Re: [MORPHMET] Question on combine datasets in MorphoJ

2017-08-14 Thread 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
<https://cran.r-project.org/web/packages/geomorph/>* has a function called
combine.subsets
<https://www.rdocumentation.org/packages/geomorph/versions/3.0.5/topics/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 <https://twitter.com/DrEmSherratt>
co-author of geomorph R package: Software website
<http://geomorphr.github.io/geomorph/> | CRAN website
<https://cran.r-project.org/web/packages/geomorph/> | googlegroups
<https://groups.google.com/d/forum/geomorph-r-package>

Caecilians are legless amphibians...

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

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


On 14 August 2017 at 15:17, Pablo Fisichella <fisichellapa...@gmail.com>
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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Re: [MORPHMET] Help needed - Extract classifiers form ID String in Geomoprh or export complete datasets from MorphoJ

2017-02-20 Thread Emma Sherratt
Dear Marcos,

1- The functions you need are in base R, not in the geomorph package.
use the function strsplit() to split a character string by any character.
See related functions for alternatives for manipulating character strings.

2- yes. In MorphoJ, choose the dataset in the file tree then go to file,
export dataset and choose all of the items you wish to export.

Emma





On Tue, 21 Feb 2017 at 08:19, marcos patricio 
wrote:

> Dear colleagues,
>
> I’m working with a 2D dataset from fly wings. I have run my analysis in
> MorphoJ where I did extract many classifiers from the ID string.
>
> Now, I’m working with the same dataset with Geomorph, because I want to do
> run some specific multivariate analysis  but I have two specific questions
> I could not find the answer to:
>
> 1 – Is there any function in Geomorph that is similar to “Extract
> classifiers from ID string…” in MorphoJ?
>
> 2 – Is it possible in MorphoJ software to export/write a file with
> procrustes coordinates, Centroid size AND all the classifiers to an .csv,
> .txt or .xls file?
>
> Kind regards,
> --
> Marcos Patrício Macedo, M.Sc.
> Laboratório de Biologia Evolutiva,
> Departamento de Genética e Morfologia
> Universidade de Brasília, Brasília, DF, 70910-900, Brasil
> 
>
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Re: [MORPHMET] Re: plotting landmarks on Morpheus?

2016-12-23 Thread Emma Sherratt
For 3D surface models, I suggest IDAV Landmark Editor (
http://graphics.idav.ucdavis.edu/research/EvoMorph) or the commercial
version Checkpoint that Dennis mentioned below. Meshlab's pick points
function works. Also digit.fixed() function in geomorph R package depending
on the specimens.

If you have lots of specimens, IDAV LE has an semiautomated placement
system that is still the best IMO.

Emma
On Sat, 24 Dec 2016 at 04:37, dslice  wrote:

> If you mean Morpheus et al., this program does not do any manual data
> collection. I have tried for years to get a scicomp student interested in
> writing such a module, but to no avail. I have written several digitizing
> programs over the decades - providing graphical feedback and interfacing to
> digitizing hardware, but cannot find the time to do this myself.
>
> I don't need to collect data that often but for 2D data, I use tpsDig by
> Rohlf. For 3D data from meshes, I use Meshlab. That has worked sufficiently
> in the past, but not always as advertised on the Mac. Others have used
> Landmark Editor. I think the old version is free, but unsupported, while
> the new version Stratovan Checkpoint may be a commercial offering -
> https://www.stratovan.com/blog/landmark-editor
>
> Others can chime in with their favorite data collection modality.
>
> -ds
>
>
> On Thursday, December 15, 2016 at 11:00:02 AM UTC-5, Gabriel Wrobel wrote:
>
> I am just beginning to work with morphometrics and have a pretty simple (I
> assume) question.  I have built several 3D models of crania and mandibles
> using photogrammetry and planned to use these to plot landmark points
> (rather than using a microscribe) suing Morpheus.  But, I can't figure out
> how to place the landmark points on the model.  I was unable to find
> (recognize) this information in the user's guide.
>
> What I would love, in fact, is a very general explanation of how to get
> started building a database.  The user's guide seems to start with the
> analyses, and assumes a basic level of familiarity that I sadly don't have.
>
> Any and all suggestions are appreciated!
>
> Gabe
>
>
>
>
>
>
>
>
>
> --
>
>
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
>
> ---
>
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>
> --
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Re: [MORPHMET] fitting lines to allometric plots?

2016-12-20 Thread Emma Sherratt
Hi Christy,

I think the "PredLine" functionality of *geomorph's* procD.allometry()
function, following the Adams & Nistri 2010 BMC paper is a safer approach.
We have to remember we are dealing with multivariate data here and a
multivariate regression where the Y axis is a univariate summary, and the
"line" is just an approximation of the trajectory in a multidimensional
space. I think that putting such a line would mislead people and wouldn't
be accurate.

