RE: [MORPHMET] Morphmet in the Future
That is an interesting suggestion. Whatever we do next it should not depend on any single individual. A problem is that we do not have a morphometrics society or an editor of a journal that could take ownership of morphmet. Jim _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution From: Murat Maga Sent: Monday, July 1, 2019 3:03 AM To: K. James Soda ; MORPHMET Subject: RE: [MORPHMET] Morphmet in the Future Dear Morphmet community, Couple weeks prior to his sudden demise, I suggested Dennis to consider moving the morphmet at some point to a modern forum platform that support markups, code formatting and inline images. You can check out https://discourse.slicer.org to see one in action. The main benefit that I see is the potential for a more community build up and engagement. For people who prefer to receive messages as emails (myself included), they can configure their accounts to subscribe to messages. Discourse is open-source and free to install and to use on ones own servers. There are various hosted options for a small fee too, https://www.discourse.org/pricing. It is sad having to talk about changes so soon after Dennis’s passing, but I thought it is an appropriate discussion to have. M From: K. James Soda mailto:k.jamess...@gmail.com> > Sent: Saturday, June 29, 2019 9:10 PM To: MORPHMET mailto:morphmet@morphometrics.org> > Subject: [MORPHMET] Morphmet in the Future Dear Fellow Morphometricians, I want to give a quick comment about the future of morphmet after Dennis's passing so that any necessary changes will not come as a surprise. Please rest assure that it is not a question of whether morphmet will continue but rather if any different procedures will be required to make or view posts. Right now, morphmet is linked to morphometrics.org <http://morphometrics.org> , which is a domain that belonged to Dennis himself. As a result, it is possible that, at some point in the future, morphmet may temporarily go down if the morphmetrics.org <http://morphmetrics.org> domain becomes unavailable. What does this mean for you as a member? Right now, very little. You can continue to post to morphmet and new members can join morphmet without interruption. If in the future, this ceases to be the case, you will receive an invitation to a near identical Google group that will function in the same manner as morphmet has operated since the 2014 transition. Invitations will likely be distributed over the course of two to three days. The invitation email will include instructions on any changes to the submission process, which will likely only include a new email address for making posts and a new web address for the forum. If you have any questions or concerns, please contact me either on or off of the list (k.jamess...@gmail.com <mailto:k.jamess...@gmail.com> ). Best regards, James Soda Interim Moderator (Soon to be) Assistant Professor Department of Mathematics Quinnipiac University Hamden, CT 06518 -- 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> . -- 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> . -- 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] Re: semilandmarks in biology
Perhaps, but Procrustes superimposition already adds lots of covariances also. It is a bit tricky (meaning that I do not know of a good solution) to preserve the "real" covariances and distinguish them from artifacts of fitting. GM works well for testing differences among means of groups but studying covariances among shape variables is a much more difficult problem. Some ML approaches have been suggested that could minimize the covariances due to superimposition but the ones I have looked at require some very unreasonable biological assumptions about their statistical properties. Such discussions will not die until there are good solutions or else someone proves that no good solution is possible. I still have hope for some clever idea. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution -Original Message- From: alcardini Sent: Tuesday, November 6, 2018 12:35 PM To: F. James Rohlf Cc: mitte...@univie.ac.at; MORPHMET Subject: Re: [MORPHMET] Re: semilandmarks in biology Yes, but doesn't that also add more covariance that wasn't there in the first place? Neither least squares nor minimum bending energy, that we minimize for sliding, are biological models: they will reduce variance but will do it in ways that are totally biologically arbitrary. In the examples I showed sliding led to the appearance of patterns from totally random data and that effect was much stronger than without sliding. I neither advocate sliding or not sliding. Semilandmarks are different from landmarks and more is not necessarily better. There are definitely some applications where I find them very useful but many more where they seem to be there just to make cool pictures. As Mike said, we've already had this discussion. Besides different views on what to measure and why, at that time I hadn't appreciated the problem with p/n and the potential strength of the patterns introduced by the covariance created by the superimposition (plus sliding!). Cheers Andrea On 06/11/2018, F. James Rohlf wrote: > I agree with Philipp but I would like to add that the way I think > about the justification for the sliding of semilandmarks is that if > one were smart enough to know exactly where the most meaningful > locations are along some curve then one should just place the points > along the curve and computationally treat them as fixed landmarks. > However, if their exact positions are to some extend arbitrary > (usually the case) although still along a defined curve then sliding > makes sense to me as it minimizes the apparent differences among > specimens (the sliding minimizes your measure of how much specimens differ > from each other or, usually, the mean shape. > > > > _ _ _ _ _ _ _ _ _ > > F. James Rohlf, Distinguished Prof. Emeritus > > > > Depts. of Anthropology and of Ecology & Evolution > > > > > > From: mitte...@univie.ac.at > Sent: Tuesday, November 6, 2018 9:09 AM > To: MORPHMET > Subject: [MORPHMET] Re: semilandmarks in biology > > > > I agree only in part. > > > > Whether or not semilandmarks "really are needed" may be hard to say > beforehand. If the signal is known well enough before the study, even > a single linear distance or distance ratio may suffice. In fact, most > geometric morphometric studies are characterized by an oversampling of > (anatomical) landmarks as an exploratory strategy: it allows for > unexpected findings (and nice visualizations). > > > > Furthermore, there is a fundamental difference between sliding > semilandmarks and other outline methods, including EFA. When > establishing correspondence of semilandmarks across individuals, the > minBE sliding algorithm takes the anatomical landmarks (and their > stronger biological homology) into account, while standard EFA and > related techniques cannot easily combine point homology with curve or > surface homology. Clearly, when point homology exists, it should be > parameterized accordingly. If smooth curves or surfaces exists, they > should also be parameterized, whether or not this makes the analysis slightly > more challenging. > > > > Anyway, different landmarks often convey different biological signals > and different homology criteria. For instance, Type I and Type II > landmarks (sensu Bookstein 1991) differ fundamentally in their notion of > homology. > Whereas Type I landmarks are defined in terms of local anatomy or > histology, a Type II landmark is a purely geometric construct, which > may or may not coincide with notions of anatomical/developmental > homology. ANY reasonable morphometric analysis must be interpreted in > the light of the correspondence function employed, and the some h
RE: [MORPHMET] Re: semilandmarks in biology
I agree with Philipp but I would like to add that the way I think about the justification for the sliding of semilandmarks is that if one were smart enough to know exactly where the most meaningful locations are along some curve then one should just place the points along the curve and computationally treat them as fixed landmarks. However, if their exact positions are to some extend arbitrary (usually the case) although still along a defined curve then sliding makes sense to me as it minimizes the apparent differences among specimens (the sliding minimizes your measure of how much specimens differ from each other or, usually, the mean shape. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution From: mitte...@univie.ac.at Sent: Tuesday, November 6, 2018 9:09 AM To: MORPHMET Subject: [MORPHMET] Re: semilandmarks in biology I agree only in part. Whether or not semilandmarks "really are needed" may be hard to say beforehand. If the signal is known well enough before the study, even a single linear distance or distance ratio may suffice. In fact, most geometric morphometric studies are characterized by an oversampling of (anatomical) landmarks as an exploratory strategy: it allows for unexpected findings (and nice visualizations). Furthermore, there is a fundamental difference between sliding semilandmarks and other outline methods, including EFA. When establishing correspondence of semilandmarks across individuals, the minBE sliding algorithm takes the anatomical landmarks (and their stronger biological homology) into account, while standard EFA and related techniques cannot easily combine point homology with curve or surface homology. Clearly, when point homology exists, it should be parameterized accordingly. If smooth curves or surfaces exists, they should also be parameterized, whether or not this makes the analysis slightly more challenging. Anyway, different landmarks often convey different biological signals and different homology criteria. For instance, Type I and Type II landmarks (sensu Bookstein 1991) differ fundamentally in their notion of homology. Whereas Type I landmarks are defined in terms of local anatomy or histology, a Type II landmark is a purely geometric construct, which may or may not coincide with notions of anatomical/developmental homology. ANY reasonable morphometric analysis must be interpreted in the light of the correspondence function employed, and the some holds true for semilandmarks. For this, of course, one needs to understand the basic properties of sliding landmarks, much as the basic properties of Procrustes alignment, etc.. For instance, both the sliding algorithm and Procrustes alignment introduce correlations between shape coordinates (hence their reduced degrees of freedom). This is one of the reasons why I have warned for many years and in many publications about the biological interpretation of raw correlations (e.g., summarized in Mitteroecker et al. 2012 Evol Biol). Interpretations in terms of morphological integration or modularity are even more difficult because in most studies these concepts are not operationalized. They are either described by vague and biologically trivial narratives, or they are themselves defined as patterns of correlations, which is circular and makes most "hypotheses" untestable. The same criticism applies to the naive interpretation of PCA scree plots and derived statistics. An isotropic (circular) distribution of shape coordinates corresponds to no biological model or hypothesis whatsoever (e.g., Huttegger & Mitteroecker 2011, Bookstein & Mitteroecker 2014, and Bookstein 2015, all three in Evol Biol). Accordingly, a deviation from isometry does not itself inform about integration or modularity (in any reasonable biological sense). The multivariate distribution of shape coordinates, including "dominant directions of variation," depend on many arbitrary factors, including the spacing, superimposition, and sliding of landmarks as well as on the number of landmarks relative to the number of cases. But all of this applies to both anatomical landmarks and sliding semilandmarks. I don't understand how the fact that semilandmarks makes some of these issues more obvious is an argument against their use. Best, Philipp Am Dienstag, 6. November 2018 13:28:55 UTC+1 schrieb alcardini: As a biologist, for me, the question about whether or not to use semilandmarks starts with whether I really need them and what they're actually measuring. On this, among others, Klingenberg, O'Higgins and Oxnard have written some very important easy-to-read papers that everyone doing morphometrics should consider and carefully ponder. They can be found at: https://preview.tinyurl.com/semilandmarks I've included there also an older criticis
