Dear Murat and Carmelo,

Thank you for your suggestions and important comments.  I will add other
specimens from the same locality and explore the variation at different
distances to assess how meaningful is the effect.

All the Best,

Anderson

On Thu, Jan 4, 2018 at 6:30 PM, Carmelo Fruciano <c.fruci...@unict.it>
wrote:

> Hi Anderson,
>
> I concur with Murat about the usefulness of having actually multiple
> specimens. Analyses on a single specimen, although in principle attractive
> (as one "isolates" error from biological variation), are not necessarily
> informative on a practical level. Also there are two problems, one of
> magnitude (e.g., how large is variation due to distance/presentation
> relative to biological variation), one of direction (e.g., if one
> distance/presentation gets consistently digitised differently from the
> other, that is, you have non-random error/bias). You can find discussions
> of these in my recent review which Murat very kindly suggested.
>
>
> I would add that, in addition to the digitization process, differences
> might have been caused by factors. However, another thing that I noticed in
> your TPS file is that you have first all the repetitions at one distance,
> then all the others. So I assume you digitized them in that order. This
> suggests that, as already pointed out by Murat, the differences might be
> due to "learning" or changes over time in the way you digitize.
>
>
> Most likely, the final error will come from a combination of various
> sources, as it's generally the case.
>
>
> In general, I would suggest you to run a larger preliminary analysis with:
>
> - multiple biological specimens
>
> - multiple distances
>
> - multiple digitizations
>
> - digitizing in random order across repetitions (there is a very useful
> function for this in tpsUtil by F.J. Rohlf)
>
> - using multiple statistical tools to gauge how large is the error
> relative to biological variation and if there are non-random patterns
>
>
> I hope this helps,
>
> Carmelo
>
>
>
> Il 2/01/2018 7:28 PM, Murat Maga ha scritto:
>
> Hi Anderson,
>
>
>
> I don’t think PCA is the tool you want to use in this context. Procrustes
> anova already tells you that your two magnification levels are done
> differently. Since your question is ‘can I combine data from different
> magnification level in the same analysis?’, the answer to that in your
> current study design (single sample measured five times at two different
> scales) is a very qualified no.
>
>
>
> But, what is more relevant, (or what I would have liked to know) the
> magnitude of this error in context of actual biological variation.
>
> For that, you have to have a study design where you have a few samples of
> different sizes measured at different magnification scales a couple times
> (not just measuring the same object repeatedly in different
> magnifications), or something along those lines.
>
>
>
> There is a really a lot of literature on this.  But you need to use a
> statistics based framework, not EDA tools like PCA to answer this.
>
>
>
> M
>
>
>
>
>
> *From:* Anderson Feijo [mailto:andefe...@gmail.com <andefe...@gmail.com>]
> *Sent:* Monday, January 1, 2018 11:02 PM
> *To:* Murat Maga <m...@uw.edu> <m...@uw.edu>
> *Cc:* MORPHMET <morphmet@morphometrics.org> <morphmet@morphometrics.org>
> *Subject:* Re: [MORPHMET] Doubt Scaling photos
>
>
>
> Dear Murat,
>
>
>
> Thank you very much for your email and time for explore my dataset. To
> perform this simple experiment, given the aim was to explore the
> magnification issue, I chose only three landmarks (as you could see in the
> tps file) easily to replicate. The reason I am trying to combine two
> magnification is that I will work with groups with different sizes; for
> example, species with 10 cm and others with 3 cm of total length of skull.
> Place the camera at a good distance to avoid parallax for the large group
> will lead a low resolution images of the small groups. Thus, my initial
> idea was to have two standardized distances and combine later after
> accounting the scale effects.
>
>
>
> In my short experiment, what intrigues me is the clear groups in PCA (and
> other exploratory analyses) based on the two magnifications (see below). At
> the beginning, I was expecting a great overlap between the two distances
> and minimum differences due to landmarks-placement error as seen within
> each of the group.
>
>
>
> Best,
>
> Anderson
>
>
>
> [image: Inline image 1]
>
>
>
>
>
> On Sat, Dec 30, 2017 at 3:57 PM, Murat Maga <m...@uw.edu> wrote:
>
> Dear Anderson,
>
>
>
> It has nothing to do with the scale of your data (or least not directly).
>
>
>
> As you can see, you actually performed those two digitization attempts
> differently. It is maybe 1-2 pixels off, but in a very consistent way
> (greens are from one scale, red is the other scale, and cross is the
> consensus shape). This type of systematic error commonly occur in
> digitization process, as one learns better or alters the way landmarks are
> digitized/defined along the process. In your case, perhaps higher
> resolution image gave a better definition (imaging sense) of landmarks, so
> you captured them very slightly differently than low-res image (but in a
> very consistent way).
>
>
>
> If you are concerned, the first step perhaps is to do the same thing (i.e.
> digitization of same sample with different magnifications several times)
> with several real specimens and get a sense of the magnitude of this error
> in context of the biological variation. Then perhaps you can decide,
> whether you can actually combine digitization’s from different
> magnification levels. There is quite a bit of literature on this,  you can
> start with a recent review.
>
>
>
> https://www.ncbi.nlm.nih.gov/pubmed/27038025
>
>
>
> Is there a reason you are not using a single magnification level for all
> your samples?
>
> M
>
>
>
>
>
> *From:* Anderson Feijo [mailto:andefe...@gmail.com]
> *Sent:* Friday, December 29, 2017 1:35 AM
> *To:* MORPHMET <morphmet@morphometrics.org>
> *Subject:* [MORPHMET] Doubt Scaling photos
>
>
>
> Hi everyone,
>
>
>
> I am starting a new project using GM working with groups with different
> sizes (eg. rodents and small carnivores). I would like to use the whole
> dataset combined in the analyses, instead of perform set of analyses for
> each sized group. So, I did a test using the same skull and place the
> camera in two distance to the object (~15 cm and ~30 cm). My expectation
> was after scaling (using tpsDig) I wouldn´t detect any meaningful
> difference in the dataset. However, I got two clear groups that were even
> statistically different. I have attached here the tps file that I used (10
> copies of the same skull, 5 at ~15 cm and 5 at ~30cm). My question is how
> can I combine two set of 2d landmarks based on photos taken from different
> distance to the object. I would greatly appreciate any suggestion.
>
>
>
> All the Best and Happy 2018!
>
>
>
> Anderson
>
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> --
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> _____________________________________________
>
>
>
> Dr. Anderson Feijó
>
>
>
> Key Laboratory of Zoological Systematics and Evolution
>
> Institute of Zoology, Chinese Academy of Science
>
> Beichen West Road, Chaoyang District, 100101
>
> Beijing, China
>
>
>
> Curriculum: *Lattes
> <http://lattes.cnpq.br/9406413385468571>; ResearchGate
> <https://www.researchgate.net/profile/Anderson_Feijo>*
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-- 
_____________________________________________

Dr. Anderson Feijó

Key Laboratory of Zoological Systematics and Evolution
Institute of Zoology, Chinese Academy of Science
Beichen West Road, Chaoyang District, 100101
Beijing, China

Curriculum: *Lattes <http://lattes.cnpq.br/9406413385468571>; ResearchGate
<https://www.researchgate.net/profile/Anderson_Feijo>*

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