semilandmarks and the like. My idea is that if the organ you're interested in is so soft and flexible that you cannot realy imagine a standard situation, then it's a bit too tricky and studying shape variation might even be not particularly meaningful in itself. On the other hand, if there is some sort of normal status that you can imagine your organ in (and you can get your organ in this status), then you can use sliding semilandmark or other outline methods. About the deformation, apart the obvious of avoiding it, if it's somewhat predictable then maybe it can be modeled and removed from your data. Sorry if I sound too vague but your question is quite general... I hope that the answer is of some help, though... Best, Carmelo -- Carmelo Fruciano Post-doc - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ Universita' di Catania - A.P.Se.Ma. Servizio di Posta Elettronica
Re: Head Shape Question
Original Message Subject:Re: Head Shape Question Date: Sun, 13 May 2012 14:15:46 -0400 From: kalpana das kkalpanaa1...@gmail.com To: morphmet@morphometrics.org Dear Dustin, I had somewhat similar kind of question.I used sliding semilandmark method to capture the snout shape in frog. You can try selecting the landmark along a curve in TpsDIG and then change those landmarks into sliding semilandamrks in TPSutil. I think this way you can be able to capture the outline. Correct me if i am wrong. Regards, Kalpana On Sun, May 13, 2012 at 9:43 PM, morphmet morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org wrote: Original Message Subject: Head Shape Question Date: Mon, 7 May 2012 15:07:29 -0400 From: Owen, Dustin A dao...@bsu.edu mailto:dao...@bsu.edu To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org morphmet@morphometrics.org mailto:morphmet@morphometrics.org I am an undergraduate researcher looking to describe differences in head shape among male and female salamanders. I have been using tpsDig, but have had no success with the outline function. I would ideally like to outline the entire head and have a set number of landmarks digitally placed along the curve. Dustin Owen dao...@bsu.edu mailto:dao...@bsu.edu -- *Kalpana* MSc.Biodiversity and Conservation(2009-11) University School of Environment Management Guru Gobind Sigh Indraprastha University Dwarka,Delhi-110075 Email- kkalpanaa1...@gmail.com mailto:email-kkalpanaa1...@gmail.com Mobile no-9620313751/8010255368 /Not everything that counts can be counted, and not everything that can be counted counts. /
Soft tissue analyse
Original Message Subject:Soft tissue analyse Date: Wed, 9 May 2012 12:55:57 -0400 From: Julia Klaczko jklac...@gmail.com To: morphmet@morphometrics.org Dear all, I would like to quantify the shape of an soft tissue organ. However I am not sure what would be the best method to use. Working with soft tissue organs, I am having two problems: one is the absent of landmarks, and the other is that sometimes the preparation of the specimens may cause some deformations on the shape. Is there any way to get around this situation? Thank you very much for your help, Julia -- Julia Klaczko Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology Harvard University 26 Oxford St. Cambridge, MA 02138 phone: 617-384-8437 tel:617-384-8437
RE: permutations in TPSRegr and asymmetry in pictures
Original Message Subject: RE: permutations in TPSRegr and asymmetry in pictures Date: Thu, 26 Apr 2012 22:07:27 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu Organization: Stony Brook University To: morphmet@morphometrics.org What the tpsRegr program does is pretty simple. For the 'all option' it just scrambles the order of the independent variable relative to the dependent variable across all individual specimens. For within blocks it simply scrambles the order within each block (it assume blocks correspond to adjacent specimens in the input files). An example could be where the blocks corresponded to individuals and a pair of observations within each block could correspond to its shape before and after some treatment that could change its shape. For the among blocks option it scrambles the order of the blocks but keeps each block intact. This would give a user an idea of how important the blocks were. I will have to add more text to the help file! I should add some more options to make the program more flexible. Jim -- F. James Rohlf, John S. Toll Professor, Stony Brook University The much revised 4th editions of Biometry and Statistical Tables are now available: http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf Please consider the environment before printing this email -Original Message- From: morphmet [mailto:morphmet_modera...@morphometrics.org] Sent: Wednesday, April 25, 2012 5:00 PM To: morphmet Subject: permutations in TPSRegr and asymmetry in pictures Original Message Subject: permutations in TPSRegr and asymmetry in pictures Date: Mon, 23 Apr 2012 07:16:58 -0400 From: andrea cardini alcard...@gmail.com To: morphmet@morphometrics.org Dear Morphometricians, please, has anyone got any experience with the different options for permutation tests in TPSRegr? I did not manage to find an example in the help file but I may have missed it and would really like to find something like the detailed protocol Jim describes for the test of common slopes etc. A second unrelated question. I was wondering how studies of asymmetries might be affected by using pictures of 3D objects (e.g., human faces). I can easily imagine biases that could spuriously introduce DA in the data and may not be obvious to detect. Even without any systematic error, I wonder whether the 2D approximation of a 3D object may affect FA. Thanks for your help. Cheers Andrea Dr. Andrea Cardini Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi 213, 41100, Modena, Italy tel: 0039 059 2055017 ; fax: 0039 059 2055548 Centre for Anatomical and Human Sciences University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of York, Heslington, York YO10 5DD, UK Centre for Forensic Science , The University of Western Australia 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: alcard...