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 <morphmet@morphometrics.org>
> > 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
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> > --
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> >
>
>
> --
> 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
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