Em

~~~

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
office tel: +61 2612 54943
mob: +61 4234 19966
Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt>
co-author of geomorph R package: Software website
<http://geomorphr.github.io/geomorph/> | CRAN website
<https://cran.r-project.org/web/packages/geomorph/> | googlegroups
<https://groups.google.com/d/forum/geomorph-r-package>

Caecilians are legless amphibians...

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

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




On 21 December 2016 at 15:12, Christy Hipsley <chips...@museum.vic.gov.au>
wrote:

> Hi all,
>
> This is a fairly simple question, but one that I am unsure of - is it
> appropriate to fit lines to plots of allometric scores, for example
> regression score or common allometric component (CAC) vs size, or the first
> residual shape component (RSC) vs CAC? If the scores represent individuals
> from different groups or species, does it make sense to add a line of best
> fit to each group to visualize trends? I've noticed in other papers that
> lines are not used, so I'm wondering if this is somehow "wrong". I realize
> the line itself is not the regression line, but if it's only used for
> visual comparison, is that technically okay?
>
> Thanks for any feedback,
> Christy
>
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Re: [MORPHMET] Curve sliding semilandmarks

2016-12-06 Thread Emma Sherratt
Dear Lawrence,

You can use geomorph's gpagen function for sliding semilandmarks during
Procrustes superimposition, by minimising bending energy or by minimising
Procrustes distance.

I would say that it is better to sample the curve in IDAV Landmark
Editorwith many semilandmarks, in order to avoid as many issues of
smoothing the curve of interest. Also, if you link two or more curves
together in IDAV Landmark Editor, then first use digit.curves function in
geomorph to resample the semilandmarks of those curves (since IDAV Landmark
Editor does not consider two curves sharing 1 landmark as linked and places
equally distant semis on each curve separately).

Details of geomorph below in my signature, including the extensive help
guide.

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
office tel: +61 2612 54943
mob: +61 4234 19966
Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt>
co-author of geomorph R package: Software website
<http://geomorphr.github.io/geomorph/> | CRAN website
<https://cran.r-project.org/web/packages/geomorph/> | googlegroups
<https://groups.google.com/d/forum/geomorph-r-package>

Caecilians are legless amphibians...

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

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




On 7 December 2016 at 05:21, Lawrence Fatica <lawrence.m.fat...@gmail.com>
wrote:

> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I used
> IDAV Landmark to place four curves of five semilandmarks each (as well as
> several fixed landmarks) along the major contours of the pelvis. I plan on
> doing the analysis in R, but I am unsure what my options are for
> semilandmarks sliding along curves. I am particularly concerned that the
> semilandmarks will slide along their tangents and off the bone when using
> sliding protocols that do not include the 3D mesh itself.
>
> Is this something I should be worried about? Has anyone else had success
> using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
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[MORPHMET] Re: Horizontally inverted aligned landmark clouds

2016-09-11 Thread Emma Sherratt
Dear Christopher,

What comes to mind is the option in geomorph's gpagen() function 
"PrinAxes". When this option is TRUE, the shape coordinates are aligned by 
their principal axes rather than how the configuration was digitized- this 
is for visualisation and isn't changing the shape infomration in any way. 
Might this be the source of your concern?

Emma

On Friday, 9 September 2016 00:54:48 UTC+10, Christopher Marshall wrote:
>
> Dear Group, 
>
> I'm digitizing landmarks for geometric morphometics using TPSDig and 
> plotting the data from a .TPS file in Geomorph in R.   
>
> For a newly digitized dataset the plot of the aligned landmarks of all 
> specimens is horizontally inverted 
>
> This is not the case for an older dataset also digitized using TPSDig.   
>
> This must be a common issue but am unable to resolve.  Any suggestions? 
>
> Thanks in advance, 
> CDM

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Re: [MORPHMET] Terminology: Morphometry or Morphometrics?

2016-09-08 Thread Emma Sherratt
Dear Chris, Norm, Alannah,

Thank you for your comments and discussion on this term! And for engaging
in a fun and different topic for this forum.

It is indeed the etymology and usage I find most fascinating. I have
noticed through my years of training in morphometrics (as I would call it)
that colleagues in Brazil and Spanish speaking countries say morphometry
usually and I'd not heard this before - at least I don't remember hearing
it said in Britain. I began to wonder why, but had not found the answer.
I'm glad I'm not the only one interested in this - thanks Mauro!

Have a lovely weekend all!

Best wishes,

Em

On Thursday, 8 September 2016, Chris Klingenberg <c...@manchester.ac.uk>
wrote:

> Dear Emma
>
> They are synonyms, with the same meaning. Incidentally, that is the same
> as for "biometry" and "biometrics".
>
> I think "morphometry" may be the older of the two (the Oxford English
> Dictiionary has a first occurrence in 1857, although it is not clear
> whether the meaning is the same, versus 1960 for "morphometrics"), and is
> the more traditional-sounding one.
> During much of the 20th century, words ending in "-ics" had the aura of
> coolness about them (perhaps from physics envy) as it now applies to those
> ending in "-omics".
>
> Also, I have a feeling (which may be wrong) that there may be a geographic
> flavour to the two words. In my impression, the word "morphometry" is
> perhaps more widespread in Britain (plus perhaps the Commonwealth), whereas
> folks in North America seems to use "morphometrics" pretty much all the
> time.
> Furthermore, "morphometry" may come more naturally to writers who
> translate from another language (French "morphométrie", German
> "Morphometrie" etc.).
>
> There would be room for linguistic research here
>
> Best wishes,
> Chris
>
>
> On 08/09/2016 06:01, Emma Sherratt wrote:
>
>> Dear Morphmet-hive mind,
>>
>> I've been curious for some time about the terms "morphometry" and
>> "morphometrics" and whether they are in fact interchangeable or quite
>> distinct. Also, is it related to the difference between phylogeny and
>> phylogenetics?
>>
>> Regards,
>>
>> Emma
>>
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
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>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org > morphmet+unsubscr...@morphometrics.org>.
>>
>
> --
> ***
> Christian Peter Klingenberg
> School of Biological Sciences
> University of Manchester
> Michael Smith Building
> Oxford Road
> Manchester M13 9PT
> United Kingdom
>
> Web site: http://www.flywings.org.uk
> E-mail: c...@manchester.ac.uk
> Phone: +44 161 2753899
> Skype: chris_klingenberg
> ***
>
> --
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>

-- 

~~~

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
office tel: +61 2612 53029
mob: +61 4234 19966
Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt>
co-author of geomorph R package: Software website
<http://geomorphr.github.io/geomorph/> | CRAN website
<https://cran.r-project.org/web/packages/geomorph/> | googlegroups
<https://groups.google.com/d/forum/geomorph-r-package>

Caecilians are legless amphibians...

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

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

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[MORPHMET] Terminology: Morphometry or Morphometrics?

2016-09-07 Thread Emma Sherratt
Dear Morphmet-hive mind,

I've been curious for some time about the terms "morphometry" and 
"morphometrics" and whether they are in fact interchangeable or quite 
distinct. Also, is it related to the difference between phylogeny and 
phylogenetics? 

Regards,

Emma


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Re: [MORPHMET] morphospace occupation

2016-08-05 Thread Emma Sherratt
Dear Patrick,

morphol.disparity function in geomorph will give you just that, as
Procrustes variance, the most common measure of disparity (amount of
morphospace occupation).