RE: [MORPHMET] How to project shape difference onto different PC
Yes, the PC axes are “comparable”. I think the best way to think about what a PCA does is to interpret it as a projection of a multidimensional space down to a low dimensional space that captures as much of the overall variation as possible. The first axis is somewhat special because it represents the best 1-dimensional space. Past that one should think of 1 and 2 giving the best 2-dimensional space and 1, 2, and 3 giving the best 3-dimensional space, etc. The axes themselves are not of a priori interest in an application – it is the space that is of interest. A consequence is that plots showing projections of points relative to PC1, PC2,etc. must be plotted to the same scale (i.e., consistent with the fact that the eigenvalues give the variances along each axis). If, as unfortunately often the case, the axes are plotted using different scales then the space has been distorted and is no longer the space that best accounts for the overall variation in the data. That also distorts the impressions one gets in looking at the plot as using different scales changes the relative distances between points. Within that reduced space one may find that particular axes can seem to be interpretable but one should really look at the space and decide which directions within the space are most interesting based on the patterns of the data. That is, the data need to suggest interesting direction unless one has some a priori groups one wishes to compares. Often the first PC is of special interest but that is often due to allometry and the relatively large impact of size variation. That is, by now, a rather boring result! The individual PC axes are defined based on convenient mathematical properties – not based on any biological models so each one should not be considered separately as things of special interest. The above also means that one need not just visualize variation along each axis separately. One can, as in tpsRelw software, visualize any specified point within the PC space or in any direction of interest within the PC space. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution From: Yinan Hu <yinanhu...@gmail.com> Sent: Friday, May 18, 2018 2:19 PM To: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] How to project shape difference onto different PC Dear James, Thanks for the reply. Yes I have completed a PCA on a GM dataset with 11 landmarks, and you got it exactly right that I'm trying to decompose shape differences onto individual PCs. The reason I was hesitating to do the vector projection is that I'm not sure if PC scores on different PCs are directly comparable to each other. For simplicity, let's say I'm only considering PC1 and PC2, which explains 80% of shape variation in total (60% + 20%). Group A has a mean PC1 score of 0.5, and PC2 score of 0.1; where as Group B has a mean PC1 score of 0.4 and PC2 score of 0.3. Then I'm looking at a 0.1 difference along PC1 and a 0.2 difference along PC2 between these two groups. Would this mean they differ twice as much along PC2 than PC1, such that in the 80% of shape variation explained by these two PCs, 1/3 is along PC1 and 2/3 is along PC2? But considering that PC1 explains three times more variation than PC2 (60% vs 20%), would this mean I should weigh the PC score difference (distance along each PC)? i.e. although the absolute difference in mean PC1 score is 0.1, it should be weighed three times more than the difference along PC2 so in the 80% of shape variation explained by these two PCs, 3/5 is along PC1 and 2/5 is along PC2? On the other hand, I agree visualizing the shape difference along each PC can be helpful, and I'm pretty sure the plotRefToTarget function from the R package geomorph can achieve this. Thanks again. Best, Yinan On Friday, May 18, 2018 at 12:53:32 PM UTC-4, K. James Soda wrote: Dear Dr. Hu, Let me begin by restating how I understand the question: You have completed a PCA on a morphological data set in which there are two subsets of interest. Now you would like to decompose the difference between the two subsets into differences along individual PCs. Here is my two cents on the issue: I would say that the literal solution to this problem would probably be something along the lines of what you proposed. For simplicity, say that you summarized each subset using its mean position in the PC space. This would be expressed as a vector where each element is a position along a single PC. The difference between these two vectors would then be a decomposition of how far you would need to move along each PC axis to move from one mean to the other. You could then standardize the elements so that their absolute values sum to one. This would be an expression of what percentage of the distance is along each PC. What I perceive as the subtext
RE: [MORPHMET] Problem creating sliding semilandmarks with tps software
Not quite the way I intended the tps software to be used. The “curves” feature was originally intended for curves to be shown but not actually used in any computations. Some now do use it to enter points intended to be semilandmarks – perhaps because the lines connecting them give the impression of belonging to cures. Appending tps curves to landmarks feature can be used but it is an extra complication. In tpsRelw only landmark points are used. If the sliders file is input then the indicated landmarks will be used as sliding semilandmarks. Note: unless a curve is very complex, 40 semilandmarks to probably too many. The tpsUtil program should not, of course, crash. Please provide me more details about the version used, the input file, and at what point the program crashed. I will then try to fix the problem. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Natalia Siomava [mailto:nat.siom...@gmail.com] Sent: Friday, December 22, 2017 12:20 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Problem creating sliding semilandmarks with tps software Hello everybody, I am trying to add some sliding semilandmarks in my analysis but got stuck with defining them. What I have done: 1) digitized normal LM (13) 2) created a curvature in tpsDig and resampled curve by length with the same number of LM (40) for each specimen 3) with tpsUtil “Append tps Curve to landmarks”, I transformed 40 curve points into LM. At this point, the file looks fine: LM=53 (13 real LM + 40 come from the curve points). I can also open it in MorphoJ but I all 53 points are shown as LM, not semiLM. However, when I use this file in tpsUtil to "Make sliders file", I get an error: "Access violation at address "00449136 in module "tpsUtil.exe". Read of address 0008." I click several times OK and get a window with "No semilandmarks" I get 3 options: "Load Semi.", "Create", and "Cancel". If I click "Create", an .NTS file is created but it's not possible to open it with MorphoJ. MorphoJ gives as error "The chosen dimentionality and the number of data columns in the file are inconsistent". Could you please explain me what I do wrong? I will appreciate any help and/or suggestions. Thank you, Best, Natalia <https://lh3.googleusercontent.com/-id2J2QGOwC4/Wj2Es42rclI/A0U/dYaVjK7IMPIY1oZsXgFWeeolNwG2wHvKwCLcBGAs/s1600/1.jpg> <https://lh3.googleusercontent.com/-Q3DoSe9ZjEU/Wj2Ew86zYdI/A0Y/lbEi_I4bEXEOaIcvkVucFgUxWOLv_8q4QCLcBGAs/s1600/2.jpg> -- 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> . -- 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] Problems with loading new files into tpsDig
1) Two possibilities: if the full path to the images option is not used then the images have to be in the same folder as the tps file (the solution is to copy the image files to the new location). Alternatively, if the full paths are used then the software will assume the images are still in the original location (solution is to edit the tps file using a simple editor such as Windows notepad and do a global search and replace to point to the new location. 2) Seems a little odd. Note that just using a "reflex camera" is not enough - you have to also set the resolution to the desired level. By default tpsDig2 should show the images to fill the screen. If they are in fact higher resolution then they should not be pixelated unless they are greatly enlarged. You could send me one image for me to look at to see if there is something special about the images. ________ F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University -Original Message- From: Lisa Krendl [mailto:lisa.maria.kre...@gmail.com] Sent: Tuesday, December 12, 2017 1:22 AM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Problems with loading new files into tpsDig Dear all, I have two problems in terms of dealing with the tpsDig program: 1) I have been using tpsDig before to set landmarks, but since I rearranged my files and folders I always get an error report when I am trying to upload TPS files into the program. The error meassage is: Image file not found: C: Cannot open file "C:.". The system cannot find the indicated path. I already tried to use different versions of tpsDig. I also deleted all the folders with my data and after transferring it back to my computer it still did not work. Why could that be? 2) Besides that, I have one more issue with the program. For initial trials I used a compact camera. These pictures worked, but the pictures (image size: 1,06 MB) are a little blurred so I decided to use a single-lens reflex camera to obtain the pictures. The new pictures (image size: 5,77 MB) do not stretch across the whole user interface of the program and when I try to zoom in they get very pixelated. For further research I want to use the reflex camera. Do you know how I could solve the problem? Your help is very much appreciated. Thank you very much in advance. Kind regards, Lisa Krendl -- 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.
RE: [MORPHMET] Issue with sliders file data
If you send me your tps and slider files (but no need to send the image files) then I can see if I can find the problem. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution -Original Message- From: Katherine Morucci [mailto:morucci...@gmail.com] Sent: Wednesday, December 6, 2017 8:16 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Issue with sliders file data Hi There, I recently decided to reuse some data from an old 2D GM project on swine tooth morphology. When I went to rerun some of my data using my project's original code, I was unable to perform a general procrustes analysis using gpagen without receiving the error message: Error in x[s[, 3], ]: subscript out of bounds. I continued to receive this message after re-running all of my old data. I'm not sure why there would be an issue with the dimensionality of my data now, that did not exist before. I decided to rebuild a TPS file for superimposition and creation of a new sliders file. This also did not work. I'm not very experienced with R or the TPS suites, so it's likely that I'm overlooking something very simple, but after spinning my wheels on this for a few days I wanted to reach out for advice. Any help would be greatly appreciated! -- 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.