@gmail.com, andrea.card...@unimore.it Webpage: http://sites.google.com/site/hymsfme/drandreacardini Editorial board for: Zoomorphology: http://www.springer.com/life+sciences/animal+sciences/journal/435 Journal of Zoological Systematics and Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/
Re: Alternatives to Geomagic (UNCLASSIFIED)
Correction as per Dr. Corner: archit...@headus.com.au should be archi...@headus.com.au. -the mod [dslice] On 5/1/12 11:38 PM, morphmet_modera...@morphometrics.org wrote: - Forwarded message from Corner, Brian D CIV (US) - Date: Tue, 1 May 2012 12:49:27 + From: Corner, Brian D CIV (US) Reply-To: Corner, Brian D CIV (US) Subject: Alternatives to Geomagic (UNCLASSIFIED) To: morphmet_modera...@morphometrics.org Classification: UNCLASSIFIED Caveats: NONE RapidForm is more expensive than GeoMagic, at least it was until GM raised its price. I’ve pretty much given up working with MeshLab, after spending a very frustrating afternoon trying to merge a couple very high density meshes. Too many crashes and quirks. In the 3d Lab here at the US Army Natick Soldier RDEC, we used CySlice and related software from Headus (http://www.headus.com.au/home). Headus is run by Phil Dench Jill Smith (Perth, Australia) who started supporting Cyberware scan merging editing way back when (1995-ish). Phil’s software is very useful and more-or-less user friendly (we call it Phil-friendly). He uses his own flavor of PLY which cannot be read by MeshLab, kind of a pain but we wrote a little converter we can share. His on-line email support is superb. Price is reasonable and within the range of most grants. He has provided 30-day trials in the past. You may contact Headus through the above link or Phil directly at archit...@headus.com.au http://mailto:archit...@headus.com.au. For full disclosure, I have an on-going contract with Headus to support the software we purchased. Cheers, -bc * Brian D. Corner, PhD Research Anthropologist WarSTAR US Army Natick Soldier RDEC Comm: 508-233-5317 DSN: 256-5317 ** * Note new email address as of 25 April 2012 * *brian.d.corner@mail.mil* Classification: UNCLASSIFIED Caveats: NONE - End forwarded message - -- /* Replies will be sent to the (moderated) list. */ For more information visit http://www.morphometrics.org
Re: Regression of Shape with size
Original Message Subject:Re: Regression of Shape with size Date: Wed, 2 May 2012 10:09:13 -0400 From: Antigoni Kaliontzopoulou ant...@gmail.com To: morphmet@morphometrics.org Hello Kaplana, if your images were not made from the same distance and you don't have a size reference within them that you can use to calibrate and calculate a scale factor, you are actually lacking information about size in your coordinates. This means that centroid size is not a correct measure of size in your case (it is OK for the Procrustes superimposition but it doesn't represent the relative size of your specimens, because it is not standardised). You could use SVL as the size measure, but that would give you a result that is difficult to interpret, as it would tell you about the allometry of the shape of the structure you are studying on total body size (but not of shape on size of the structure, which can be tricky because you can have different allometry components in your system). The best solution would be if you have some size measure you can use to calibrate your photographs. This does not need to be necessarily millimetric paper or a ruler: if you have in your pictures a structure that you have measured (a linear biometric variable you can see well and without distortion in the photos), you can use that (you would need to set the reference lengths for each specimen in tpsDig, say by indicating the distance between the eyes of each animal and inputting the equivalent measure). Hope this helps Antigoni On Wed, May 2, 2012 at 8:38 AM, morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org wrote: - Forwarded message from kalpana das __ - Date: Wed, 2 May 2012 06:13:10 -0400 From: kalpana das __ Reply-To: kalpana das __ Subject: Regression of Shape with size To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org Dear all, I want to regress the size on shape and want to see how shape is changing with respect to size. But i have images without scale factor. So ,I was just wondering if it is appropriate to use SVL (snout to vent length in frogs which is equivalent to total body length) as size instead of centroid size in Tpsregr Programm. Or is there any other way i can put the scale in images .? Any kind of suggestion is welcome. Thank you Regards, Kalpana -- *Kalpana* MSc.Biodiversity and Conservation(2009-11) University School of Environment Management Guru Gobind Sigh Indraprastha University Dwarka,Delhi-110075 Email- kkalpanaa1...@gmail.com http://mailto:email-kkalpanaa1...@gmail.com Mobile no-9620313751/8010255368 /Not everything that counts can be counted, and not everything that can be counted counts. / - End forwarded message - __ -- Antigoni Kaliontzopoulou CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Campus Agrário de Vairão, 4485-661 Vairão PORTUGAL Department of Ecology, Evolution, and Organismal Biology Iowa State University, Ames, Iowa 50011, USA tel: +351 91 3086188 mail to: ant...@gmail.com mailto:ant...@gmail.com antig...@mail.icav.up.pt mailto:antig...@mail.icav.up.pt