Emma

On Friday, 5 August 2016, Patrick Arnold <patrick.arn...@uni-jena.de> wrote:

> Dear morphometrics,
>
> I am doing GMM in R and wonder if their is a simple function or package to
> calculate a quantity of morphospace occupation when I have, for example, 3
> groups (i.e. which of the groups is the most variable).
>
> Thanks in advance
> Cheers
> Patrick
>
> --
> Patrick Arnold, M.Sc.
>
> wissenschaftlicher Mitarbeiter und Doktorand
> Institut für Spezielle Zoologie und Evolutionsbiologie
> mit Phyletischem Museum
> Friedrich-Schiller-Universität Jena
> Erbertstraße 1
> 07743 Jena
> Germany
>
> Phone:  +49 (0)3641 9-49165
> Fax:+49 (0)3641 9-49142
> E-mail: patrick.arn...@uni-jena.de
>
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~~~

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
office tel: +61 2612 53029
mob: +61 4234 19966
Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt>
co-author of geomorph R package: Software website
<http://geomorphr.github.io/geomorph/> | CRAN website
<https://cran.r-project.org/web/packages/geomorph/> | googlegroups
<https://groups.google.com/d/forum/geomorph-r-package>

Caecilians are legless amphibians...

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

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

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[MORPHMET] geomorph R package users forum

2016-07-27 Thread Emma Sherratt
Dear Colleagues,

We have followed in the footsteps of this extremely useful MORPHMET 
discussion forum and have started our own, specifically for geomorph R 
package questions, discussions and troubleshooting. This replaces the 
archaic system we had on the blog site 
. You can sign up 
here: https://groups.google.com/d/forum/geomorph-r-package

We encourage users of geomorph to post their specific questions about the 
software there rather than here, and to keep all general morphometrics 
discussion to here, MORPHMET.

We are in the midst of switching all of our material to a new website also, 
so please bear with us in this transition.

Best wishes,

Emma, on behalf of the geomorph team.

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Re: [MORPHMET] Cannot load STL file into Landmark Editor software

2016-07-17 Thread Emma Sherratt
Patrick,

The icon against your "sample" file indicates that the .stl is not being
read as a 3D model but as a coordinate file. You might need to resave it as
a .ply file using meshlab, or something similar.

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 18 July 2016 at 12:52, lv xiao <lxia...@gmail.com> wrote:

> Dear all,
>
> I have 3D dental model files in STL format (a sample file is attached
> below). I wish to load these files into Landmark Editor (available from
> http://www.idav.ucdavis.edu/research/EvoMorph) for landmark and
> semilandmark digitization. However, I do not know why I cannot successfully
> load these files.
>
> The steps I took was as follows (please help me find out where I was
> wrong, thank you!):
>
> 1. Open Landmark Editor and create a new project named project.land
>
>
> <https://lh3.googleusercontent.com/-zy06GSff_E4/V4xAnhFuTzI/AL8/cZVsb7PwHQElJHkbnE0ztDFlAEmAu8aPwCLcB/s1600/1.jpg>
>
>
> 2. Click "OK" and the following window appears
>
>
> <https://lh3.googleusercontent.com/-bf0XRzF4-ro/V4xA8sTDVyI/AMA/AlLKHOBCvJMaYHEfHkpTPbZWUn6daqowgCLcB/s1600/2.jpg>
>
>
> 3. Right click the "project" folder and choose "Import"
>
>
> <https://lh3.googleusercontent.com/-r3a2BU1SX6Y/V4xBWSjYdfI/AME/gshC5SbNPKMmKuSq4BGoI6ye6qv1E5i5gCLcB/s1600/3.jpg>
>
>
> 4. Choose the intended STL file and click "open"
>
>
> <https://lh3.googleusercontent.com/-77HZ5q4EMgg/V4xBvZA1lhI/AMM/-CUCHpSbYVIfAvNop48uUa98D7cXu_umQCLcB/s1600/4.jpg>
>
>
> 5. The STL file appears in the leftmost pane as follows
>
>
> <https://lh3.googleusercontent.com/-Zi-IhaB-Co8/V4xCWkXJTeI/AMU/t4bs_juVlz8bkIJsArYeWEKt8neXqJGugCLcB/s1600/5.jpg>
>
>
> 6. BUT The "Load into A" and "Load into B" options are still deactivated
>
>
> <https://lh3.googleusercontent.com/-oWA8wEHvR0I/V4xDB2PVrwI/AMg/XA-ZhtPRP1okaMJUUzVb-mg-jWlBPuAhACLcB/s1600/6.jpg>
>
>
> Therefore, I do not know how should I proceed to load surface files into
> Landmark Editor.
>
>
> The above steps were performed following the user manual of Landmark
> Editor available from
> http://www.idav.ucdavis.edu/research/projects/EvoMorph/supplement/LandmarkDoc_v3_b6.pdf
>
>
> Thank you very much if you could try opening the attached sample.stl file
> on your Lanmark Editor to help me figure out where I was wrong or if any
> other files are needed.
>
>
> Best regards,
>
> Patrick
>
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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
<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.
>
> --
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Re: [MORPHMET] PC scores of ancestral nodes/MorphoJ/Square change Parsimony

2016-05-19 Thread Emma Sherratt
Hi Filipe,

I believe you cannot directly. When you use the "Map onto phylogeny" option
in MorphoJ, you will have appear in the scene tree the tree icon, and two
dataset icons below that. "BranchDiffs" and "IndContrasts". From the
MorphoJ helpGuide:
*Each analysis produces two output data sets: one with the values of the
changes along the branches of the phylogeny for the values of shape
variables, centroid sizes and covariates in the original dataset, and the
other with scores for phylogenetically independent contrasts (Felsenstein
1985) for the same variables.*

You could retroactively calculate node position in PC space based on the
IndCont and branch lengths. However it may be simpler to run
plotGMPhyloMorphoSpace in *geomorph* in R and extract the ancestral states
(which although are calculated by maximum likelihood using *phytools*
fastanc *) - note that the anc.states matrix returned are states prior to
PCA, so all you'd need to do is:

all.data <- rbind(two.d.array(mydata), anc.states) # combine tips and
nodes
pcdata <- prcomp(all.data)$x # PCA