RE: [MORPHMET] Appending tps curves to landmarks
Please send me a copy of the tps file you are having a problem with (I do not need all of the images). Should be an easy fix but I would like to check your file to be sure. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution From: Candice Neves [mailto:536...@students.wits.ac.za] Sent: Friday, November 10, 2017 5:26 AM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Appending tps curves to landmarks Hi All I'm currently trying to append curves to landmarks using the function in tpsUtil (I want to use the curve information as sliding landmarks) however any time I try to do this tpsUtil gives me an error message saying '0.004149' is not a valid floating point value.' I take this to mean that one of the points I made when digitizing is not "valid" and so tpsUtil cannot read the file? Is this right? When I was digitizing tpsDIG kept popping up error messages but I couldn't figure out what I was doing wrong, I was just tracing the outline using the 'draw curve' function. I'd delete the curve and start over, but it happened every time I outlined a molar so eventually I jut kept going. Did this mess me up? Was there a way to fix what I was doing that would have meant my curves would be read in tpsUtil? Is there a way I can manually append my curve data as landmarks that could still be read into Geomorph or Momocs as sliding landmarks? Could I edit the tps file manally to do this or am I going to have to start over redrawing the curves? I need to delete some landmarks as well, so I'm having the same problem with tpsUtil, I was planning on manually deleting the landmarks I no longer want for my specimens (or should I just tell the R packages I use to exclude certain landmarks? I think this might be better). Any help would be greatly appreciated Thanks Candice Neves MSc Candidate -- 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> . -- 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] morphometrics courses
The web page at http://life.bio.sunysb.edu/morph/notices.html has just been updated to list the upcoming courses. You may find this to be a convenient list. This will be a busy Fall and Winter! _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Depts. of Anthropology and of Ecology & Evolution -- 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] number of landmarks and sample size
Another, though non-statistical, approach to judge whether one has an appropriate number of landmarks or perhaps too many is to use the tpsSuper software. One could start with many landmarks and confirm (one hopes) that the average unwarped image is clear implying that the landmarks have captured the variation of not only the landmarks but the structures around them. You can then remove landmarks and see whether the average looks fuzzier. If so, that reflects variation not well tracked by the chosen landmarks. If there is little change then the landmarks you removed are not really necessary to track the variation in the sample. One could then continue the process. Clearly the issue is not just the number of landmarks but where they are located relative to the variation among the specimens. This process could be automated to try combinations of landmarks such that some measure of variation in pixels of the unwarped images are minimized. I seem to remember that Mardia made a suggestion like that many years ago. _ _ _ _ _ _ _ _ _ F. James Rohlf, Distinguished Prof. Emeritus Stony Brook University Depts. of Anthropology and of Ecology & Evolution -Original Message- From: Murat Maga [mailto:m...@uw.edu] Sent: Wednesday, May 31, 2017 12:33 PM To: Mike Collyer <mlcoll...@gmail.com>; Lea Wolter <leawolter...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> Subject: RE: [MORPHMET] number of landmarks and sample size I want to chime in on Mike's comment about density of landmarking changing the effect size. Nicolas Navarro and I did something similar in context of quantitative genetics of mandible shape and came to a similar conclusion using 2D, 3D and 3D semi-landmarks sets on same dataset. Navarro N, Maga AM. 2016. Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape? G3: Genes, Genomes, Genetics 6:1153–1163. -Original Message- From: Mike Collyer [mailto:mlcoll...@gmail.com] Sent: Wednesday, May 31, 2017 7:43 AM To: Lea Wolter <leawolter...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] number of landmarks and sample size Dear Lea, I see others have responded to your inquiry, already. I thought I would add an additional perspective. Your question about statistical significance requires asking a follow-up question. What statistical methods would you intend to use to evaluate “significance”? If you are worried about the number of landmarks, your concern suggests you might be using parametric test statistics frequently associated with MANOVA, like Wilks lambda or Pilai trace. Indeed, when using these statistics and converting them to approximate F values, one must have many more specimens than landmarks (more error degrees of freedom than shape variables, to be more precise), if “significance” is to be inferred from probabilities associated with F-distributions. Therefore, limiting the number of landmarks might be a goal. When using resampling procedures to conduct ANOVA, using fewer landmarks can paradoxically decrease effect sizes, as an overly simplified definition of shape becomes implied. We demonstrated this in our paper: Collyer, M.L., D.J. Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for phenotypes described by high-dimensional data. Heredity. 115: 357-365. This is consistent with Andrea’s comment about quality over quantity with the caveat that limited quantity precludes quality. In other words, too few landmarks translates to limited ability to discern shape differences, because the shape compared is basic. In the paper, we used two separate landmark configurations: one with few landmarks and the other with the same landmarks plus sliding semilandmarks between fixed points, on different populations of fish. We found that adding the semilandmarks increased the effect size for population differences and sexual dimorphism. But if we constrained our analyses to parametric MANOVA for our small samples, we would have to use the simpler landmark configurations and live with the results. I do not wish to suggest that adding more landmarks is better. Overkill is certainly a concern. I would suggest though that statistical power would be for me less of a concern than a proper characterization of the shape I wish to compare among samples. If I suspect curvature is important but am afraid to use (semi)landmarks that would allow me to assess the curvature differences among groups, opting instead to use just the endpoints of a structure because I am worried about statistical power, then I just allowed a statistical procedure to take me away from the biologically relevant question I sought to address. Andrea is correct that quality is better than quantity, but quantity can be a burden in either direction (too few or too many). Additionally, statistical power will vary among statistical met
RE: [MORPHMET] Interpreting PCA results
What is important is not the fact that one is going +/- one standard deviation along each axis. When shape changes are subtle one may need to go beyond the observed range to make it more obvious to the eye what the changes are. Exactly how far one goes away from the mean is arbitrary. It is a visualization – not statistics. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 WWW: http://life.bio.sunysb.edu/morph/rohlf P Please consider the environment before printing this email From: mahendiran mylswamy [mailto:mahenr...@gmail.com] Sent: Monday, May 15, 2017 2:31 AM To: f.james.ro...@stonybrook.edu Cc: morphmet@morphometrics.org; dsbriss_dmd <orthofl...@gmail.com>; K. James Soda <k.jamess...@gmail.com> Subject: RE: [MORPHMET] Interpreting PCA results Dear all, I read interesting comments and the attached manuscript as well. I find David question us interesting. If any one could answer David question in a simple way? I am quoting his question below?. "What I do not quite understand is what exactly is the purpose of applying standard deviation(s) to the PCA and then warping the Procrustes average shape to these standard deviations? " On 15 May 2017 6:08 a.m., "F. James Rohlf" <f.james.ro...@stonybrook.edu <mailto:f.james.ro...@stonybrook.edu> > wrote: I agree with these comments but would like to add another point. I prefer to think that the purpose of the PCA is to produce a low-dimension space that captures as much of the overall variation (in a least-squares sense) as possible. Within that space there is no need to limit the visualizations to the extremes of each axis – one can investigate any direction within that space if there is a pattern in the data that suggests an interesting direction. The directions of the axes are mathematical constructs and not bases on any biological principles. Perhaps one sees some clusters in the PCA ordination but the variation within or between clusters need not be parallel to one of the PC axes. One can then look in other directions. That is why the tpsRelw program allows one to visualize any point in the ordination space – not just parallel to the axes. That means for publication one has to decide which directions are of interest – not just mechanically display the extremes of the axes. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu <mailto:f.james.ro...@stonybrook.edu> Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 WWW: http://life.bio.sunysb.edu/morph/rohlf P Please consider the environment before printing this email From: K. James Soda [mailto:k.jamess...@gmail.com <mailto:k.jamess...@gmail.com> ] Sent: Sunday, May 14, 2017 7:28 PM To: dsbriss_dmd <orthofl...@gmail.com <mailto:orthofl...@gmail.com> > Cc: MORPHMET <morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> > Subject: Re: [MORPHMET] Interpreting PCA results Dear David, Great question! I disagree with the statement that the samples' variance in shape space is not biologically real or, perhaps more accurately, is less real than the variance in any other space. As far as I see it, the basic strategy in any biostatistical study, be it GM or otherwise, is that a researcher represents a real biological population as an abstract statistical population. They then use this abstract statistical population as a proxy for the real one so that inferences in the statistical space have implications for the real world. For example, a PCA finds a direction in the statistical space in which the statistical population tends to be spread out. This is interesting to the researcher because this direction has a correspondence to certain real world variables. As a result, the PCA tells the researcher in what ways the real population tends to vary. The key point, though, is that the researcher transitioned from the statistical space to the real world. Moving from shape space to the real world is no different in principle. We have a real population of specimens, whose shape are of interest to us, and we represent them using vectors of shape variables. The vectors are abstractions; it is not as if we can hold a vector in our hands. However, this is irrelevant because they are just proxies, no less real than any other quantitative representation. What matters is if we can tie them back to the real world. This is why morphometricians implement a visualization step. In a PCA, the PCs describe how our proxies vary, and we visualize in order to see how this variation appears in the real world. It is infeasible to visualize every point along this
RE: [MORPHMET] Interpreting PCA results
I agree with these comments but would like to add another point. I prefer to think that the purpose of the PCA is to produce a low-dimension space that captures as much of the overall variation (in a least-squares sense) as possible. Within that space there is no need to limit the visualizations to the extremes of each axis – one can investigate any direction within that space if there is a pattern in the data that suggests an interesting direction. The directions of the axes are mathematical constructs and not bases on any biological principles. Perhaps one sees some clusters in the PCA ordination but the variation within or between clusters need not be parallel to one of the PC axes. One can then look in other directions. That is why the tpsRelw program allows one to visualize any point in the ordination space – not just parallel to the axes. That means for publication one has to decide which directions are of interest – not just mechanically display the extremes of the axes. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 WWW: http://life.bio.sunysb.edu/morph/rohlf P Please consider the environment before printing this email From: K. James Soda [mailto:k.jamess...@gmail.com] Sent: Sunday, May 14, 2017 7:28 PM To: dsbriss_dmd <orthofl...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] Interpreting PCA results Dear David, Great question! I disagree with the statement that the samples' variance in shape space is not biologically real or, perhaps more accurately, is less real than the variance in any other space. As far as I see it, the basic strategy in any biostatistical study, be it GM or otherwise, is that a researcher represents a real biological population as an abstract statistical population. They then use this abstract statistical population as a proxy for the real one so that inferences in the statistical space have implications for the real world. For example, a PCA finds a direction in the statistical space in which the statistical population tends to be spread out. This is interesting to the researcher because this direction has a correspondence to certain real world variables. As a result, the PCA tells the researcher in what ways the real population tends to vary. The key point, though, is that the researcher transitioned from the statistical space to the real world. Moving from shape space to the real world is no different in principle. We have a real population of specimens, whose shape are of interest to us, and we represent them using vectors of shape variables. The vectors are abstractions; it is not as if we can hold a vector in our hands. However, this is irrelevant because they are just proxies, no less real than any other quantitative representation. What matters is if we can tie them back to the real world. This is why morphometricians implement a visualization step. In a PCA, the PCs describe how our proxies vary, and we visualize in order to see how this variation appears in the real world. It is infeasible to visualize every point along this axis, so we instead visualize a handful. Since the core goal in PCA (at least in this context) is to describe variance, we generally describe the locations where a visualization occurs in units of standard deviations from the mean. We could use absolute distances along an axis, but this is probably more arbitrary than standard deviation units. The standard deviations come from the data's distribution, whereas the absolute distance is really only well-defined in the mathematical space. To summarize: i) Nearly all quantitative analyses involve an abstraction to a mathematical space. ii) The description of points in a mathematical space is useful to the researcher because the researcher is able to translate the abstract mathematical space into a real world interpretation. iii) In GM, the shape variables are traditionally translated into the real world via visualization. Ergo, morphometricians often interpret PCA results via visualizations along individual PCs. To aid in interpretation, this tends to occur in standard deviation units because the standard deviation is more easily tied to the real world relative to arbitrary selecting a unit of distance. Perhaps some of these points are up for debate, but remember that statistics is largely the study of VARIATION. If the variation in shape space did not have any biological significance, almost no analysis after alignment would be possible. Hope somewhere in this long commentary, you found something helpful, James On Tue, May 9, 2017 at 4:56 PM, dsbriss_dmd <orthofl...@gmail.com <mailto:orthofl...@gmail.com> > wrote: Good afternoon all, I have a question about interpretat
RE: [MORPHMET] question about form space
tpsRelw has an option (on the “Options” menu) to specify the use of form space when doing an analysis of relative warps (PCA). -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 WWW: http://life.bio.sunysb.edu/morph/rohlf P Please consider the environment before printing this email From: marcelo cardillo [mailto:marcelo.cardi...@gmail.com] Sent: Thursday, May 11, 2017 12:47 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] question about form space Dear Colleagues, I´m interested to work in the form space (shape plus size) with the ouput data of the tpsrewl. Should I use the scale aligned specimen matrix.?, also which is the proper method to display this matrix (a PCA with the covariance matrix maybe) ?. best! M -- Dr.Marcelo Cardillo IMHICIHU-CONICET-UBA Saavedra 15, 5to piso cp (1083) Teléfono: (011) 4953-8548 - Interno 212 Buenos Aires. Capital Federal. Argentina http://conicet.academia.edu/MarceloCardillo -- 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> . -- 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] tpsDig2 update
I have just uploaded version 2.30 of tpsDig2 to the http://life.bio.sunysb.edu/morph server. It fixes a problem with the decimal character when reading coordinates of curves. Thanks to Jessica Grahn for reporting the problem. 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.
