Re: [MORPHMET] Newly added samples as outliers in TPS file

2016-06-27 Thread Emma Sherratt 
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

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 

Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians




On 28 June 2016 at 05:07, Collyer, Michael  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 
> 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.

Re: [MORPHMET] Newly added samples as outliers in TPS file

2016-06-27 Thread Collyer, Michael 
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 
> 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] Newly added samples as outliers in TPS file

2016-06-27 Thread Anurag Mishra 
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.