-------- Original Message -------- Subject: Re: Visualization of non-allometric shape change in MorphoJ Date: Fri, 20 Jan 2012 03:27:17 -0500 From: andrea cardini <[email protected]> To: [email protected] Dear Marko, Viscosi and I (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025630) tried to provide a simple (and sometimes simplistic) step by step guideline to this and some other analyses in taxonomic studies using GMM. We also describe how to first use TPSRegr (for 2D data) to test slopes, as described by Rohlf in the help file, before trying any 'size-correction'. In the paper you'll find refs pointing to more sophisticated and potentially more accurate approaches. I would try to replicate the analysis following that guideline. If you still have problems, let me know. I'll do my best to find a spare moment to see if I can help (after the next week!). The V&C paper is on tree leaves but most of what we describe is pretty general. I can send you a pdf of that paper with a comment on how to modify one of the analyses for studies on animals. However, this does not concern the 'size-correction', which is the same regardless of whether it's leaves, bones or other structures. Good luck. Cheers Andrea At 14:21 19/01/2012 -0500, you wrote:
-------- Original Message -------- Subject: Visualization of non-allometric shape change in MorphoJ Date: Tue, 17 Jan 2012 08:24:36 -0500 From: Marko Djurakic <[email protected]> To: Morphmet <[email protected]> Dear morphometricians, Iâd like to compare sexual shape dimorphism and its patterns among four groups after size correction. I have some struggle regarding visualization of non-allometric shape changes in MorphoJ. Here is step-by-step procedure that I used in analysis: My dataset contain four groups (A, B, C and D) and within each of them there were two sexes (male and female) as subgroups. 1. I did the GPA on the whole dataset. 2. First I was interested in SShD within each group and therefore I subdivided dataset by âgroupâ factor in preliminaries menu, unchecking the âseparate procrustes fitâ, resulting in four new datasets (A, B, C and D). Each of them contains 2 classifiers (sex and group). Please consider that group classifier was invariant then. 3. I performed regression analysis pooled by sex in each group (regression slopes between sexes were homogeneous) â overall four separate regressions. To visualize shape changes of allometric and non-allometric component âaveraged observation byâ option was used in preliminaries menu. As averaging factor I used âsexâ and âgroupâ, respectively. I did the same averaging procedure *for* each group. Averaging by sex results: MorphoJ showed predicted and residuals shape changes for both females and males (4 graphs at all per group) Averaging by group results: MorphoJ showed predicted and residuals shape changes for a group (2 graphs per group), but they appeared precisely the same regarding direction and magnitude of the shape change which was unusual. Main objective is to visualize allometric and nonallometric shape change of each group. Did I miss some step or it is just a bug in the program MJ? If so, how I can visualize non-allometric shape change in MJ? I used 1.04a version of MorphoJ. Additionally, I did the same analysis on other dataset and results were the same. -- MarkoÄurakiÄ, PhD student, University of Novi Sad Faculty of Sciences Department of Biology and Ecology Dositej ObradoviÄ Square 2 21 000 Novi Sad Serbia e-mail:[email protected]
Dr. Andrea Cardini Researcher in Animal Biology Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi 213, 41100, Modena, Italy tel: 0039 059 2055017 ; fax: 0039 059 2055548 Honorary Fellow Functional Morphology and Evolution Unit, Hull York Medical School University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of York, Heslington, York YO10 5DD, UK Adjunct Associate Professor Centre for Forensic Science , The University of Western Australia 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: [email protected], [email protected], [email protected], [email protected] Webpage: http://sites.google.com/site/hymsfme/drandreacardini Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata 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=0947-5745&site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/