RE: [MORPHMET] tpsDig2 and closed curves
Yes, that was the intended behavior. As mention on a prior posting, the closed curve option is only for esthetics – it displays a line to connect the first and last points but coordinates on the first point is not added to the end of the list. In GM one must avoid the chance that two points would have identical coordinates as a deformation in their positions would require an infinite amount of bending energy. However I could change the interpolation rule if users request it. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: J Coelho [mailto:joaopedrocoe...@gmail.com] Sent: Sunday, February 26, 2017 3:41 AM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] tpsDig2 and closed curves Greetings morphometricians, I noticed a strange behaviour while attempting to obtain closed curves from tpsDig2. When I resample the curve, the first and last point remain fixed, and only other points get repositioned. This is the correct behaviour for open curves. However - to my understanding - in closed curves only one of these points (ex. first) should be fixed. To reproduce it, follow: 1. Options > Close Curve 2. Modes > Draw Curve 3. Now, draw anything you wish, ex. an ellipse. 4. Right click on your closed curve > Resample Curve 4.1 Input a far bigger number of points (I know, I know, but it's easier to notice this way) 4.2 Chose [By Length] > Ok. The distance between last and first landmark remains fixed. Again, a behaviour I'd only expect in open curves. Am I wrong to expect the resampling to effect all points except the first one in the specific case of closed curves?? Thanks in advance, Best Regards, -- 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> . -- 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] Problems visualizing curves across versions of tpsDig
This is most likely caused by not setting the decimal character (. Or ,) to agree with what is used in the tps file. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Luis Ruedas [mailto:rue...@pdx.edu] Sent: Tuesday, February 21, 2017 12:49 PM To: morphmet@morphometrics.org Subject: [MORPHMET] Problems visualizing curves across versions of tpsDig I have been digitizing data from some 2D images on a computer where I had loaded tpsDig 2.16 (yes, a long time ago, I know) then tried to work on a laptop with tpsDig 2.29. Initially, I was unable to see the curves I had created. When I changed to a high vis color, I noticed a thick line on the bottom edge of the image in tpsDig. The file remains unchanged, with the original curve coordinates. Anyone know what may be going on? Help is welcome... All the best, Luis -- Luis A. Ruedas, Ph.D. Associate Professor of Biology Portland State 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 <mailto: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] tpsdSuper update
I have just uploaded version 2.04 of tpsSuper to the http://life.bio.sunysb.edu/morph server. It fixes a problem in saving aligned specimens that was noticed by Jennifer Valvo. 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] tpsUtil and tpsRelw updates
I have just uploaded the following to the http://life.bio.sunysb.edu/morph server: tpsUtil version 1.74. Adds a feature suggested by Sonja Windhager. The reorder specimens option can now read a vector of 0 or 1 values to indicate which specimens should be deleted or kept in a file. tpsRelw version 1.67. A number of small problems fixed. Also updated the help file. tpsSuper - still version 2.03 but recompiled with the newer version of the compiler. The problems with the 64 bit versions (for 64 bit Windows versions) of the tps software seem to have been fixed in the new compiler version. As always, let me know of any problems or suggestions for the tps software. 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] tpsUtil update - version 1.73
I have updated the tpsUtil program to version 1.73 and uploaded it to the life.bio.sunysb.edu/morph server. At the suggestion of T.J. Slezak I have extended the "compute area" option to also include the computation of the length of the perimeter and a measure of circularity of the outline points. He has also suggested that I remind users that the "complete curve" option in tpsDig2 is just esthetic - the curve will be seen as a closed outline but the first point will not be duplicated in the output file. ________ 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.
RE: [MORPHMET] eliminating the effect of population differences
Is the assumption that these are all provide estimates of the same covariance matrix? If so, one could test for homogeneity of covariance matrices and then compute a common (i.e., average) covariance matrix. The test will require adequate sample sizes (more samples within each population than the number of shape variables). F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Ariadne Schulz [mailto:ariadne.sch...@gmail.com] Sent: Wednesday, January 18, 2017 10:27 AM To: Elahe <ellie.parv...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] eliminating the effect of population differences I would like to hear any responses to this as well. I did something similar and I wasn't sure how to approach this question. In future studies I would like to address precisely this issue. My inclination would be that first you would want to determine how much morphological variation you're getting between sites. You could then look at sexual dimorphism within each site and/or you could look at variation of only females and only males over all sites. But this is all rather clunky and does not eliminate any interpopulation variation. If anyone has already proposed or can propose a better methodology I'd be interested in it as well. Best, Ari On Wed, Jan 18, 2017 at 5:29 PM, Elahe <ellie.parv...@gmail.com <mailto:ellie.parv...@gmail.com> > wrote: Dear all, I have pooled samples from 7 different populations of one species in order to study the allometric growth and sexual dimorphism in that species. As different populations may have subtle differences in terms of body dimensions with each other, I want to remove their effects. Can anyone suggest a way to eliminate population effects and maybe finding some residuals that are homogeneous and can be used for further analyses? I would appreciate any helps :) -- 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> . -- 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> . -- 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] tpsUtil update
I have just uploaded version 1.71 of tpsUtil to the http://life.bio.sunysb.edu/morph server. It adds better error messages to handle the cases where the decimal separator character in the data does not match the option set in the software. 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.
RE: [MORPHMET] the problem with CVA... or is it?
