Re: [MORPHMET] Question on combine datasets in MorphoJ

[Emma Sherratt]

Dear Pablo,

MorphoJ's user manual has this to say about combining datasets:
"Combining datasets *only makes sense if the datasets contain observations
with compatible landmark data*. This means that the datasets must contain
corresponding landmarks in the same order, have the same dimensionality and
the same type of symmetry. Moreover, if the configurations have object
symmetry, the pairing of landmarks must be the same. MorphoJ checks for
these conditions. However, this does not make the procedure foolproof! For
instance, it might still be possible to combine data from fly wings and
mouse mandibles, both with 15 landmarks in 2D and with matching symmetry,
into a single dataset. The user is responsible for ensuring that only truly
compatible datasets are combined."

In the R environment, *geomorph
* has a function called
combine.subsets

that
could help you. However, be aware that combining landmark data from
different structures, as Chris Klingenberg points out above, is to be done
with extreme caution.

For more information about combing datasets, see this paper:
Davis, M.A., M.R. Douglas, M.L. Collyer, & M.E. Douglas, M. E. 2016.
Deconstructing a species-complex: geometric morphometric and molecular
analyses define species in the Western Rattlesnake (Crotalus viridis). PloS
one, 11(1), e0146166.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146166

Emma


~~~

Emma Sherratt, PhD.

*University Research Fellow*
Department of Genetics and Evolution
School of Biological Sciences
The University of Adelaide
Adelaide, SA 5005
AUSTRALIA

*Honorary Researcher*
South Australia Museum
Adelaide, SA 5005
AUSTRALIA

email: emma.sherr...@gmail.com
mob: +61 4234 19966
Twitter: @DrEmSherratt 
co-author of geomorph R package: Software website
 | CRAN website
 | googlegroups


Caecilians are legless amphibians...

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On 14 August 2017 at 15:17, Pablo Fisichella 
wrote:

> Dear All
>
> I am analyzing 3D coordinates from non-human primate molars. I have in the
> same dataset coordinate data for M1, M2 y M3. I performed multivariate
> analysis using the size and shape (form) of all teeth together (M1, M2 and
> M3). Now I am interested in perform analysis comparing individual teeth, so
> I used the option Subdivide Dataset by and I divided my dataset by tooth
> class. Subsequently, in order to perform multivaraite analysis I used the
> option combine data set and I combined my M1 data for all species in one
> dataset. The same procedure was used for M2 and M3. Since I am interested
> in the shape component I done a  multivariate regression of the procrustes
> coordinates on the CS. I obtained  a new dataset free of the allometric
> component. I followed the same procedure to subdivide the general dataset
> into individual datasets representing each molar teeth. However, when I
> tried to combine my shape dataset is not posible, simply the shape dataset
> was not present in the datasets available to combine the datasets, only the
> form datasets are available to make the combination. So I cant performed
> statistical analysis by individual teeth using the residuals of the
> multivariate regression (i.e.,shape).
>
> Somebody have suggestions on how I can divide my dataset in indidivdual
> teeth in order to perform statistical analyses? and why the combine dataset
> option apparently doesnt work for my shape data?
>
> any suggestion or advise is more than wellcome
>
> best regards
>
> Pablo
>
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> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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[MORPHMET] Question on combine datasets in MorphoJ

[Pablo Fisichella]

Dear All

I am analyzing 3D coordinates from non-human primate molars. I have in the
same dataset coordinate data for M1, M2 y M3. I performed multivariate
analysis using the size and shape (form) of all teeth together (M1, M2 and
M3). Now I am interested in perform analysis comparing individual teeth, so
I used the option Subdivide Dataset by and I divided my dataset by tooth
class. Subsequently, in order to perform multivaraite analysis I used the
option combine data set and I combined my M1 data for all species in one
dataset. The same procedure was used for M2 and M3. Since I am interested
in the shape component I done a  multivariate regression of the procrustes
coordinates on the CS. I obtained  a new dataset free of the allometric
component. I followed the same procedure to subdivide the general dataset
into individual datasets representing each molar teeth. However, when I
tried to combine my shape dataset is not posible, simply the shape dataset
was not present in the datasets available to combine the datasets, only the
form datasets are available to make the combination. So I cant performed
statistical analysis by individual teeth using the residuals of the
multivariate regression (i.e.,shape).

Somebody have suggestions on how I can divide my dataset in indidivdual
teeth in order to perform statistical analyses? and why the combine dataset
option apparently doesnt work for my shape data?

any suggestion or advise is more than wellcome

best regards

Pablo

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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