Re: Regression of Shape with size
Original Message Subject: Re: Regression of Shape with size Date: Wed, 2 May 2012 17:01:05 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu To: Morphmet morphmet@morphometrics.org If you have the SVL for each specimen then you can use that to set the scale for each specimen in tpsDig - assuming that you can see the entire distance in each image. You then can use centroid size. --- Sent remotely by F. James Rohlf, John S. Toll Professor, Stony Brook University -Original Message- From: morphmet morphmet_modera...@morphometrics.org Date: Wed, 02 May 2012 16:51:27 To: morphmetmorphmet@morphometrics.org Reply-To: morphmet@morphometrics.org Subject: Re: Regression of Shape with size Original Message Subject:Re: Regression of Shape with size Date: Wed, 2 May 2012 10:09:13 -0400 From: Antigoni Kaliontzopoulou ant...@gmail.com To: morphmet@morphometrics.org Hello Kaplana, if your images were not made from the same distance and you don't have a size reference within them that you can use to calibrate and calculate a scale factor, you are actually lacking information about size in your coordinates. This means that centroid size is not a correct measure of size in your case (it is OK for the Procrustes superimposition but it doesn't represent the relative size of your specimens, because it is not standardised). You could use SVL as the size measure, but that would give you a result that is difficult to interpret, as it would tell you about the allometry of the shape of the structure you are studying on total body size (but not of shape on size of the structure, which can be tricky because you can have different allometry components in your system). The best solution would be if you have some size measure you can use to calibrate your photographs. This does not need to be necessarily millimetric paper or a ruler: if you have in your pictures a structure that you have measured (a linear biometric variable you can see well and without distortion in the photos), you can use that (you would need to set the reference lengths for each specimen in tpsDig, say by indicating the distance between the eyes of each animal and inputting the equivalent measure). Hope this helps Antigoni On Wed, May 2, 2012 at 8:38 AM, morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org wrote: - Forwarded message from kalpana das __ - Date: Wed, 2 May 2012 06:13:10 -0400 From: kalpana das __ Reply-To: kalpana das __ Subject: Regression of Shape with size To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org Dear all, I want to regress the size on shape and want to see how shape is changing with respect to size. But i have images without scale factor. So ,I was just wondering if it is appropriate to use SVL (snout to vent length in frogs which is equivalent to total body length) as size instead of centroid size in Tpsregr Programm. Or is there any other way i can put the scale in images .? Any kind of suggestion is welcome. Thank you Regards, Kalpana -- *Kalpana* MSc.Biodiversity and Conservation(2009-11) University School of Environment Management Guru Gobind Sigh Indraprastha University Dwarka,Delhi-110075 Email- kkalpanaa1...@gmail.com http://mailto:email-kkalpanaa1...@gmail.com Mobile no-9620313751/8010255368 /Not everything that counts can be counted, and not everything that can be counted counts. / - End forwarded message - __ -- Antigoni Kaliontzopoulou CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Campus Agrário de Vairão, 4485-661 Vairão PORTUGAL Department of Ecology, Evolution, and Organismal Biology Iowa State University, Ames, Iowa 50011, USA tel: +351 91 3086188 mail to: ant...@gmail.com mailto:ant...@gmail.com antig...@mail.icav.up.pt mailto:antig...@mail.icav.up.pt
CT Scan + MorphoJ
Original Message Subject: CT Scan + MorphoJ Date: Wed, 18 Apr 2012 23:14:11 -0400 From: Gabrielle Openshaw gabrielle.opens...@gmail.com To: morphmet@morphometrics.org Hi all, Has anybody tried using CT scan data in MorphoJ? I want to analyse skull shape disparity and really need to avoid damaging specimens so am using a CT scanner to acquire shape data. However, I am only really familiar with 2D analysis in MorphoJ, and most 3D studies that use MorphoJ seem to use a surface scanner (digitizer). Can MorphoJ handle large CT files, or do I need to change them in some way? If anybody has any suggestions for landmark digitization or an alternative program for analysis of CT data, please let me know! Thanks in advance!! Gabi Openshaw (gabrielle.opens...@gmail.com)
permutations in TPSRegr and asymmetry in pictures