While you do have more sample than variables, it is too close. One prefers to have many more samples than the number of variables. Another problem is that a CVA with 144 variables will mostly involve a covariance matrix that is close to being singular. One way I like to check for problems (and is provided in NTSYSpc) is to first project the data onto the PCA axes based on the pooled within-groups covariance matrix. If the CVA suggests that the PC axes with the smallest eigenvalues are the most important for distinguishing groups then you are very likely to be in trouble. In that case, apparent large differences between some groups may be due to rounding errors in the computations. One solution is to drop PCA dimensions with small eigenvalues (of course you will then not be able to detect any real differences in those dimensions but in most studies that is not likely to be a problem). That also improves the ratio of the number of samples relative to the number of variables. It is nice to produce a CVA type plot showing the relative distances among group means. One could just do a PCA of the group means. However, the purpose of the CVA plot is to show distances that are a function of how close the means are statistically (in the sense of how easily they can be distinguished). Distances in such a plot do not correspond to the absolute amount of shape difference as measured by Procrustes distances. The choice of distance is important. One could also do a PCOORD of a matrix of generalized distances but for visualization of shapes you will need information about the shape variables themselves. That can be done after a PCOORD analysis but using a CVA is more straight-forward. Depends of the purpose of your study. Note that if projections onto the PCA axes were used as variables then the results of the CVA will have to be back-transformed. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 WWW: http://life.bio.sunysb.edu/morph/rohlf P Please consider the environment before printing this email From: Christy Hipsley [mailto:chips...@museum.vic.gov.au] Sent: Monday, November 28, 2016 6:04 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] the problem with CVA... or is it? Dear Morphmet-ers, I'm seeking advice on methods for visualizing shape features that distinguish multiple groups using GM. I know CVA has fallen out of favor for a number of reasons discussed here - e.g., more variables than groups, nonisotropic variation: Mitteroecker, P., and Bookstein, F. 2011. Linear discrimination, ordination, and the visualization of selection gradients in modern morphometrics. Evol. Biol. 38:100–114. Klingenberg, C. P., and Monteiro, L. R. 2005. Distances and directions in multidimensional shape spaces: Implications for morphometric applications. Syst. Biol. 54:678–688. Although given these limitations, is it really expected to give completely false results regarding the visualization of shape changes? In my study sytem, I show that ecological groups have statistically different cranial shapes, using both Procrustes ANOVA and PGLS. Now I simply want to visualize what the main features are that distinguish them, preferably using warps or wireframes, so that those changes must be directly relateable to the original landmark coordinates. I did that using individual specimens instead of species means, so I have 161 individuals vs 144 variables (48 landmarks*3D). I also did a between-group PCA on the species means which shows the same pattern, so is it technically "wrong" to show both? Thanks for any feedback on this issue, and I would appreciate to hear any alternative methods that people might use. I use MorphoJ and Geomorph for analyses. Best, Christy -- 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> . -- 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] Problems with min-dsquare sliding in tpsRelw
An advantage of the bending energy approach is that it minimizes the chance of collapsing landmarks because changes in the positions of landmarks that are close together requires much more bending energy. This is not usually a problem but it can be if the outline has a sharp corner - which seems likely for a beak. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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: Guillermo Navalón [mailto:guiyelm...@gmail.com] Sent: Monday, August 22, 2016 9:34 AM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Problems with min-dsquare sliding in tpsRelw Hi everyone, In a very disparate sample of bird skulls I am using a configuration with both lnmdks and smlndmks. Specifically, to capture the lateral morphology of the beak (likely the most variable area) I digitized 2 curves with 15 evenly-spaced semilandmarks. The 2 curves are constrained by 3 regular lndmks forming a triangle, the tip-of-the-beak landmark (landmark 1) is the anterior end of both curves. When I slide the smlndmks in tpsRelw with min-dsquare slide method some of the anterior smlndmks collapse in a very narrow section in both of the 2 curves in the Procrustes superimposition. This effect is not affecting to the other curve in the configuration (midline of the neurocranium) that is apparently much less variable in my sample. Also, minimum bending energy slide method does not affect the superimposition in this way, but I want to try to use min-dsquare. I have tried to change the slide maximum iterations and slide recursive options but still recover the same effect. Any idea what is going on here? Is it a bug of the program or is it a proper statistical effect? Thank you! Guillermo Navalón -- 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] RE: tpsDig2 version 2.28 available
Oh, and there was another important change to tpsDig2. Some uses have reported that the landmark labels were no longer visible. Actually they were present but very small because their size was in terms of the size of the pixels in the image (which would be very small if the image was very large). There is now an option to specify the label size in terms of screen pixels so they should remain visible even when the image is zoomed. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email From: F. James Rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Tuesday, August 23, 2016 4:59 PM To: 'Morphmet (morphmet@morphometrics.org)' <morphmet@morphometrics.org> Subject: tpsDig2 version 2.28 available I have just uploaded version 2.28 of tpsDig2 to the http://life.bio.sunysb.edu/morph site. The new version again does a proper screen copy and save of both the image and any landmarks or curves currently on the screen. One can also now specify the color of the line to be used for measurement. A few other minor things were also fixed. Thanks to Mauro Cavalcanti for the suggestions. ------ F. James Rohlf New email: f.james.ro...@stonybrook.edu <mailto:f.james.ro...@stonybrook.edu> Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsDig2 version 2.28 available
I have just uploaded version 2.28 of tpsDig2 to the http://life.bio.sunysb.edu/morph site. The new version again does a proper screen copy and save of both the image and any landmarks or curves currently on the screen. One can also now specify the color of the line to be used for measurement. A few other minor things were also fixed. Thanks to Mauro Cavalcanti for the suggestions. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsSuper update to 2.03
I have just uploaded version 2.03 of the TpsSuper program to the life.biol.sunysb.edu/morph server. The only change is to add the ability to directly save all of the unwarped images to files. There is a new menu item for this on the plot unwarped images window. Thanks to Jennifer Valvo for suggesting this addition. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsRelw update to version 1.65
I have just uploaded version 1.65 of tpsRelw to the http://life.bio.sunysb.edu server. Several important changes were made. Problems with printing, saving, and copying the plot of the variance of partial warp scores against bending energy were fixed. Thanks to Shibu Vardhanan for reporting the problem. I also made a number of additions to the help file. Some options are, perhaps, somewhat easier to understand now. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsUtil (v. 1.70) & tpsDig2 (v. 2.27) updates
I have just made small but important changes in tpsUtil and tpsDig2 and
uploaded them to the http://life.bio.sunysb.edu/morph server. Again, fixing
problems with the decimal character ("," vs. "."). The most important
problem was that the scale factor could be written to the tps file by
tpsDig2 using a "," even though a "." Was used for the coordinates of the
landmarks. The tpsUtil program had a problem showing which character was to
be used for the decimal character. Thanks to Claudia Wrozyna for pointing
out the problem. I was also just reminded about it by Katerina Papayiannis.
Please keep notifying me if you find a problem using my software. I greatly
appreciate comments, suggestions, and even complaints about something not
working correctly as it helps me improve the software.
--
F. James Rohlf New email: f.james.ro...@stonybrook.edu
Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.
& Research Professor. Dept. of Anthropology
Stony Brook University 11794-4364
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/biometry-fourthedition-sokal
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf
P Please consider the environment before printing this email
--
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] tpsRelw update 1.64
I have just uploaded version 1.64 to the http://life.bio.sunysb.edu/morph server. It fixes a problem in the visualization of shapes implied by different positions in the PCA plot. The problem was than when the plot was printed or saved to a file it did not match the correct plot shown on the screen. Thanks to Weimin Si for reporting the problem. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsRelw update
I have just uploaded version 1.63. It fixes a problem reported by Carlo Meloro. When saving aligned specimens in the .nts format the number of columns in the matrix was set to 0 rather than twice the number of landmarks. 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] tpsDig2 update to version 2.26
I have just uploaded version 2.26 of tpsDig2 to the http://life.bio.sunysb.edu/morph server. This fixes some problems and suggestions reported by Miriam Zelditch. There is now an option on the Options menu so that the current zoom will be kept when moving from one specimen to another. The 'go to specimen' window now allows for files with of up to 9 specimens - I assume that will be large enough for most users. Please let me know of other changes that would make using the program easier. Thanks again, Miriam! 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.
RE: [MORPHMET] replacing df with principal components for MANOVA tests
Note: to give statistically reliable results it needs to do more than just “culls the dimensions of x to match the number of positive non-zero eigenvalues”. You need to have the number of degrees of freedom much larger than the number of dimensions of the space or else you are likely to find that the PC dimensions with the smallest eigenvalues apparently account for most of the differences among groups. Simply using randomization tests do not solve this problem. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Collyer, Michael [mailto:michael.coll...@wku.edu] Sent: Tuesday, April 5, 2016 5:29 AM To: Brenna Hays <bkhays...@gmail.com> Cc: MORPHMET <morphmet@morphometrics.org> Subject: Re: [MORPHMET] replacing df with principal components for MANOVA tests Brenna, The PCA you performed produces a list of objects, one of which is a matrix of PC scores. Change AIS.PC to AISPC$x, and it should work. In this case, $x is the matrix of scores. The help files for the functions you use tell you the objects that are returned. You can also use attributes() to see the list of objects returned. The $ indicate that you are going to the list and extracting the object that follows. Just as a cautionary note, you might make sure that the number of columns for x is not the same as the number of landmarks times the dimensions (2 or 3). I cannot remember if R automatically culls the dimensions of x to match the number of positive non-zero eigenvalues. If not, you might have to do that yourself. There are also non-parametric MANOVA options that do not rely on degrees of freedom, which would make theses steps unnecessary, if you are comfortable with using randomization tests. Good luck! Mike Michael Collyer Associate Professor Biostatistics Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: michael.coll...@wku.edu <mailto:michael.coll...@wku.edu> On Apr 5, 2016, at 10:16 AM, Brenna Hays <bkhays...@gmail.com <mailto:bkhays...@gmail.com> > wrote: I have been reading up on MANOVA and come across the common complication requiring a large number of degrees of freedom. After performing Procrustes superimpositions on my landmark configurations, along with my small sample sizes, is not allowing me to perform MANOVA tests. I have read that one can fix this problem by replacing the coordinates with principal components. The coding from my information source is very vague, but I've been trying some different things. Below is my code - note the error message at the bottom. AISarray <- two.d.array(AIS.shape) ID <- c(1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3) Depth <- c(3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5) Region <- c(7, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5) RR <- c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2) CDR <- c(2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1) AISdf <- cbind(AISarray, ID, Depth, Region, RR, CDR) specs <- as.factor(AISdf[,51]) depth <- as.factor(AISdf[,52]) region <- as.factor(AISdf[,53]) rr <- as.factor(AISdf[,54]) cdr <- as.factor(AISdf[,55]) AIS.PC <- prcomp(AISarray) summary(manova(lm(AIS.PC~specs*region))) #NOT WORKING Error in model.frame.default(formula = AIS.PC ~ specs * region, drop.unused.levels = TRUE) : invalid type (list) for variable 'AIS.PC' It seems MANOVA requires a data frame, but replacing the coordinates with principal components turns it into a list. I cannot find any other information on this matter. Any help would be much appreciated. Thanks, Brenna Hays Research Assistant, Master's Student Nova Southeastern University -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org <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> . -- 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> . -- 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] Richard Reyment (1926-2016)