Em

* ML and weighted squared change parsimony are equivalent assuming BM model
of evolution

~~~

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 17 May 2016 at 01:32, filipe oliveira <filipe.fi...@gmail.com> wrote:

> Hi,
>
> do you know how to save the PC values of the ancestral nodes estimated
> with Square change Parsimony in MorphoJ?
>
> Thank you.
> Best
> Filipe
>
> --
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Re: [MORPHMET] Using Semilandmarks

2016-05-11 Thread Emma Sherratt
Dear Edgar,

Semilandmarks should be slid during Procrustes superimposition; treating
them as fixed landmarks will only add error into your analyses. Therefore
the answer is simply a) use software that supports semilandmark sliding.
Your options are great. And when it comes to deciding whether to minimise
for bending energy or Procrustes distance, I suggest reading Gunz &
Mitteroecker 2013 here
<http://www.italian-journal-of-mammalogy.it/article/view/6292>. For GPA and
further analyses, I suggest using the TPS suite and MorphoJ, or geomorph if
you are confident with script-based analyses.

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 12 May 2016 at 09:26, Edgar Esteban Herrera Collazos <
edgaresteba...@gmail.com> wrote:

> Dear Morphometricians,
>
> I'm conducting a study on fish taxonomy using integrative taxonomy, my
> first approach is using Geometric Morphometrics.
>
> For GM I decided to use Landmarks and Semilandmarks. My question is: Is
> there any difference or advantage between using a) a software that supports
> semilandmark sliding or b) by entering each semilandmark as a landmark?
>
> Best regards
>
> --
> Edgar Esteban Herrera Collazos B.Sc.
>
> Postgraduate Student at Pontificia Universidad Javeriana
> Ichthyology Laboratory 108B Ed 53 - 3208320 Ext 4127
> ---
> Estudiante de Posgrado en la Pontificia Universidad Javeriana
> Laboratorio de Ictiología 108B Ed 53 - 3208320 Ext 4127
>
>
> --
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Re: [MORPHMET] writing .nts files from geomorph

2016-01-19 Thread Emma Sherratt
Dear Ari,

geomorph uses the following code to write an .nts from the digtizing
functions. It's an .nts file for single specimens

# Write .nts file for output of digitize2d(), buildtemplate() digit.fixed()
and digitsurface()
# A is an nx2 or nx3 matrix of the output coordinates. To be used
internally only.

writeland.nts <- function(A, spec.name, comment=NULL){
  ntsfile=paste(spec.name,".nts",sep="")
  file.create(file=ntsfile)
  if(is.null(comment)){
cat(paste('"',spec.name,sep=""),file= ntsfile,sep="\n",append=TRUE)
  }
  else if(!is.null(comment)){
cat(paste('"',spec.name,sep=""),file= ntsfile,sep="\n")
cat(paste('"',comment,sep=""),file= ntsfile,sep="\n",append=TRUE)
  }
  dims <- dim(A)
  if (dims[2] == 2){
cat(paste(1,dims[1],2,0,"dim=2"),file= ntsfile,sep="\n",append=TRUE)
  }
  else if (dims[2] == 3){
cat(paste(1,dims[1],3,0, "dim=3"),file= ntsfile,sep="\n",append=TRUE)
  }
  write.table(A ,file= ntsfile,col.names = FALSE, row.names = FALSE,sep="
 ",append=TRUE)
}

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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




On 19 January 2016 at 20:19, Ariadne Schulz <ariadne.sch...@gmail.com>
wrote:

> Hi all,
>
> I'm hoping this will be a quick and easy question. I've even done it
> before and then forgotten how.
>
> I need to create quite a few .nts files. The easiest way to do this I
> think is in R. I read in my .dta file, got my landmarks all switched the
> way I want them but now for each of my elements I need to create a .nts
> file. I've searched about online and the only things I could find were how
> to read a .nts file and the "digitize" functions. I know it's possible to
> simply write .nts files, because I have done it before ... but I've
> forgotten what I did.
>
> Help?
>
> Best,
> Ari
>
> --
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Re: [MORPHMET] Read .landmarkAscii file into R

2016-01-19 Thread Emma Sherratt
Hi David,

Not sure what the file actually looks like since you’ve not included a sample 
here. However I suggest taking a look at the readland functions in geomorph R 
package to see how we tackle the different types. If you want, send it through 
to us and we can take a look. If there’s a lot of people using AVIZO for 
digitising, we can include a function in geomorph.

Regarding a read function writing? Nope, never heard of that.

Em

~~~
Emma Sherratt, PhD.
Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science, 
Room L112 Bldg C02, 
University of New England, 
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...
  __
    (\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
      `"`   `"`   `"`
learn more about them here: www.emmasherratt.com/caecilians

On 20 January 2016 at 14:50:38, David Katz (dck...@ucdavis.edu) wrote:

Hi everyone, 

I've collected 3D landmarks on a series of cranial surface models in Avizo. 
Avizo's landmark editor outputs .landmarkAscii files, which I would like to 
read into R. The way I've done the reading has the following very unexpected 
effect: sometimes, it writes additional data to my .landmarkAscii files. I'd 
like to understand why, but am mostly interested in finding a solution.

To read in the landmark files for a specimen...

# Below, avz.file is the filepath for the .landmarkAscii  
# file for a single specimen.
# The code reads the .landmarkAscii file with read.csv. 
# This is useful because the object created lays out 
# the informational data that precedes the coordinate data 
# predictably. This makes it easy to lop off the 
# informational data. 
  read.lms <- read.csv(avz.file, header=FALSE)[,1]

  # The last row of informational data will contain the 
  # text "@1" and nothing else. 
  lm.start <- which(read.lms=="@1")+1

  # Now it is possible to create an object with landmark 
  # data only. R interprets each landmark (all three 
  # coordinates together) as a factor. I convert the factor 
  # vector to a character vector.
  lm.char <-
     as.character(droplevels(
         read.lms[(lm.start):length(read.lms)]))

  # Then I create an empty matrix for the landmark data    
  lm.mat <- matrix(NA, nrow=length(lm.char), ncol=3)

  # Then fill lm.mat with the landmark data. As mentioned, 
  # lm.char is a vector. Each element of that vector 
  # contains the X, Y, and Z coordinate for a landmark.
  # The coordinates are separated by spaces 
  # (or maybe tabs)
  for(i in 1:nrow(lm.mat))
     {lm.mat[i,] <- 
         as.numeric(unlist(strsplit(ctlm.char[i], " ")))}
 
That's it. The code above will read in the data and make a landmark matrix. 
Unfortunately, it sometimes also writes additional lines to the .landmarkAscii 
file. The first added element is "@2." Thereafter, the landmark file adds as 
many three-coordinate triplets as there are landmarks in the original data 
file. The values of these triplets are 0,0,1 (or maybe 1,0,0).

This is really strange behavior. A read function shouldn't write. 

My issue may be better suited to an R forum, but I am hoping someone here has 
reliable code for reading Avizo landmarks into R.

Thanks in advance. 

