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.

Reply via email to