Oh, that is a great loss. He has done very important early work in multivariate morphometrics. His work had a large influence on me when I was a graduate student. A very enthusiastic worker on many subjects - quite impressive! I very much enjoyed my interactions with him especially when I visited him in Uppsala for two months. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University -Original Message- From: Eric Delson [mailto:eric.del...@lehman.cuny.edu] Sent: Thursday, March 31, 2016 5:51 AM To: morphmet@morphometrics.org Subject: Re: [MORPHMET] Richard Reyment (1926-2016) I also am saddened to hear of Prof. Reyment's death. He kindly aided me in Uppsala when I was traveling as a grad student to observe fossil primate specimens, and he showed me Chinese material from several sites including Zhoukoudian. I recall how he was complaining about the infighting between Stalinist and Maoist radical student groups on campus. It was only much later that I learned about his morphometric work through Les Marcus and others. He will be missed. Eric Delson CUNY & AMNH On 3/31/2016 11:41 AM, Norman MacLeod wrote: > It is with great sadness that I inform this community of the death of Richard > Reyment, who passed away at his home in Sollentuna, Sweden, just outside > Stockholm, on 30 March. A brief autobiography of Richard’s life and work is > available > at:https://urldefense.proofpoint.com/v2/url?u=http-3A__richardreyment.com_index.html=BQIFaQ=uxRm7bTqKzXs8e5WpHvdhQ=QsvmrqJR0YtjwRsCcawJg9FfJ-6mHfFhAx1IUIyo7A8=_1Nri_WOtwk2NSubYPK_nLTwqmbWMKYoFN67cslzX24=YWOQofIGSixW0D0Jq6wSq4Jj-VsjJ51nqZjcCk4LokY= > . I would not presume to improve on the information he has already provided > there other than to add that he was my good friend, a valued colleague and > true intellectual of unusually broad interests, abilities and > accomplishments. I often wince when I hear someone described as a “polymath” > these days as the term has become devalued through overuse. However, Richard > was a genuine polymath as his bibliography all too readily attests. Over a > career that spanned more than half a century Richard assimilated a vast body > of knowledge of about quantitative data analysis, morphometrics, > palaeontology, geology and a variety of other fields by remaining an active > and engaged researcher as well as a teacher, editor, author and > administrator. In pursuing these interests he had the good fortune to be able > to undertake this assimilation piece-by-piece, paper-by-paper, book-by-book > as these fields were developing; through their heydays at it were. Now, there > is simply too much information being published by too many people on too many > topics to allow anyone to develop the sort of synoptic understanding Richard > achieved for even a single speciality, much less half-a-dozen. People like > Richard are now passing from the scene. That is a tragedy for us all. > Possibly with one or two rare exceptions, we’ll not see their like again. > > Richard’s daughter Britt-Louse has informed me that his funeral will be held > in the next few weeks and will be attended only by the family. > > Norm MacLeod -- 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] tpsRelw update to 1.62
I have just uploaded version 1.62 of tpsRelw to the http://life.bio.sunysb.edu/morph server. It fixes a problem with saving aligned specimens in the .nts format. Thanks to Carlo Meloro for reporting the problem. 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] another tpsDig2 update
I have just uploaded version 2.25 of tpsDig2 to the http://life.bio.sunysb.edu/morph server. This fixes some problems (e.g., errors selecting some operations when no specimens had yet been loaded). I also added an option to sound a "beep" when a landmark is digitized. Thanks to Mauro Cavalcanti for bringing these to my attention. ____ 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] tpsDig2 update to version 2.24
I have just uploaded version 2.24 of tpsDig2 to the http://life.bio.sunysb.edu/morph server. This fixes a problem in the context menu where the option to delete a landmark was not listed after on resampled the points in a curve. Thanks to Miriam Zelditch for letting me know that there was this problem. Reminder: use just the 32 bit versions of the tps software for now. 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] tps series - 64 bit problems
It is apparent that the compiler I used to generate the 64 bit versions of the tps software has some serious problems. If you run into any problems using them please try switching back to the normal 32 bit versions until I can obtain an updated version of the compiler and associated libraries. If they work for you then they are ok to use but many experience crashes. 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] tpsUtil update
I have just uploaded version 1.68 of tpsUtil to the http://life.bio.sunysb.edu/morph server. Small change: I just added another error message for an inconsistency in the numbers of landmarks in a tps file. 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.
RE: [MORPHMET] Mahalanobis distance in cluster analysis of shape variables
The distinction is that Mahalanobis distance should be thought of as a statistical distance. For a single variable it is like a z-score (a difference divided by a standard deviation). It is not a measure of the absolute amount of difference. In the multivariate case Mahalanobis distance is relative to the amount of the amount of variation in the direction of the difference (that is what taking into account within-group covariation gives you). Both Mahalanobis and Euclidean distances are valid. It depends on what you wish “distance” to mean. In morphometrics do you want to cluster based on how similar shapes are (in terms of distance in Kendall shape space) or based on the degree of statistical overlap in population samples (e.g., the degree to which specimens from the two groups might be misidentified). A practical problem with Mahalanobis distance in many morphometric studies is that it requires large sample sizes within groups because landmark data is usually high dimensional and thus very large samples are needed for reliable results. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Elahep [mailto:ellie.parv...@gmail.com] Sent: Saturday, January 30, 2016 7:14 AM To: MORPHMET <morphmet@morphometrics.org> Cc: ellie.parv...@gmail.com; jkunk...@une.edu Subject: Re: [MORPHMET] Mahalanobis distance in cluster analysis of shape variables Dear Joseph, Thanks for your detailed explanation. As it is recommended by Claude in "morphometrics with R" (2008) it's better to use the Mahalanobis distance for clustering group means, because this will be scaled by the within-group variance-covariance. In my analysis, I calculated the mean value of relative warp scores for each population and then carried out a UPGMA cluster analysis based on the Euclidian distance and results were satisfying for me and they were congruent with my other results. According to the book and other articles I ran the same analysis but based on the Mahalanobis distance in PAST software, but unfortunately whenever I ran the analysis the software error "Invalid floating point operation" appeared!! so I couldn't see the Mahalanobis's cluster!! (I couldn't realize why this error happens) Euclidian distance worked for me, but I was just curious to understand if my analyses is statistically meaningful!! Thanks again for your answer, Elahe On Saturday, January 30, 2016 at 5:12:46 PM UTC+3:30, Joseph Kunkel wrote: I can not speak directly to why it is frequently used in GM cluster analysis but I would like to mention how I look at Mahalanobis distance based on its calculation. Mahalanobis distance is not a pure distance metric like Euclidian or Manhattan distance, as you have stated it is ‘standardized’. What doe that really mean? It sounds supeficially good. One way of computing it is to rotate the k-landmark data set to simplest form treating the landmarks as factors. This way would consider all landmarks to have a common covariance structure in XY or XYZ in three dimensions. That is a already a streetch, since not all landmarks can be assumed to have the same covariance structure. In addition the landmarks have all been already centered about their centroid and rotated to coincide, which has eliminated a dgeree of freedom of variability that can have consequences. Furthermore not all species landmarks can be expected to have the same covariance structure, which is an assumption made in the ordinary Mahalanobis distance application to strut analysis between populations or species. The assumption of similar data structure of course applies to the null hypothesis where there is no difference. The typical statistical test explodes when the null hypothesis is falsified so just when you want the Mahalanobis distance metric to be accurate it starts misbehaving. After rotation to simplest axes one does an 1 df F-test between each of the landmarks. These tests are all independent so they can be summed together to produce a k df F-test which is Mahalonobis D squared.So Mahalonobis D is the square root of the sum of independent F-tests, but those F-tests are based on all sorts of assumptions about the variance of the landmarks. I immagine on could modify calculation of D by limiting the sum over the top 95 or 99% variance components of the principal components. Many times applications of analytical techniques are judged by whether they ‘work’ or not. If a clustering method works for you, use it(?). I am of the opinion that I use statistics to convince myself rather than the audience. A confluence on many arguments is used to make a case. Joe -·. .· ·. .><º>·. .· ·. .><º>·. .· ·. .><º> .··.· >=- =º}>< Joseph G. Kunkel, Re
[MORPHMET] tpsRelw update
I have just uploaded version 1.62 of tpsRelw to the http://life.bio.sunysb.edu/morph site. Just one change - a problem that caused the scale factor to be ignored in computing centroid size was fixed. (In the prior version I had tried to be a little too clever in making the software tolerant of using the wrong decimal separation character.) Thanks to Luciano Brambilla for discovering the problem. I hope everyone has a healthy and productive 2016! -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] Invalid floating point operation
I can't tell unless I see the tps file but such problems are usually due to the setting for the decimal character: . or ,. There is an option in tpsRelw that allows you to set it to match what is in your tps file. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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: Kandace Hugentobler [mailto:kandace.hugentob...@gmail.com] Sent: Friday, December 11, 2015 8:34 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Invalid floating point operation Hi, I am currently working on a tps file and trying to do the relative warps and I keep getting an "Invalid floating point operation." error. I looked over the tps file and couldn't see errors, but I may be missing something. TpsRelw is working with a different tps file. I tried restarting the computer and redownloading tps relw. Do you have any suggestions? Thanks, Kandace -- 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] tpsDig2