David


--
David Katz
University of California, Davis
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Re: [MORPHMET] Geomorph R package: digit.curves (several curves with different starting points at once)

2015-11-09 Thread Emma Sherratt
Pere,

>From what I can see it's a simple mistype:

for(i in 1:100){
equi[,,i]<-digit.curves(allcurves[1,,i], allcurves[,,i], 20, closed=F)
}

You need two commas in both brackets because you are working with a 3D
array. I have been very busy marking exams which is why I didn't answer you
sooner on the geomorph blog.

Emma

On Monday, 9 November 2015, Pere Ibáñez <perei...@gmail.com> wrote:

> Hello everybody,
>
> I need to ask something in relation to digit.curves in R package geomorph,
> because I think that there must be a really fast way to do something that I
> was going to do specimen by specimen.
>
> I created a (p x k x n) array using readland.tps from a tps file
> containing coordinates of a curve in n=100 specimens (this array is called
> allcurves). Now I want to use digit.curves to find 20 equidistant
> semilandmarks in the curve of each specimen defined by the coordinates of
> my array allcurves.
>
> I can use a for loop for that. But the start point of the curve of each
> specimen is different. The start point of each curve is the first row (the
> first landmark) of each specimen in the array allcurves. Is there any way,
> using the for loop, to use the first row of each specimen as the start
> point for each curve? I tried this:
>
> equi<-array(NA, dim=c(22,3,100)) #22 because I want to get the start and
> end points and 20 equidistant points in the outcome
>
> for(i in 1:100){
> equi[,,i]<-digit.curves(allcurves[1,i], allcurves[,,i], 20, closed=F)
> }
> This error occurs: Error in allcurves[1, i] : incorrect number of
> dimensions
>
> I know this happens because I am not getting right how to tell the program
> to use the first row of each specimen of the array as start point for each
> curve. Is there any way to do this? It would be extremely time-saving for
> my analyses.
>
> Thank you so much in advance. I really appreciate any advise!
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org <javascript:;>.
>


-- 

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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

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

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Re: [MORPHMET] Error with read.ply in geomorph

2015-08-23 Thread Emma Sherratt
Hi Claire, sorry for the delay- I'm travelling.

this looks like an issue with the normals. How does it work with addNormals
=F ?

Emma

On Friday, August 21, 2015, Claire Terhune claire.terh...@gmail.com wrote:

 Hi Emma-
 I seem to be having a different problem with the read.ply function that
 I'm hoping to get some help with. I've made sure my files are in ASCII
 format and I have removed texture information, but when I try to import
 them into geomorph I am getting the following error: *Error in if
 (sum(normals[1:3, it[j, i]] * normal)  0) normals[, it[j,  :   missing
 value where TRUE/FALSE needed*

 The files I'm working with were generated from CT scans rather than via a
 surface scanner, so I wonder if that has something to do with it? If so,
 does anyone have any suggestions as to how I might fix this?
 Thanks,
 Claire Terhune

 _

 Claire E. Terhune, Ph.D.

 Assistant Professor

 Department of Anthropology

 Old Main 336

 University of Arkansas

 Fayetteville, AR 72701



 Office: (479) 575-3529

 Lab: (479) 575-5296

 Email: cterh...@uark.edu
 javascript:_e(%7B%7D,'cvml','cterh...@uark.edu');

 Web page: terhunelab.uark.edu



 On Monday, December 15, 2014 at 10:02:39 PM UTC-6, Emma Sherratt wrote:

 Dear David and Stefan,

 The issue was that the PLY file of David has textures, which our read.ply
 function currently does not support. Resaving the file without the texture
 information made the file readable.

 FYI Stefan, the original file read fine with your vsgImport function, but
 only when readcolor=FALSE. When TRUE, it crashed R.

 Emma

 On Tuesday, 16 December 2014 05:34:00 UTC+11, Stefan Schlager wrote:

 Hi David,
 You can use either vcgImport from Rvcg or file2mesh from Morpho (which
 is basically the same) to import all kinds of meshes (stl, obj, ply) binary
 and ascii into an object of class mesh3d

 Best
 Stefan

 On 15/12/14 01:52, David Katz wrote:

 Hello,

 When I try to read a 3D surface file (ply ascii format) into geomorph, I
 get the following error:

 Error in dim(points) - c(ncolpts, npoints) :
   dims [product 6426920] do not match the length of object [5784228]

 For what it's worth, length of object is *exactly *90% of dims.

 Does anyone have an idea where this problem is coming from and how to
 fix it? Note that the model opens without difficulty as a binary ply in
 Geomagic.

 Thanks.

 David Katz

 --
 David Katz
 Doctoral Candidate
 Department of Anthropology--Evolutionary Wing
 University of California, Davis
 Young Hall 204
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Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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

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Re: [MORPHMET] Estimating Ontogenetic Trajectories

2015-08-23 Thread Emma Sherratt
Dear Miranda,

Using procD.lm is the correct function for what you want to do. Since you
have just two groups it's a simple Procrustes Anova. Your implementation
should be:

procD.lm(shape~ age*group)

This will give you:

Effect of age; where significant means the shape scales allometrically

Effect of group; where significant means the groups differ in intercept

The interaction term of age and group to tell you if the two groups have
the same slope (interaction term not significant) or the slopes differ (sig
interaction term)

Then from this you will be able to deduce whether the two groups follow the
same allometric trajectory or not. But remember, you are dealing with
multivariate regression here so there is no positive or negative allometry,
since the slope is a multivariate vector in shape space.

The same formula into trajectory.analysis should then lead you to where you
were hoping to go with that.

Emma

On Monday, August 24, 2015, Karban, Miranda E miranda-utzin...@uiowa.edu
wrote:

 Hello morphometricians,

 I am relatively new to morphometrics, and I am attempting to assess
 ontogenetic trajectories from a longitudinal sample of growth study x-rays.
 My subjects are divided into 2 groups, and I would like to determine
 whether there are developmental differences in cranial shape between these
 groups. I have precise ages for each subject, so I hope to use age as a
 variable (following McNulty et al., 2006) rather than centroid size.



 From what I gather from the literature, I can estimate ontogenetic
 trajectories by regressing the Procrustes aligned shape coordinates onto
 the independent variable of age. So far, I have attempted to do this in the
 geomorph package in R using the procD.lm and the trajectory.analysis
 functions. I am wondering if I am doing this correctly, or if there is a
 better function to use.