Original Message Subject: permutations in TPSRegr and asymmetry in pictures Date: Mon, 23 Apr 2012 07:16:58 -0400 From: andrea cardini alcard...@gmail.com To: morphmet@morphometrics.org Dear Morphometricians, please, has anyone got any experience with the different options for permutation tests in TPSRegr? I did not manage to find an example in the help file but I may have missed it and would really like to find something like the detailed protocol Jim describes for the test of common slopes etc. A second unrelated question. I was wondering how studies of asymmetries might be affected by using pictures of 3D objects (e.g., human faces). I can easily imagine biases that could spuriously introduce DA in the data and may not be obvious to detect. Even without any systematic error, I wonder whether the 2D approximation of a 3D object may affect FA. Thanks for your help. Cheers Andrea Dr. Andrea Cardini Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi 213, 41100, Modena, Italy tel: 0039 059 2055017 ; fax: 0039 059 2055548 Centre for Anatomical and Human Sciences University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of York, Heslington, York YO10 5DD, UK Centre for Forensic Science , The University of Western Australia 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: alcard...@gmail.com, andrea.card...@unimore.it Webpage: http://sites.google.com/site/hymsfme/drandreacardini Editorial board for: Zoomorphology: http://www.springer.com/life+sciences/animal+sciences/journal/435 Journal of Zoological Systematics and Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/
No Subject: one of the most remarkable, scientific artifacts of our time -the mod
Original Message Date: Sun, 22 Apr 2012 07:59:15 -0700 From: Fred Bookstein f...@brainmap.stat.washington.edu To: morphmet_modera...@morphometrics.org April 22, 2012 Dear colleagues, Anybody who finds themselves anywhere near Vienna during the next eight weeks should make a side trip to the Ring to see one of the most remarkable scientific artifacts of our time: a four-meter-tall (lifesize) cast of the surface of a living 2000-year-old olive tree. This remarkable object is not in the Naturhistorische Museum where it ought to be, but instead finds itself in the Theseustempel, the little building inside the Volksgarten that originally housed the statue Theseus and the Centaur before it was moved to the landing of the grand staircase in the then-new Kunsthistorische Museum in 1891. Here in the Tempel the cast of the tree is displayed as an art object, entitled wisdom? peace? blank? all of this?, by the contemporary Swiss conceptual artist Ugo Rondinone, of whom I had never previously heard. I found some good views of it on Google Image, particularly this one, which shows the scale (and the ceiling of the Tempel): http://derstandard.at/1334795666279/Wiener-Volksgarten-Der-Wind-als-Bildhauer [the German phrase there means The wind as sculptor]. Whether a representation of a particular superannuated organism or instead a work of art, this object forces us to keep in mind the immense complexity of organismal form (a trope first treated in biomathematical terms by Walter Elsasser around 1975) and the likewise immense difficulty of saying, in any abstract language, what the form of an organism actually is. In this role the Rondinone piece supplies an endlessly paradoxical series of challenges to the foundations of any competent morphometrics, whether zoological or botanical. I recommend the images to anybody on this mailing list and the object itself to anyone within a couple of hundred miles of Vienna anytime from now through June 24, when the exhibit closes and the object is removed. The exhibit is free, by the way. If you like olive trees as symbols of human transience, here's another photo: http://www.dhm.de/ausstellungen/mueller/k_0.htm. The human is the dying ex-chancellor of Austria, Bruno Kreisky. The tree is 1000 years old, not 2000, but the idea is the same, this time photographed by Konrad Mueller. Fred Bookstein
MorphoJ and CVA
Original Message Subject: MorphoJ and CVA Date: Wed, 25 Apr 2012 13:46:30 -0400 From: Robert Ward r.w...@bangor.ac.uk To: morphmet@morphometrics.org Please forgive me if I'm making an obvious error. I'm trying to reconcile different outputs relating to CVA results in MorphoJ. The analysis is looking for sex differences in a 6-landmark shape and the output from MorphoJ is shown below (I left out the Procrustes tests and canonical coefficients). The MorphoJ output seems to suggest that CVA was not able to find a set of shape features to make a highly reliable discrimination, p=.06, not terrible but not great. On the other hand, if I export the CV1 scores from that analysis, and compare the male and female scores, then I get highly significant differences with either a two-sample t-test, t(85)=3.8, p=.0002, or a two-sample permutation test, Z=3.55, p=.0004. So I reckon I am misunderstanding something somewhere. If CVA is finding a vector through shape space that best discriminates the two groups, and the CV1 score reflects position on this vector, then shouldn't it be fine to test for a sex difference by a two-sample test of some kind? If so, then I wonder why the big discrepancy between the MorphoJ results, and tests using the CV1 scores? Thanks for your help, Rob Canonical Variate Analysis: CVA x6 ... Sex Dataset: mouthx6 Classification criterion: Sex Groups Observations 1. F 40 2. M 48 Variation among groups, scaled by the inverse of the within-group variation Eigenvalues % Variance Cumulative % 1. 0.16891938 100.000 100.000 Mahalanobis distances among groups: F M 0.8160 P-values from permutation tests (1 permutation rounds) for Mahalanobis distances among groups: F M 0.0621
categorical variables in pls