For some reason people have not been able to download the tpsDig2 32 bit software (a server warning). I just uploaded a fresh copy of the same version (2.22) and it seems to download ok now. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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 interpretation of PCs individually
I recently responded privately to a message at interpretation of individual PCs but I thought my response might be of interest to the group. The problem with highlighting and interpreting the "most important" PCs is that it implies that the individual PCs are likely to have special biological meaning. There is no reason for that to be true (although people can and commonly do find interpretations of almost any pattern). One should remember that PCA is a mathematical/statistical tool to project as much as possible of the variation in a multivariate space down onto as few dimensions as possible. Because it is a projection it is essential that the scales of the axes are the same when plotting PC1 vs. PC2, etc.). No biological model is involved in the definition of a PCA. It is just an elegant mathematical partitioning of the overall variance into orthogonal (uncorrelated, not independent) components. There undoubtedly are interesting directions in that space but for biological applications it does not seem likely that the underlying dimensions should happen to be perfectly uncorrelated. A user would have to justify that assumption before they should try to interpret individual PCs. It is often done but that does not make it correct. A related thing to remember is that within the plot of the low-dimensional space is that the interesting directions to interpret need not be parallel to the axes. Especially true for data with samples within and among species. The PCs may not align to either the main directions of variation within species or among species. They will be some compromise and thus even the first axis may not be that interpretable except for relatively homogeneous samples. I saw an interesting example of that a few years ago in a study in which the variation within one group of species was parallel to PC2 but variation within the other major group of species was equally along PC1 and PC2 (i.e., the major dimension of variation in the 2nd group was at an angle of about 45 degrees to the PC1 and PC2 axes. ------ F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] Appending TPS files
That option in tpsUtil will do what you wish. The trick is just that the files must be in the same directory. You just select the directory – not individual files because the program will then display a list of all the tps files in that directory and you can select which ones should be combined and in which order. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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 P Please consider the environment before printing this email From: Daniel Svozil [mailto:dpsvo...@gmail.com] Sent: Tuesday, October 20, 2015 2:03 AM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Appending TPS files Hi All, So I am facing a dilemma, where I have digitized landmarks on 90 individuals, for each of 11 populations. The images and the associated TPS file for each population is located in a separate folder (i.e. one folder per population). Now, I want to combine the TPS files from each population, into one single TPS file. Is this possible? If so, how do I do it? I have tried clicking append, (File>Save data>Append) in TPS Dig2, as well as the Append files option in the drop down menu of TPS Util. In both cases, I get the dialog box, where it asks for an input directory and an output directory, however, no option to select multiple TPS files is available. It occurred to me that perhaps the separate TPS files had to be located in the same folder, (I did not check the "include path" option when I created each individual TPS file), but even so, when I repeat the Append files steps listed above, I am still presented with the input/output directory options and only the one TPS that was originally associated with that folder (i.e. pop1 TPS file is the only one available in the pop1 directory, even though I have copied the pop2 TPS file and images over, as well). Any suggestions? Or will I have to start over with a TPS file containing all images from all the populations as one? Kind regards, Daniel. -- 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> . -- 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] tpsUtil update - 1.64
A new update, 1.64, has just been uploaded to the http://life.bio.sunysb.edu/morph server. This fixes a problem in the "Delete/reorder landmarks" option. Thanks to Andrea Cardini for reporting the problem. ------ F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsDig2 update 2.20
A new version of tpsDig2 has been uploaded to http:life.bio.sunysb.edu/morph. The only changes reflect an observation made by Ingrid Grueso that one may unknowingly click on the "M" button to indicate a missing landmark when one intends to click on the landmark digitizing button right next to it. I have added a new entry on the Options menu where one can specify whether a pop-up confirmation window should be displayed when one clicks on the "M" button. Click on "OK" to add a missing landmark or "Cancel" to ignore and return to digitizing landmarks. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsUtil update 1.63
I have just uploaded tpsUtil 1.63 to the life.bio.sunysb.edu/morph server. It adds a feature recently suggested by Andrea Cardini. There is now a plot that shows which landmarks are being deleted or retained and what their new numbers of the retained landmarks will be. Note: this module works for both 2D and 3D data though the plot only uses the X & Y coordinates. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. & Evol. & Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal <http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsUtil again
I have uploaded version 1.62 to the SBU server. It fixes a problem with appending NTS files that contain blank lines. I have also modified the delete/reorder specimens and the landmarks options so they allow a more convenient (and standard) multiple selection. Thanks again to Andrea Cardini for pointing out the problem and making the suggestions. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. Evol. Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] one more update: tpsTree
Version 1.22 now has 32 and 64 bit executables. Relatively minor changes to the program (mostly fixing memory leaks) but many changes were made to the help file. It should be more helpful now. Again, the files can be downloaded from http://life.bio.sunysb.edu/morph. This will be the last of the high priority updates to the tps programs. The other programs (e.g., tpsSplin, tpsBias, tpsPower, consistency) will be updated later - unless there is a specific request for one or more of the other tps programs. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. Evol. Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsDig2 update to version 2.19
An update to tpsDig2 has just been uploaded to the http://life.bio.sunysb.ed/morph server. Some relatively small changes to both the program (both 32 and 64 bit versions) and the help file. A printable version of the help file is also included to serve as a user manual -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor, Emeritus. Dept. of Ecol. Evol. Research Professor. Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] change of email
In case viewers did not notice the note below next to my name in prior postings on morphmet, my email address is changing. The new one is f.james.ro...@stonybrook.edu mailto:f.james.ro...@stonybrook.edu The old one (ro...@life.bio.sunysb.edu mailto:ro...@life.bio.sunysb.edu ) is now being forwarded to the new address so that will also work for a while - but that will end in early September. Sorry for any inconvenience. Now I have to find all the places where my old address is displayed. The http://life.bio.sunysb.edu/morph server will still function as before - just the email is changed. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsUtil update to 1.61
Continuing progress: I have just uploaded version 1.61 of tpsUtil to the Stony Brook server. Both 32 and 64 bit versions are now available. Small changes to the program and useful changes to the help file were made. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] More tps updates
I have just uploaded to http://life.bio.sunysb.edu/morph new versions of tpsSmall, tpsRelw, and tpsRegr for both 32 and 64 bits. tpsRegr has a problem with the 'most recently used files' feature of the files menu fixed. Its help file has also been updated. The other programs had just minor tweaks. The main change was to use a new version of the compiler and a more automated way to create the install files - which should reduce the chance of errors in the creation of these files. Changes to the other programs in the tps series should be available soon. Now is a good time to send me suggestions and/or complaints. Note my new email address shown below. The present one should continue to work until early September. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu mailto:f.james.ro...@stonybrook.edu Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 -- 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] Update of tpsPLS to 1.23
I have just uploaded version 1.23 of tpsPLS to the http://life.bio.sunysb.edu/morph server. A 64 bit version is now available. Minor changes to the program. An option to specify the decimal character is included. Fixed some corrupted equations in the details topic in the help file. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsTri update
Version 1.28 of tpsTri has been uploaded to the http://life.bio.sunysb.edu/morph server. It now includes both 32 and 64 bit versions. The help file has been updated and minor changes to the program itself (allows for selection of the decimal character and location of the tpsTri.ini file. -- F. James Rohlf New email: f.james.ro...@stonybrook.edu Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsSmall update + more soon
I have just uploaded ver. 1.33 of tpsSmall. As before, there are 32 and 64 bit versions. The installations are now setup so that one can, if one wishes, install both versions on the same computer. However, for most users there is no real point to install 32 64 bit versions on the same computer but handy for those who wish to test software and find problems that they can report back to me. Note: the file names have been changed slightly so it is important that the old version be uninstalled. I am using a new program to generate install files and I expect it to do a better job of uninstalling. Note also that the 64 bit version does require a 64 bit version of Windows. tpsSmall is the simplest program in the tps series so I have uploaded it first. I am now using a more automatic method for building both versions and their installation files. If no installation problems are reported then I will be uploading similar updates to most of the rest of the tps programs. For users, this is an optional update as there are no important changes in the computations performed by the software. -- F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsDig2 update
I have just uploaded version 2.19 of the tpsDig2 program to the http://life.bio.sunysb.edu/morph server. This version includes both 32 and 64 bit versions. It also fixes the INI file storage problem (the help file also describes a way to force the program to still use the program's folder - seems necessary on some computers). Using the user's documents folder is more standard and also more desirable because it enables different users of the same computer to save different preferences. There were also a number of small changes. For example, there are now additional image enhancement options. The fit to window option is now retained when moving from one image to the next. A printable user manual is also included as a PDF file. It has identical information as contained in the help file. It is just a different format that some may find more convenient. Thanks to Lucia Alarcon Rios for letting me know that at least some Windows 7 computers still require the INI file to be placed with the program. Again, please let me know if there are problems with this latest version. -- F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology Stony Brook University 11794-4364 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsRelw one more time!
I have just uploaded version 1.58 to the life.bio.sunysb.edu server. The only important change is that it now works with Windows XP. Thanks to Mauro Cavalcanti for testing it on his WinXP computers. Also thanks to Jesus Marugán and others for their help with passing along the exact text of the error messages. -- F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsRelw problem fixed!