 I have tried the following:

 lateral.gpa - gpagen(vaultlandmarks)

 procD.lm(two.d.array(lateral.gpa$coords) ~ age, iter = 999)



 where “vaultlandmarks” refers to the 2D landmark and semi-landmark
 coordinates in my tps file, and “age” refers to a column in my metadata csv
 file which gives the age of each specimen to the nearest 1/10 of a year.
 This provides a sum-of-squared Procrustes distances, a mean square, and a
 highly significant p-value. I am not sure, however, how to compare the
 results I get from the 2 groups.



 When I try the trajectory.analysis function:

 lateral.gpa - two.d.array(gpagen(vaultlandmarks)$coords)

 trajectory.analysis(lateral.gpa~age)



 I get the error message: “Error in trajectory.analysis(lateral.gpa ~ age)
 :   X-matrix does not specify enough model factors (see help file).”



 Thank you for any advice or help you might provide.



 Best,

 Miranda Karban

 PhD Candidate, University of Iowa

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~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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

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Re: [MORPHMET] Stuck on creating new dataset

2015-07-11 Thread Emma Sherratt
Abel,

One problem that arises from surface scanning is that the integrity of the
ply files is less that perfect- there could be duplicated vertices or holes
and non-manifold edges (disconnected faces and vertices). I do not know
Morpheus well, but perhaps it is worth checking your files with Meshlab
first.

Emma

On Thursday, July 9, 2015, Abel Bosman bosman.a...@gmail.com wrote:

 Dear all,

 My name is Abel Bosman and I am quite new (as of 2 weeks ago) to geometric
 morphometrics, so my question might be a bit silly.

 I wanted to use the program Morpheus et al. to analyze my data on human
 mandibles, obtained from a NextEngine 3D scanner. I stored this data as a
 .ply file and selected new from images and then 3D. When I select the
 appropriate file, the program seems to be stuck on creating new dataset.
 Is this because my files are too large? (15.9 MB) or am I doing something
 wrong?. The data that is supplied with the program in the 3d section of the
 file folder (.ply files on monkey skulls) seems to work properly, so I am
 quite sure that the program is working as it should.

 If you have any suggestions or other tips, I would be very glad to hear
 them.

 With kind regards,
 Abel

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 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org javascript:;.



-- 

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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

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Re: [MORPHMET] Re: physignal in geomorph

2015-06-15 Thread Emma Sherratt
Anneke,

I'm gad you've managed to solve your issue but I need to say that making
your data a 3D array shouldn't be the fix.

 library(geomorph)
Loading required package: rgl
 data(plethspecies)
 Y.gpa-gpagen(plethspecies$land)#GPA-alignment

 #Test for phylogenetic signal in shape using data in a 3D array
 physignal(plethspecies$phy, Y.gpa$coords, method=Kmult,iter=99)
$phy.signal
  [,1]
[1,] 0.9572538

$pvalue
 [,1]
[1,] 0.04

 #Test for phylogenetic signal in shape using data in a 2D matrix
 physignal(plethspecies$phy, two.d.array(Y.gpa$coords),
method=Kmult,iter=99)
$phy.signal
  [,1]
[1,] 0.9572538

$pvalue
 [,1]
[1,] 0.02

So there must have been something wrong with your 2D matrix to not work
previously. Check that it is numeric, check that the rownames were assigned
properly, and that it contained only the data you wanted to input.

FYI, in geomorph, we use the 3D array format to specify that the data are
coordinate data, and the 2D matrix for multivariate data, not necessarily
shape data. This allows several of the functions to be used with non-shape,
multivariate datasets.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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




On 15 June 2015 at 20:24, Anneke van Heteren a.h.vanhete...@gmail.com
wrote:

 Dear all

 Thank you very much to those who have replied to my question. It turned
 out that my data was a 2D matrix instead of a 3D array and that that was
 causing the problem.

 Best wishes,

 Anneke


 On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote:

 Dear friends and colleagues



 I am trying to run physignal in geomorph (R), but I am running into a
 problem I do not understand. Here is the code I am using and the error
 message:

  physignal(ursid_phyl, Regr_res_av, iter=99)

 Error in match.names(clabs, names(xi)) :

   names do not match previous names



 However:

  name.check(ursid_phyl,Regr_res_av)

 [1] OK



 But:

  match(ursid_phyl,Regr_res_av)

 [1] NA NA NA NA

  match(Regr_res_av,ursid_phyl)

  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

 [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA



 This suggested to me that physignal might need the columns to carry the
 same names rather than the rows (as my phylogeny is list of 4 and I have 15
 landmarks=45 variables), but when I transposed my data, I get a different
 error message:

  trans_regr_res_av -t(Regr_res_av)

  physignal(ursid_phyl, trans_regr_res_av, iter=99)

 Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) :

   Number of taxa in data matrix and tree are not not equal.



 I do not know what I could try next to calculate physignal. Any help
 would be appreciated. This is the phylogeny that I am using:



 (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);


 Thanks in advance.



 Best wishes,



 Anneke van Heteren




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 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


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Re: [MORPHMET] Landmark Editor -- MorphoJ problem

2015-06-15 Thread Emma Sherratt
Ari,

This issue is probably due to having spaces in the names of your specimens.
Find and replace with _ then try again

Emma


On Monday, June 15, 2015, a.l.schulz ariadne.sch...@gmail.com wrote:

 Hello All,

 I need to ask a rather silly question for which I imagine there is a
 simple solution ... but I just can't figure it out. I've created a landmark
 file in IDAV Landmark Editor and exported an NTSYSpc (.dta) file for it. I
 then tried to upload that into MorphoJ, but to no avail. I keep getting the
 message There appear to be too many row labels in the file. I then tried
 to create the same dataset using text files exported from Landmark Editor
 but got roughly the same message. I have opened the files and looked at
 them and as far as I can tell there is nothing wrong.

 Has anyone else encountered and overcome this issue? For the time being I
 am stumped.

 Best,
 Ari

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 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org
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~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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

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

To unsubscribe from this group and stop receiving emails from it, send an email 
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[MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

2015-06-15 Thread Emma Sherratt
Dear Edouard,

You can find a comprehensive guide by David Polly 
here: http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf

And a few tips on digitizing 2D data can be found 
here: 
http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-describe-the-shape-of-my-favourite-structure

Best,

Emma

On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote:

 Hello,

 Is there a guide for the complete beginner on how to use ImageJ instead of 
 tpsdig, especially on how to set the scale before digitizing?