Original Message Subject: categorical variables in pls Date: Wed, 25 Apr 2012 16:46:51 -0400 From: Rodrigo Lima rodrigo.l...@mail.mcgill.ca To: morphmet@morphometrics.org morphmet@morphometrics.org Dear morphometricians, Does it make sense to use categorical variables in a PLS analysis? I have landmark configurations of animals collected in 3 ecozones, and these ecozones succeed each other in a (more or less) latitudinal gradient. I think it doesn't make sense to give them values 1, 2, and 3, but would it make sense to code them as dummy variables and use these in PLS together with other environment variables? Thank you, Rodrigo
Announcement of Robert R. Sokal's Death from Mike Bell
Original Message Subject: Announcement of Robert R. Sokal's Death from Mike Bell Date: Sun, 15 Apr 2012 23:01:28 -0400 From: Michael A. Bell mab...@life.bio.sunysb.edu Reply-To: mab...@life.bio.sunysb.edu To: morphmet@morphometrics.org CC: mab...@life.bio.sunysb.edu We are sad to report that Distinguished Professor Emeritus Robert R. Sokal passed away in Stony Brook on Monday, April 9, 2012 at the age of 86. Prof. Sokal was a founding member of the Department of Ecology and Evolution at Stony Brook University, co-founder of the methodological school of Numerical Taxonomy, and the principle investigator for major research programs in the spatial variation of insects and humans and the evolutionary response to selection in insects. He supervised the training of numerous Ph.D. students and taught biometry to a much larger number. He was a member of the National Academy of Sciences of the USA and received many other honors during his remarkable career. We in the Department of Ecology and Evolution at Stony Brook will miss his insights, support, and friendship. Prof. Sokal was born into a middle class Jewish family on January 13, 1926 in Vienna, Austria, the only child of Klara and Siegfried Sokal. He fled the looming Nazi menace with his family in 1938 to Shanghai, China, which became the refuge for tens of thousands of European Jews during World War II. Robert attended secondary school and college in Shanghai, earning his B.S. degree in Biology from St. Johns University in 1947. There he also met a young Chinese student, Julie Chenchu Yang, who became his wife and lifelong love. A book entitled Letzte Zuflucht Schanghai (Final Refuge Shanghai) by Stefan Schomann (2008) in German and translated into Chinese chronicled Roberts flight from Vienna, his familys refuge in Shanghai, and the start of his life with Julie, before he came to the United States for his graduate education. Prof. Sokal received his graduate training at the University of Chicago, where he earned his Ph.D. in Zoology in 1952 under the direction of entomologist Alfred E. Emerson and was strongly influenced by Sewall Wright. He joined the Entomology Department at the University of Kansas in 1951 as an instructor, and rose rapidly through the academic ranks to Professor of Statistical Biology in 1961. He was recruited by Lawrence B. Slobodkin to the fledgling Department of Ecology and Evolution at the State University of New York at Stony Brook in 1968, where he spent the remainder of his career. Prof. Sokals scientific publications span a broad range of subjects and seven decades. He published major papers in ecology, evolution, anthropology, geography, statistics, and of course systematics. His papers appeared in Science, Nature, PNAS USA, and many of the best specialty journals in ecology, evolution, systematics, anthropology, and statistics. He is probably best known to evolutionary biologists and ecologists for his Biometry textbook with F. James Rohlf, the fourth edition of which he completed less than a year before his death. A recent search of Google Scholar indicated that the third edition of Biometry had been cited 19,851 times. Prof. Sokal is also well known as the co-founder of Numerical Taxonomy with Peter H. A. Sneath in 1963. This work promoted statistical methods for classification and was controversial both because it advocated abandonment of traditional evolutionary systematics and led to the debate between the advocates of phenetic and cladistic methods. Regardless, it is undeniable that Prof. Sokal pioneered the use of rigorous, objective statistical methods and the employment of computers in systematics. Prof. Sokal started his career with dissertation research on patterns of geographical variation in Pemphigus aphids. Later, he initiated research on the evolutionary response to selection in laboratory populations of Tribolium beetles and house flies. His last major empirical project, which he pursued for more than two decades, focused on analysis of patterns of spatial variation in human populations for a variety of traits and the development of new methods for these analyses. Prof. Sokal published 12 books (5 translated) and 206 articles, and his publications have been cited tens of thousands of times. Prof. Sokal came to Stony Brook University as a Professor in 1968. He was named Leading Professor in 1972 and Distinguished Professor in 1991. He retired in 1995 and became a very active Distinguished Professor Emeritus. He served as the Chair and Graduate Program Director of the Department of Ecology and Evolution at Stony Brook University from 1980 to 1983 and as Vice Provost for Research and Graduate Studies from 1981 to 82. He remained very active in scientific research, the Department of Ecology and Evolution, university affairs, and the National Academy of Sciences, even attending departmental colloquia until the last year of his life, when his declining health precluded it. Prof. Sokal
MorphoJ
Original Message Subject: MorphoJ Date: Fri, 13 Apr 2012 09:31:57 -0400 From: John Elizabeth Cook jpc...@ptialaska.net To: morphmet@morphometrics.org Are there any online tutorials for MorphoJ?
