Dear All, Morpheus et al. also has a data imputation feature. Ann
Ann H. Ross, Ph.D., D-ABFA > On Nov 14, 2016, at 3:42 AM, Thomas O'Mahoney <[email protected]> wrote: > > Hi all, > Both the R packages 'Morpho' and 'Geomorph' will allow you to estimate > missing landmarks using either thin plate splines or regression. It's about 3 > lines of code, fully explained in each package, to import your data and then > estimate the missing data. Both packages accept a variety of file formats, > and can also export a variety as well, so you can do the remaining analysis > in MorphoJ if you prefer. > Kind regards, > Tom O'Mahoney > >> On Mon, 14 Nov 2016 at 07:34, alcardini <[email protected]> wrote: >> 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. >> 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]. -- 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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