 Many thanks

 Edouard


 -
 Edouard Masson-MacLean
 PhD Candidate
 Room 119
 Department of Archaeology
 School of Geosciences
 University of Aberdeen
 St. Mary's, Elphinstone Road
 Aberdeen, AB24 3UF
 Scotland, UK


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Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
Anneke,

You are using match() incorrectly. See below:

 library(geomorph)
Loading required package: rgl
 data(plethspecies)
 Y.gpa-gpagen(plethspecies$land)
 physignal(plethspecies$phy,Y.gpa$coords,method=Kmult,iter=99)
$phy.signal
  [,1]
[1,] 0.9572538

$pvalue
 [,1]
[1,] 0.03

 match(plethspecies$phy, Y.gpa$coords) # doesn't work
[1] NA NA NA NA
 match(plethspecies$phy$tip.label, dimnames(Y.gpa$coords)[[3]]) # works
[1] 7 1 8 3 9 5 4 2 6

By specifying $tip.label and dimnames() you will be able to see the problem
with your dataset. It's likely to be a trailing space or _.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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




On 11 June 2015 at 18:29, Anneke van Heteren a.h.vanhete...@gmail.com
wrote:

 Dear friends and colleagues



 I am trying to run physignal in geomorph (R), but I am running into a
 problem I do not understand. Here is the code I am using and the error
 message:

  physignal(ursid_phyl, Regr_res_av, iter=99)

 Error in match.names(clabs, names(xi)) :

   names do not match previous names



 However:

  name.check(ursid_phyl,Regr_res_av)

 [1] OK



 But:

  match(ursid_phyl,Regr_res_av)

 [1] NA NA NA NA

  match(Regr_res_av,ursid_phyl)

  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

 [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA



 This suggested to me that physignal might need the columns to carry the
 same names rather than the rows (as my phylogeny is list of 4 and I have 15
 landmarks=45 variables), but when I transposed my data, I get a different
 error message:

  trans_regr_res_av -t(Regr_res_av)

  physignal(ursid_phyl, trans_regr_res_av, iter=99)

 Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) :

   Number of taxa in data matrix and tree are not not equal.



 I do not know what I could try next to calculate physignal. Any help would
 be appreciated. This is the phylogeny that I am using:



 (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);


 Thanks in advance.



 Best wishes,



 Anneke van Heteren




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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


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Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
However Anneke, the error that you first get is not our catch of the names
not matching, but is instead coming from somewhere within, but where I
cannot immediately tell. Perhaps send me the traceback.

Also note that name.check() only works with data in a 2d matrix and not a
3d array.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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




On 11 June 2015 at 22:39, Emma Sherratt emma.sherr...@gmail.com wrote:

 Anneke,

 You are using match() incorrectly. See below:

  library(geomorph)
 Loading required package: rgl
  data(plethspecies)
  Y.gpa-gpagen(plethspecies$land)
  physignal(plethspecies$phy,Y.gpa$coords,method=Kmult,iter=99)
 $phy.signal
   [,1]
 [1,] 0.9572538

 $pvalue
  [,1]
 [1,] 0.03

  match(plethspecies$phy, Y.gpa$coords) # doesn't work
 [1] NA NA NA NA
  match(plethspecies$phy$tip.label, dimnames(Y.gpa$coords)[[3]]) # works
 [1] 7 1 8 3 9 5 4 2 6

 By specifying $tip.label and dimnames() you will be able to see the
 problem with your dataset. It's likely to be a trailing space or _.

 Emma

 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L112 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.sherr...@une.edu.au
 Twitter: @DrEmSherratt

 Caecilians are legless amphibians...

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

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




 On 11 June 2015 at 18:29, Anneke van Heteren a.h.vanhete...@gmail.com
 wrote:

 Dear friends and colleagues



 I am trying to run physignal in geomorph (R), but I am running into a
 problem I do not understand. Here is the code I am using and the error
 message:

  physignal(ursid_phyl, Regr_res_av, iter=99)

 Error in match.names(clabs, names(xi)) :

   names do not match previous names



 However:

  name.check(ursid_phyl,Regr_res_av)

 [1] OK



 But:

  match(ursid_phyl,Regr_res_av)

 [1] NA NA NA NA

  match(Regr_res_av,ursid_phyl)

  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

 [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA



 This suggested to me that physignal might need the columns to carry the
 same names rather than the rows (as my phylogeny is list of 4 and I have 15
 landmarks=45 variables), but when I transposed my data, I get a different
 error message:

  trans_regr_res_av -t(Regr_res_av)

  physignal(ursid_phyl, trans_regr_res_av, iter=99)

 Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) :

   Number of taxa in data matrix and tree are not not equal.



 I do not know what I could try next to calculate physignal. Any help
 would be appreciated. This is the phylogeny that I am using:



 (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);


 Thanks in advance.



 Best wishes,



 Anneke van Heteren




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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.




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Re: [MORPHMET] Centroid size and isometric scaling

2015-05-31 Thread Emma Sherratt
Dear Blake,

In short, isometry, positive allometry and negative allometry cannot be
studied using multivariate regressions of multivariate data (such as
geometric morphometric coordinate data). These are concepts that only exist
in bivariate plots of size and a single variable.

Suggested reading on Multivariate Allometry, see Klingenberg 1996 in
Advances in Morphometrics (available here:
http://www.flywings.org.uk/papers_page.htm) and Monteiro 1999 Systematic
Biology, and and then also read this important review
Sheets  Zelditch 2013 Hystrix (in the Yellow Book).

You should perhaps be more be thinking about comparing trajectories in
shape space (e.g. Adams  Collyer 2009 Evolution).

See for example comparing different ontogenetic trajectories in Adams 
Nistri 2010 BMC Evo Bio, Klingenberg  Spence's study of heterochrony in
waterstriders (1993, Evolution).

Best,

Emma


~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt

Caecilians are legless amphibians...

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

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




On 1 June 2015 at 08:51, Blake Dickson bdick...@g.harvard.edu wrote:

 Hey all,

 So I have a question regarding using centroid size in analyses of scaling.

 I want to test how something scales with increasing body size in a 3D GM
 context. If I use centroid size, gained from 3D landmarks, as a measure of
 the size of my object and skull length as a measure of body size, what
 scaling would I assume to be isometric? Do I treat centroid size as a
 single dimension unit (length) and assume isometry is 1:1; or rather
 centroid size as a multidimensional unit?

