Anurag, Just a quick addition to Mike's email: if the specimens have matching symmetry (i.e. left side of head or right side) that you are using the same side each time, since geomorph does not flip configurations to make a better fit during GPA.
Lastly, I'd do a check by redigitising one of the previous specimens to see where that falls. Emma ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Emma Sherratt, PhD. Postdoctoral Researcher in the Keogh Lab <http://biology-assets.anu.edu.au/hosted_sites/Scott/> Division of Evolution, Ecology & Genetics Research School of Biology 116 Daley Road The Australian National University Acton, ACT 2601 AUSTRALIA email: emma.sherr...@gmail.com tel: +61 2612 53029 mob: +61 4234 19966 Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt> Caecilians are legless amphibians... * __ (\ .-. .-. /_") \\_//^\\_//^\\_// `"` `"` `"`* learn more about them here: www.emmasherratt.com/caecilians On 28 June 2016 at 05:07, Collyer, Michael <michael.coll...@wku.edu> wrote: > Anurag, > > I assume you are doing one GPA for the combined data and not combining the > data after GPA has been performed separately on both subsets. The latter > surely could lead to the problem you describe. > > I recommend, if you have not done so already, using the plotOutliers > function. It will provide specimen numbers for outliers. Then you can use > plotRefToTarget, following the examples in the help file but with your data > and the specific specimen numbers that concern you, so that you can get a > visual idea of why these specimens are divergent in shape from the others. > You should be able to ascertain whether there was a procedural error (like > flipping the order of two landmarks), digitizing bias (like one person > tends to put landmarks more to the left, and another more to the right for > vague anatomical points), or natural variation (maybe the specimens are > just different). > > There is nothing in the gpagen function - or Generalize Procrustes > analysis, in general - that would inherently introduce a bias to only > certain configurations. > > Good luck solving this! > > 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 > > On Jun 27, 2016, at 1:45 PM, Anurag Mishra <anuragmishra1...@gmail.com> > wrote: > > I had assigned landmarks to a group of specimen images (lizard heads) in > tpsDIG and stored them as a .TPS file. I later wished to add a few more > samples (of specimens from other locations, images photographed by others > that were sent to me via mail) so I added the same landmarks in the same > order and appended the new specimens to my existing .tps file. > > However, after applying a Generalized Procrustes Analysis (gpagen function > in Geomorph package), when I generate a PCA plot, I get the new samples as > outliers. I am quite positive that the newly acquired specimens should not > be so different from the data I already had. Is there anything I am doing > wrong? To my understanding, the images being taken by different sources > should not matter because gpagen function transforms all the landmarks > orientations to represent only shape data. > > -- > 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 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.