Re: Strange tpsDig2 problem
Original Message Subject:Re: Strange tpsDig2 problem Date: Tue, 10 Apr 2012 02:08:25 -0400 From: Saber Sadeghi sabersade...@yahoo.com To: morphmet@morphometrics.org Dear Karl at first you have to make a file for your samples' pictures with separate names using tpsUtil before digitizing, then you can see your pictures and back and forth your digitized pictures using tpsDig toolbar. hope it can help saber --- On *Mon, 4/9/12, morphmet /morphmet_modera...@morphometrics.org/* wrote: From: morphmet morphmet_modera...@morphometrics.org Subject: Strange tpsDig2 problem To: morphmet morphmet@morphometrics.org Date: Monday, April 9, 2012, 9:50 PM Original Message Subject: Strange tpsDig2 problem Date: Tue, 3 Apr 2012 14:13:39 -0400 From: Karl Fetter karl.fet...@gmail.com http://us.mc1133.mail.yahoo.com/mc/compose?to=karl.fet...@gmail.com To: morphmet@morphometrics.org http://us.mc1133.mail.yahoo.com/mc/compose?to=morphmet@morphometrics.org Hi Morphometricians, I have a strange problem in tpsDig2 I want to bring up and see if anyone has experienced the same problem. I have a file that contains images I've scanned and images I've photographed with an overhead camera set up. The images are all named with unique names and are contained in one file. When I make the tps file, and view the images in tpsDig2, it will skip come images if I'm scrolling though the images with the red Get next image button, and then skip through different images if I'm using the red Get previous images button (these buttons are the one at the top left that you use to scroll through images in your tps file). tpsDig2 seems to have a preference to skip my scanned images, but not all of them. It behaves like this on my mac (running VirtualBox) and on my office computer that runs windows. So, there are a few images that are in the folder and written to the tps file that I cannot view or digitize landmarks. Has anyone experienced this? I downloaded tpsDig2 again, but the problem remains. Any ideas? Thanks Karl Fetter
update to tpsUtil
Original Message Subject:update to tpsUtil Date: Wed, 4 Apr 2012 22:28:00 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu Organization: Stony Brook University To: morphmet@morphometrics.org I have just uploaded version 1.48 of tpsUtil to the life.bio.sunysb.edu/morph server. It fixes a problem in the ‘compute area’ function (thanks to Etienne Low-Décarie) for finding the problem. It also now includes the ability to transform landmark coordinates in an .NTS file into a .TPS file (a feature requested by Kevin Parsons). -- F. James Rohlf, John S. Toll Professor, Stony Brook University The much revised 4^th editions of Biometry and Statistical Tables are now available: http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf PPlease consider the environment before printing this email
Next Engine scanner protocol
Original Message Subject:Next Engine scanner protocol Date: Mon, 9 Apr 2012 18:01:31 +0200 From: Javier Santos javiersant...@hotmail.com To: Morphomet New Mailing List morphmet_modera...@morphometrics.org Hello morphometricians, I am working with snow vole skulls and have been provided a Next Engine surface scanner to obtain my shape data. I have done various tests with the scanner, but I still don't achieve the resolution I was expecting in the quality of the scans after alignment. I was hoping that somebody who has used or is using this scanner could give me some tips on how they program the scanner to obtain their images, such as number of divisions, starting angle, starting tilt, etc. As well, any tip on what to use to position and maintain the skull still during scanning (especially as I use the optional robotic arm for the Next Engine scanner). I would also appreciate any other useful information you might know on how to obtain fine morphological data from micromammal skulls using other techniques, software, etc. Thank you a lot in advance! All the best, Javier Santos Museo Nacional de Ciencias Naturales (MNCN-CSIC) Biodiversity and Evolutionary Biology Department
Question about integration indices compared at a common level of sampled population variance
