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 <alcard...@gmail.com> 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 <m...@uw.edu> 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:rmper...@ncsu.edu] > > Sent: Saturday, November 12, 2016 9:53 PM > > To: MORPHMET <email@example.com> > > 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 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. > > > > > > > -- > 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: alcard...@gmail.com, andrea.card...@unimore.it > WEBPAGE: https://sites.google.com/site/alcardini/home/main > > --------------------------------------------------------------- > FREE Yellow BOOK on Geometric Morphometrics: > > http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf > --------------------------------------------------------------- > 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 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. 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