Not exactly: another user-friendly option is the 'old Morpheus et al.', which estimates missing landmarks (with coordinates, for instance, coded in NTS as -9999 -9999 -9999, for each 3D landmark) using mean substitution, regression, tps or mirror reflection. The last option is a bit more complicated, I believe, and I never tried it, but the other 3 are easy to select: import the NTS file and first use the command SET FULLPRECISION ON; then try the command LIST PMISS OPTIONS, and then SET PMISS IMPUTATION REGRESSION (for instance); finally use SUPER GPA followed by PMISS IMPUTE; if you restore scale (SUPER RESTORE SCALE), you'll get size back in the data (and also estimated for specimens with missing landmarks). You just need to re-export the nts file and remove, in the first line, the code (1 -9999) for the missing landmarks (replace with simply 0): check any description of NTS in the TPS Series and you'll see what I mean.
In a couple of my old papers (the one with Thorington on marmots ontogeny, 2007, and the one with Elton, 2008, BJLS on guenon skulls - pdfs in my webpage) there might be something on this and how we estimated the accuracy of missing landmarks estimates. Much more on this topic is in several papers by Gunz and the others from the Viennese school (including, if I am correct, one of their two papers in the Hystrix, 2013, open access special issue). As someone was also interested in the truss method (implemented in the old Morpheus et al. as well), I've uploaded the software here: https://www.dropbox.com/sh/ee5gu0qiqe6hz0v/AABLZkLs98uD8aXr79VaxbWma?dl=0 That should be the latest version I have, which Dennis gave us in Vienna 10 years ago. To be honest, I suspect it's still on the web, in its official page, but haven't check the link for a while. Dennis can help more with the 'secret commands', and check if I made mistakes above. There should be a few other people on the list with experience on this, and certainly someone who has used the mirror reflection option (on which, I can't help). Good luck. Cheers Andrea On 13/11/2016, Murat Maga <[email protected]> wrote: > MorphoJ handles missing landmarks, but I don't think it has a function to > estimate them. SO without an estimation of your landmark position, your > options are either to drop the sample from the analysis (if you want to > retain full set of landmarks) or to remove the landmark from your analysis > (to keep full set of individuals). > > You can also experiment with trying to estimate them based on reflection (if > it is a symmetrical structure) or based on bunch of reference samples. Both > Morpho and gemorph in R have functions for estimating missing landmarks. See > if they give you reliable estimates, and then you can proceed with your > analysis. > > Otherwise your options are limited to those two. > M > > > -----Original Message----- > From: Rosa Perez [mailto:[email protected]] > Sent: Saturday, November 12, 2016 9:53 PM > To: MORPHMET <[email protected]> > Subject: [MORPHMET] Re: Problem with missing data using MorphoJ > > On Thursday, August 11, 2016 at 4:06:01 PM UTC-4, Jade Racine wrote: >> Dear all, >> >> >> >> I digitized 108 craniofacial landmarks on human skulls from an >> archaeological context using a MicroScribe G2X. I have a lot of random >> missing values due to postmortem damage. I am currently trying to >> analyze my data using MorphoJ. I followed the instructions from the >> user’s guide, entering "-9999" in the data files for missing values. I >> then combined the dorsal and ventral views using FileConverter. The files >> I get can be read in MorphoJ. >> However, nothing else works. I can’t visualize the landmarks or >> perform any kind of analysis. If I try to find outliers, I get the >> message "Finding outliers is not possible because only a single >> observation or none at all is available". I get this message >> regardless of whether I upload one file with all individuals in it or >> multiple files with one individual each. The problem seems to be with >> the "-9999" code because if I remove the missing landmarks from my >> data files, MorphoJ runs correctly. I tried to substitute "-9999" for >> "9999" or "-999". MorphoJ runs fine with those but generates odd >> results that do not look like the shape of a skull. I really want to >> be able to analyze my dataset with missing values, otherwise I lose >> too much landmarks and I can’t afford to remove individuals since my >> sample is already small. Does anyone know what I am doing wrong or how I >> can fix the problem? I attached an example of my data files. >> >> >> >> >> >> Any help would be greatly appreciated. >> >> >> Thank you, >> >> >> >> >> >> Jade Racine >> >> >> Master’s student >> >> >> Department of Anthropology >> >> >> University of Montreal, Canada > > Hi Jade, > > I am also a masters student attempting to use MorphoJ and am having a > difficult time with the missing data. I collected 3D landmarks for a cranial > asymmetry project and cannot get MorphoJ to run. It keeps giving me an error > message. Did you happen to figure out what the issue was? I would truly > appreciate any advice you might be able to share. > > Thank you, > > Rosa Perez > Masters Student > NCSU > Dept of Anthropology > > -- > 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 [email protected]. > > -- > 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 [email protected]. > > -- Dr. Andrea Cardini Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy tel. 0039 059 2058472 Adjunct Associate Professor, Centre for Forensic Science , The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: [email protected], [email protected] WEBPAGE: https://sites.google.com/site/alcardini/home/main --------------------------------------------------------------- FREE Yellow BOOK on Geometric Morphometrics: http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf --------------------------------------------------------------- Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata --------------------------------------------------------------- Editorial board for: Zoomorphology: http://www.springer.com/life+sciences/animal+sciences/journal/435 Journal of Zoological Systematics and Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/ -- 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. 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