Original Message Subject:Question about integration indices compared at a common level of sampled population variance Date: Mon, 9 Apr 2012 14:41:49 -0400 From: Makedonska, Jana jmakedon...@albany.edu To: morphmet@morphometrics.org morphmet@morphometrics.org Dear Morphometricians, I would like to inquire if some of you are familiar with a method for comparing magnitudes of morphological integration between species at a common level of sampled population variance. This method was first presented in Young et al. (2010) Development and the evolvability of the human limbs (PNAS 107) and subsequently applied to cranial integration in papers such as this by Shirai and Marroig (2010). If you are familiar with this method, I would like to ask how to interpret the following results: Two species have integration indices (ICVs in my case calculated as the standard deviation in eigenvalues divided by the mean eigenvalue) whose bootstrap distributions extensively overlap, yet their bootstrap distributions for the average trait coefficients of variation differ significantly from each other. As expected, both species show a positive association between the integration indices and average trait CVs (although the slope is quite steep). Would this result mean that the species characterized by a lower average trait CV has a more integrated structure, because its significantly less variable traits co-vary more consistently to produce a similar integration magnitude? Thanks very much in advance for your input! Best regards, Jana
Re: Strange tpsDig2 problem
Original Message Subject: Re: Strange tpsDig2 problem Date: Mon, 9 Apr 2012 14:58:15 -0400 From: Liu Idárraga liuidarr...@gmail.com To: morphmet@morphometrics.org Hi Karl, I also have files .tps with a mixture of images: obtained with scanner and also with camera. I haven't had any problems; however, what I did was to make two files: one for scanner images, and the other for the camera images. I did the digitalization and then joined them with the TPSutil. And if I open the new file, showing me all the images with their landmarks, without problem. I suggest that you try to do the same with your images. Regards, Liu On 9/04/12 14:20, morphmet wrote: Original Message Subject: Strange tpsDig2 problem Date: Tue, 3 Apr 2012 14:13:39 -0400 From: Karl Fetter karl.fet...@gmail.com To: morphmet@morphometrics.org Hi Morphometricians, I have a strange problem in tpsDig2 I want to bring up and see if anyone has experienced the same problem. I have a file that contains images I've scanned and images I've photographed with an overhead camera set up. The images are all named with unique names and are contained in one file. When I make the tps file, and view the images in tpsDig2, it will skip come images if I'm scrolling though the images with the red Get next image button, and then skip through different images if I'm using the red Get previous images button (these buttons are the one at the top left that you use to scroll through images in your tps file). tpsDig2 seems to have a preference to skip my scanned images, but not all of them. It behaves like this on my mac (running VirtualBox) and on my office computer that runs windows. So, there are a few images that are in the folder and written to the tps file that I cannot view or digitize landmarks. Has anyone experienced this? I downloaded tpsDig2 again, but the problem remains. Any ideas? Thanks Karl Fetter
Re: Re: Next Engine scanner protocol
Original Message Subject:Re: Re: Next Engine scanner protocol Date: Mon, 9 Apr 2012 16:22:25 -0400 From: Caley Orr caley@gmail.com To: morphmet@morphometrics.org I concur with Heather that the HD Pro software is absolutely essential and also that doing the final alignment in Geomagic or another software program usually works better. Be sure to download the updates to the HD software as they are released, because NextEngine has made a lot of improvements over the last few years. However, with your small samples, you'll probably want to use one of the standard or high definition settings (so slower speed) depending on how small your specimens are, but not necessarily the maximum. Try the highest SD or first or second notch in the HD zone. You can offset the long scan time by doing fewer divisions. Nine divisions seems to work out pretty well in most cases and 16 on the HD setting will probably oversample the surface and make the files too large to work with. The HD settings have gotten much better and there seems to be less noise than there used to be. Use the Macro setting and pay attention to the suggested distance from the scanner (ends up being ~16cm, I believe). I would try the Align function for putting together the divisions using the colored 'pins' to match homologous points, use the Volume Merge as Heather suggests, and then output the merged divisions as a PLY file. If you are attempting to get the whole skull scanned, then reorient the specimen, repeat the scan steps and output that second merged scan as a separate PLY file. Then do the merge the two PLYs in Geomagic or similar. I don't bother with the tilt or anything (doing mostly hand bones), so have no advice there. Unless these skulls are really tiny (and depending on what anatomy you need to see), the NextEngine can do a decent job, but can take some fiddling. Good luck! -Caley -- Caley M. Orr, PhD Research Instructor Department of Anatomical Sciences Health Sciences Center T-8 040 Stony Brook University Stony Brook, NY 11794-8081 http://www.wix.com/caleyorr/phd On Mon, Apr 9, 2012 at 3:41 PM, morphmet morphmet_modera...