I just uploaded a new version (1.57) of tpsRelw to the life.bio.sunysb.edu/morph site. The problem with being unable to close a window should now be fixed. As always, it is best to uninstall the old version before installing the new one. Sorry for the delay in fixing the problem but my Internet access was not very good at the Galapagos or Machu Picchu. The rocking of the boat and then the thin oxygen did not help either. However, they were very interesting places to visit! -- F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] Problem with tpsRelw v1.56
Sorry for the problems with tpsRelw. Unfortunately i an in Equador now and soon will be in Peru. I will probably not be able to upload a fix until i return on the 26th. I would appreciate info about those computers with a problem as i cannot get it to fail on any of my computers using win7 or win8.1. ---F. James RohlfDistinguished Professor Emeritus,Ecology EvolutionResearch Professor, Anthropology Stony Brook University Original message From: Mauro Cavalcanti mauro...@gmail.com Date: 06/19/2015 9:20 AM (GMT-05:00) To: Nico Posnien nico.posn...@gmail.com Cc: MORPHMET morphmet@morphometrics.org Subject: Re: [MORPHMET] Problem with tpsRelw v1.56 Dear Nico ALL, Running the program in administrador mode does not solve the problem for me, under WinXP. And I insist -- this problem does *not* appear in any other program from Jim Rohlf's TPS Series. It affects only the latest version of tpsRelw. Best regards, 2015-06-19 6:34 GMT-03:00 Nico Posnien nico.posn...@gmail.com: Dear all, Same problem here. Same error message. For me it is not even possible to do any analysis. Does not seem to be a Windows XP specific problem since I run Windows 8.1. Is it possible to re-upload a previous version of tpsRelw? Thanks a lot! Cheers,Nico Von: Mauro Cavalcanti [mailto:mauro...@gmail.com] Gesendet: Mittwoch, 17. Juni 2015 23:28 An: MORPHMET Betreff: [MORPHMET] Problem with tpsRelw v1.56 Dear ALL,I just installed the latest version of tpsRelw (v1.56) on my old (but faithful) Windows XP computer but stumbled upon a strange problem: Every time I attempt to close either the program's main window or the About dialog box, I got the error message: Unable to write to C:\Documents and Settings\Mauro Cavalcanti\tps\tpsRelw.ini. This means that I cannot exit the program except by killing the running process using Windows task manager. I do not have such problem with any other program in the tpsSeries, installed on the same machine.Any hints?Best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio-- MORPHMET may be accessed via its webpage at http://www.morphometrics.orgTo 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. -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- 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] new publication
for those using my tps software, the following publication may be a convenient thing to site. http://dx.doi.org/10.4404/hystrix-26.1-11264 - F. James Rohlf, Distinguished Professor, Emeritus Dept. of Ecology Evolution Research Professor, Dept of Anthropology Stony Brook University -- 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] another tpsRelw update - 1.56
I have uploaded a new version of tpsRelw with several annoying problems fixed (I hope). Please let me know if you have difficulty using this software. Note: I may not be responsive right away because I expect to have only intermittent Internet service for the next two weeks. -- F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol. Evol. Research Professor, Dept. of Anthropology 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] An important update for tpsRelw
Version 1.55 of tpsRelw has been uploaded to the http://life.bio.sunysb.edu/morph server. This version is available for both 32-bit and 64-bit versions of Windows. New features include Bookstein's (2015) suggestion of plotting the log of the variance of the partial warps against the log their corresponding bending energies (this seems quite useful and informative for my data). You can now select subsets of landmarks. Problems with the display of equations in prior versions has been fixed. Note: it is best to uninstall the old version before installing the new version. Note that the executables have the same names so both versions cannot be installed on the same computer without some careful renaming of files. Please let me know of any problems or additions that would be useful. -- F. James Rohlf, Distinguished Professor Emeritus, 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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: tpsDig on a Mac using wine
Thanks! Does that also work for 64 bit versions of the programs? tpsSmall is a simple program, would you mind testing the 64 bit version? I am also, of course, curious about how it works on the other emulators. I try to program in a very standard way for maximum compatibility with Windows. -- F. James Rohlf, Distinguished Professor Emeritus, 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 P Please consider the environment before printing this email From: Joseph Kunkel [mailto:j...@bio.umass.edu] Sent: Tuesday, May 19, 2015 3:35 PM To: ro...@life.bio.sunysb.edu; morphmet@morphometrics.org Cc: Joe Kunkel Subject: tpsDig on a Mac using wine Dear Jim and Morphmet, I just want to comment on using tpsDig on a Mac. tps Dig is my go-to software for 2-D landmark digitizing of images. To digitize I would previously have to use one of my PCs in my lab which was often a pain. I was reluctant to use several of the PC-on-your-Mac options because they meant partitioning your disc or in some sense running two separate worlds on your Mac which always made me nervous for several security software reasons. Using the emulation program, wine (https://www.winehq.org/), has changed everything. It works as a unix program run from your Mac Terminal console. I have tested several of the tps suite of software from Rohlf and they work like a charm. One trick however to get around the need for a ‘right-click’ in tpsDig is to redefine the right-click as something else such as a track-pad tap which works like a charm. Thank you wine for allowing me to ‘go home’ and do tpsDig on my Macs! -·. .· ·. .º·. .· ·. .º·. .· ·. .º .··.· =- =º} Joseph G. Kunkel, Emeritus Professor Biology Department UMass Amherst Amherst MA 01003 j...@bio.umass.edu mailto:j...@bio.umass.edu -- 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] tpsSmall and tpsSuper updates - 64bit also
I have just uploaded new versions of the tpsSmall and tpsSuper programs to the life.bio.sunysb.edu/morph server. These make it easier to specify the character (. or ,) that is to be used as the decimal separator character. I have received a number of questions lately due to mismatched decimal characters. I have also uploaded 64 bit versions of these two programs. The 64 bit version is unlikely to make much difference in running the tpsSmall program but can be important for the tpsSuper program if you have a large number of large images. Similar updates are planned for the other tps programs. Including 64 bit versions is an experiment. I would appreciate feedback about whether including 64 bit versions is useful. If not, then I will not bother with 64 bit versions for the other tps programs as it does take a little more effort to keep track of two versions. -- F. James Rohlf, Distinguished Professor Emeritus, 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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] tpsDig2 update to 2.18
I have just uploaded version 2.18 of tpsDig2 to the life.bio.sunysb.edu/morph server. At the suggestion of Dean Adams, I have added a provision for missing landmarks. They are coded as the coordinates -1,-1 in the output file. Check the help file for more information. The geomorph package will have an option that will convert them to its format. However, the other tps programs do not yet know how to handle such missing landmarks. I have also added an option so that the image will be zoomed + or - as necessary to fit the window. Should make the usage more convenient. Please keep sending me suggestions and bug reports! 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 To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
RE: [MORPHMET] PC Ranks in Evolutionary PCA
Procrustes superimposition only removes isometric size variation. Shape changes that are a function of size (allometry) are not removed so a regression of some sort is needed. F. James Rohlf, Distinguished Professor, Emeritus. Ecology Evolution Research Professor, Anthropology Stony Brook University -Original Message- From: Ryan Felice [mailto:ryanfel...@gmail.com] Sent: Friday, March 27, 2015 7:34 AM To: Alex Marshall Cc: morphmet@morphometrics.org Subject: Re: [MORPHMET] PC Ranks in Evolutionary PCA Hi Alex, I'm assuming that your shape data are landmark configurations that have been subjected to a Procrustes superimposition. is that correct? If so, I dont think the regression you described is really necessary- Procrustes analysis will remove the effects of size, orientation, and position. What software are you using for your analysis? you might find it easier/more streamlined to use the phyl.pca function in the phytools R package. If you use that function, make sure that you are using the original shape data and not the independent contrasts of shape data. Good luck! -Ryan Ryan N. Felice, PhD Ohio University Department of Biological Sciences 107 Irvine Hall Athens, OH 45701 www.rnfelice.com ryanfel...@gmail.com (201)981-8642 On Fri, Mar 27, 2015 at 7:49 AM, Alex Marshall alpmar...@googlemail.com wrote: Hello everyone, I'm a MSci student new to morphometrics and this group. I'm studying morphological integration in squamate crania and one of the things I'd like to do is an Evolutionary PCA of all my species, accounting for phylogeny and allometry. I think I do this correctly but in the PCA results the PCs are not ranked by proportion of variance e.g. PC5 has greater % variance that PCs 3 4. Is this normal? To conduct the evolutionary PCA I created independant contrasts of all my shape data, regressed centroid size on shape and conducted PCA on the residuals. After this I applied the resultant PC scores to another PCA of my original data. Would anyone kindly confirm if this is the right way to do it? Many thanks, Alex Marshall MSci Student University College London alexander.marshall...@ucl.ac.uk -- 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 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] tpsUtil update
Another update to tpsUtil upload to the Stony Brook server. This fixed a problem in the calculation of areas option. Thanks to Russell Minton for pointing out the problem. New version is 1.60. 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 To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] tpsUtil update 1.59
I have just uploaded a new version (1.59) to the Stony Brook Morphometrics server. It enables the delete reorder landmarks operation to be applied to 3D data. Thanks to Andrea Cardini for noticing the problem. 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 To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] updates
tpsPLS, tpsTri, tpsSmall, tpsRegr, and tpsRelw have been updated and are available on the Stony Brook Morphometrics server. These now include a small change prompted by Andrea Cardini to make them more compatible with older versions of Windows (such as WinXP). As needed, I will update some of the other tps programs. -- F. James Rohlf, Distinguished Professor Emeritus, 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/biometry-fourthedition-sokal http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro hlf http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh lf P Please consider the environment before printing this email -- 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.
tpsDig2 update
I have just uploaded ver. 2.14 to the Stony Brook Morphometrics server. This version adds the ability to save the area and the length of a hand drawn curve to the listing file. Note that the length of the curve is just for the points drawn - it is not the length of the closed curve even if the curve is drawn as closed (I may change that in the future). Thanks to Dean Adams for the suggestion. -- F. James Rohlf, Distinguished Professor Dept. Ecology and Evolution, Stony Brook University, NY 11794-5245
RE: Tangent Space
If you have saved the consensus configuration from the prior GPA, then all you need to do is to align the new specimen with that consensus configuration. --- F. James Rohlf, Distinguished Professor State University of New York, Stony Brook, NY 11794-5245 www: http://life.bio.sunysb.edu/ee/rohlf -Original Message- From: L C Morecroft [mailto:[EMAIL PROTECTED] Sent: Wednesday, April 06, 2005 11:28 AM To: morphmet@morphometrics.org Subject: Tangent Space Dear morphometricians, I have 2000 configurations of 30 landmark points in 3D space. I have carried out a Generalized Procrustes Alignment (GPA) on these configurations and now I have a query relating to the tangent space..as I read that the points in the tangent space can be related back to actual shapes in the original 3D space... So, if I obtain one additional configuration of the same 30 landmark points, is there some method available to find out where abouts in the tangent space (for the original 2000 configurations) this new configuration will lie, without having to repeat the GPA on 2001 configurations? If you don't want to reply to the list my e-mail address is: [EMAIL PROTECTED] Thanks in advance Lucy Morecroft Research Associate University of Sheffield
