I'd tend to follow the guidelines in MorphoJ and
in the references Chris reported there.
Be careful with SPSS. I've not used it for years
but in 2010-11 there seemed to be no option for
replicating the design implemented in MorphoJ on
shape (i.e., multivariate). The univariate design
was fine and replicable; the multivariate wasn't
as one could not select the same options as in
the univariate (individual as random factor and,
say, sex as fixed effect, if I remember well ... which I am not sure!).
SPSS might have changed since then, however, and maybe now it's doable.
Also give a look at the assumptions of these
models (well described in Klingenberg et al.,
2002) and be aware that in all these types of
(M)ANOVAs the order of the factors matters:
population first and sex second is not the same
as sex first and population second.
Cheers
Andrea
At 11:49 15/12/2015, Ariadne Schulz wrote:
No problem! Actually, I'm pretty new to this
stuff too, so explaining kinda helps it gel.
Anyway, I'm writing something up now so I'm
going to come back to this later, but I think
what you want to do to get asymmetry is run a
MANOVA or an ANOVA with size as your variable.
You can do MANOVA in SPSS and there's quite a
few tutorials online for how to do that. An
ANOVA is possible in MorphoJ and probably your
simplest and quickest option. Once you have
everything in go to the "Variation" tab and it
will be your last option. If you've loaded your
classifiers you'll be able to assign "side" to
the box that - most helpfully - is marked
"side". If that's what you're trying to do it's
quite easy. Many of the people on this list have
published on it as well so the method is very nicely supported.
Best,
Ari
On Mon, Dec 14, 2015 at 7:55 PM, Jay Devine
<<mailto:[email protected]>[email protected]> wrote:
Hi, Ari-
Thank you so much for input. I can't believe how
helpful you are, ha. Your advice is not basic
whatsoever - I'm fairly new to this, so laying
everything out as you did is wonderful.
Essentially what I'm trying to do is compare
bilateral asymmetry of left and right humeri in
males and females. My classifiers are population
(NP), side (R, L), specimen (random #), and sex
(M, F). This is all part of a directed study
course I'm currently taking, which is meant to
provide me with some knowledge for my honours
thesis. It's all a bit overwhelming, but people like you make it easier!
Ahh, I see, I see. I don't have experience with
Morphologika, but I'll try this out. I've used
R, so perhaps I'll try using geomorph as well.
Once again, I can't thank you enough.
Best wishes,
Jay
On Mon, Dec 14, 2015 at 7:55 AM, Ariadne Schulz
<<mailto:[email protected]>[email protected]> wrote:
Hi Jay,
I'd be interested if MorphoJ had that option but
I don't think it does. To do it in Morphologika
you'll have to first create a Morphologika file
which includes your wireframes. It took me a bit
of doing to figure it out and actually I'm
wondering if one can do multiple classifiers or
"labels" in a Morphologika file without putting
it through geomorph. But anyway, I'll lay it out
for you in case you don't know and also so those
with more experience here can critique.
Basically, you just want to list things under
their categories as sketched out below.
[individuals]
(n individuals)
[landmarks]
(n landmarks)
[dimensions]
(n Dimensions)
[names]
(Specimen_1
Specimen_2
...)
[labels]
(name of label)
[labelvalues]
(specimen 1 label value
specimen 2 label value
...)
[wireframe]
(1,2
2,3
1,3
...)
[rawpoints]
'#1
(landmarks for Specimen 1)
'#2
(landmarks for Specimen 2)
...
I should note as it's not very clear, "labels"
are your classifiers. I think yours was
"species" if I remember from before, so your
label values will be the species names. Mine is
sex so my label values are "female,"
"possiblefemale," "unknown," "possiblemale," and
"male." There's also a category for "polygons"
but I haven't yet gotten that to work so I won't
confuse matters by trying to tell you about it.
Make sure all your wireframe points correspond
to landmarks that are included in your final set
in Morphologika or you will get an error. You
can eliminate individuals or landmarks or
polygons and so forth before you get into the
meat of things. Once you do a Procrustes fit and
PCA, you'll want the TPS tab in the control
panel. Sometimes the image comes up blank, but
if you just click on it it will solve itself.
Morphologika also allows you to "Explore Space"
which is really helpful. Make sure that button
in the Control Panel is toggled and then click
on any spot in the PC chart. You'll note that
the landmarks in the viewer change to correspond
with the position in the PC chart you've
chosen.Given what you're trying to do though, I
think you might want to try geomorph in R. It's
really quite versatile if a little daunting. I
hope this wasn't too basic ... let me know how you get on.
Best,
Ari
On Mon, Dec 14, 2015 at 5:18 AM, Jay Devine
<<mailto:[email protected]>[email protected]> wrote:
Hello again, Morphmet!
I received an immense amount of help with my
last question, so I figured I would try again!
My silly question this time concerns 3D visualization of shape change.
I've been able to successfully create wireframe
graphs for my data, but for some reason I can
not create transformation grids. I'm aware that
you need to right-click on the "PC shape
changes" background to change the type of graph.
Unfortunately, transformation grids doesn't
appear as an option for me to choose. Is there
perhaps a preliminary step I need to do?
Does anyone know why this could be happening?
Thanks in advance for your time and consideration.
Respectfully,
Jay
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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
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E-mail address: [email protected], [email protected]
WEBPAGE: https://sites.google.com/site/alcardini/home/main
FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
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
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Mammalogy: http://www.italian-journal-of-mammalogy.it/
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