@morphometrics.org mailto:morphmet_modera...@morphometrics.org wrote: Original Message Subject:Re: Next Engine scanner protocol Date: Mon, 9 Apr 2012 14:09:32 -0400 From: Heather Garvin heama...@aol.com mailto:heama...@aol.com To: morphmet@morphometrics.org mailto:morphmet@morphometrics.org I haven't scanned anything that small(I was scanning human skulls),but I can tell you that paying the extra money for the HD Pro software makes a world of a difference. Not only does it give you higher quality scans, but it cuts your scanning time pretty much in half. Besides that, I was given advice by Matt Tocheri to use the maximum number of divisions under the highest speed. This may sound counter-intuitive, but the rationale is that you get better accuracy when you have more regions of overlap (from different angles). With a high degree of overlap you can obtain just as many surface points than going more slowly over less divisions. Also in the slower speeds (higher dpi), it was suggested to me because the laser is going over each region more slowly, there's more of a chance it will pick up noise or reflect back oddly, creating more inaccuracies. So I followed this advice with human skulls (using the HD program, highest number of divisions, fastest speed). I'm not sure how it would work out on the smaller skulls. Finally, the NextEngine software does okay aligning the divisions from a single scan (given that the object doesn't move). I use the Volume Merge instead of any of the fusion options, to get a uniform mesh. But I found that it really sucked at aligning more than one 360 degree scan together (for example, if you took one 360 scan, changed position and took another). So after each scan I would save the .ply and open it in another program, such as GeoMagic or Rapidworks, and do the rest of the aligning and merging in there. The problem is, these programs are expensive, but if you have an associated engineering program they may already have an institutional copy. Hope this helps a little. Goodluck! --Heather * ~~__ Heather Garvin* PhD Candidate Center for Functional Anatomy Evolution Johns Hopkins School of Medicine http://www.hopkinsmedicine.__org/fae/HMG.htm http://www.hopkinsmedicine.org/fae/HMG.htm hmgar...@gmail.com mailto:hmgar...@gmail.com -Original Message- From: morphmet morphmet_moderator@__morphometrics.org mailto:morphmet_modera...@morphometrics.org To: morphmet morphmet@morphometrics.org mailto:morphmet@morphometrics.org Sent: Mon, Apr 9, 2012 1:56 pm Subject
Re: Strange tpsDig2 problem
Original Message Subject: Re: Strange tpsDig2 problem Date: Mon, 9 Apr 2012 16:25:09 -0400 From: F. James Rohlf ro...@life.bio.sunysb.edu Reply-To: ro...@life.bio.sunysb.edu To: Morphmet morphmet@morphometrics.org Send me a copy of the tps file (not the actual images) and perhaps I can find the problem. --- Sent remotely by F. James Rohlf, John S. Toll Professor, Stony Brook University -Original Message- From: morphmet morphmet_modera...@morphometrics.org Date: Mon, 09 Apr 2012 13:20:12 To: morphmetmorphmet@morphometrics.org Reply-To: morphmet@morphometrics.org Subject: Strange tpsDig2 problem Original Message Subject:Strange tpsDig2 problem Date: Tue, 3 Apr 2012 14:13:39 -0400 From: Karl Fetter karl.fet...@gmail.com To: morphmet@morphometrics.org Hi Morphometricians, I have a strange problem in tpsDig2 I want to bring up and see if anyone has experienced the same problem. I have a file that contains images I've scanned and images I've photographed with an overhead camera set up. The images are all named with unique names and are contained in one file. When I make the tps file, and view the images in tpsDig2, it will skip come images if I'm scrolling though the images with the red Get next image button, and then skip through different images if I'm using the red Get previous images button (these buttons are the one at the top left that you use to scroll through images in your tps file). tpsDig2 seems to have a preference to skip my scanned images, but not all of them. It behaves like this on my mac (running VirtualBox) and on my office computer that runs windows. So, there are a few images that are in the folder and written to the tps file that I cannot view or digitize landmarks. Has anyone experienced this? I downloaded tpsDig2 again, but the problem remains. Any ideas? Thanks Karl Fetter