 Thanks,
 Blake

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

 To unsubscribe from this group and stop receiving emails from it, send an
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Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
Dear Mike,

One way you can do this is by using the canonical variates analysis
function. Between two groups you will get the shape change graph associate
with the difference between groups. Or you can go to Preliminaries 
average observations by... and choose the groups classifier, and then right
click and disply graphs.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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




On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote:

 Hi All,
 I am running MorphoJ on Mac OSX. I am looking at morhological variation
 between two datasets. In each dataset, each specimen has four replicates. I
 combined the datasets, made classifier files and ran the Procrustes fit and
 generated the covariance matrix.  How then do I make a vector diagram/warp
 grid that visualizes shape change between the average shape of the two
 datasets? Thanks in advance for your help.

 Mike


 Michael W. Holmes

 Ph.D. Candidate
 University of California, Berkeley
 Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

 Museum of Vertebrate Zoology
 3101 Valley Life Sciences Building
 University of California
 Berkeley, CA   94720  USA

 http://ib.berkeley.edu/labs/lacey/holmes2.html

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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


-- 
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Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
Oh sorry, I think the latter way just shows the group mean from the overall
mean - so you may need to do some cutting and pasting...
Contact Chris Klingenberg, he might have an easier way up his sleeve.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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




On 13 February 2015 at 09:02, Emma Sherratt emma.sherr...@gmail.com wrote:

 Dear Mike,

 One way you can do this is by using the canonical variates analysis
 function. Between two groups you will get the shape change graph associate
 with the difference between groups. Or you can go to Preliminaries 
 average observations by... and choose the groups classifier, and then right
 click and disply graphs.

 Emma

 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L120 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.sherr...@une.edu.au

 Caecilians are legless amphibians...

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

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




 On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote:

 Hi All,
 I am running MorphoJ on Mac OSX. I am looking at morhological variation
 between two datasets. In each dataset, each specimen has four replicates. I
 combined the datasets, made classifier files and ran the Procrustes fit and
 generated the covariance matrix.  How then do I make a vector diagram/warp
 grid that visualizes shape change between the average shape of the two
 datasets? Thanks in advance for your help.

 Mike


 Michael W. Holmes

 Ph.D. Candidate
 University of California, Berkeley
 Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

 Museum of Vertebrate Zoology
 3101 Valley Life Sciences Building
 University of California
 Berkeley, CA   94720  USA

 http://ib.berkeley.edu/labs/lacey/holmes2.html

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

 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

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] CVA and Discriminant Analysis in Morpho J

2015-02-10 Thread Emma Sherratt
Gabi,

While Michael is correct i how you can export the CV scores from MorphoJ, I
would highly recommend against exporting the CV scores to plot against
other parameters. The reason being that CVA should not be used like
Principal Components Analysis. CVA axes should be used for inspecting the
data for the aspects of shape that delimit and discriminate between two or
more groups. Not as reduced axes for use in correlation tests.

Emma



~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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




On 11 February 2015 at 08:33, gnavas gna...@mlml.calstate.edu wrote:

 Dear Morphometrics Wizards,

 I have 2 questions for which I am hoping to get help on:

 Question 1. CVA analysis: I have 6 sites. Within each site I have at least
 22 samples. When I ran a CVA comparison on these 6 sites in Morpho J. I was
 hoping to find a way to get an actual value for each of my samples that
 plotted. So, for instance, CV1 values for each specimen, and the same for
 CV2. In the results tab, I can only find data relevant to my landmarks and
 canonical variates coefficients relating to lanmarks.

 I would love to figure out a way to export my CV1 and CV2 values for each
 specimen to then plot that against other parameters that may be effecting
 shape at those 2 or more canonical variate axes. Has anyone run into this
 problem, and found a solution?

 Question 2. Discriminant Analysis:
 Again, 6 sites with 22 samples, but this time I was only able to compare 2
 sites at a time. Has anyone ever been able to run 1 site against all
 remaining sites? It would be great to get an idea of how my sites compare
 to all others, rather than to just one other at a time. I suspect I have to
 play with my classifier variables, but I am not sure how to go about that.
 At this point, I have made 1 classifier variable that allows me to
 distinguish the different sites.

 If any of you have run into this or simply know how to do this, please let
 me know. I am also happy to give more detail on my study if that would help?

 Thank you in advance!
 Gabi

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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


-- 
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to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] CVA and Discriminant Analysis in Morpho J

2015-02-10 Thread Emma Sherratt
Gabi,

If you are interested in the relationship between a set of shape variables
(your Procrustes coordinates) and a single variable (e.g. precipitation),
you could use a Multivariate Regression in MorphoJ, or better, a Procrustes
ANOVA (which is procD.lm() in geomorph. Not sure if the Procrustes ANOVA in
morphoJ can do this...). If you have a set of environmental variables and
wish for them to be treated together, maybe 2 block partial least squares
can be used.
I would NOT use a single PC axis in a bivariate analysis of correlation
with an environmental variable. Use all the shape variables and a
Multidimensional method such as multivariate regression or Procrustes
ANOVA.

Good luck!

Emma

P.S. It my own personal opinion, but every time shape data is reduced to a
few PC axes and used in an analysis, a fairy dies... ;)

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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




On 11 February 2015 at 09:28, gnavas gna...@mlml.calstate.edu wrote:

 Hi guys,

 Thanks a ton for your quick responses. Emma, the CV scores were so
 tempting to use for comparison to other variables...What would you suggest
 would be a more appropriate index to use in order to compare the shape
 ordination results to say, environmental variables, such as sediment size
 (I am studying clam morphology differences)?

 On Tuesday, February 10, 2015 at 2:00:04 PM UTC-8, Emma Sherratt wrote:

 Gabi,

 While Michael is correct i how you can export the CV scores from MorphoJ,
 I would highly recommend against exporting the CV scores to plot against
 other parameters. The reason being that CVA should not be used like
 Principal Components Analysis. CVA axes should be used for inspecting the
 data for the aspects of shape that delimit and discriminate between two or
 more groups. Not as reduced axes for use in correlation tests.

 Emma



 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L120 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.s...@une.edu.au

 Caecilians are legless amphibians...

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

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




 On 11 February 2015 at 08:33, gnavas gna...@mlml.calstate.edu wrote:

 Dear Morphometrics Wizards,

 I have 2 questions for which I am hoping to get help on:

 Question 1. CVA analysis: I have 6 sites. Within each site I have at
 least 22 samples. When I ran a CVA comparison on these 6 sites in Morpho J.
 I was hoping to find a way to get an actual value for each of my samples
 that plotted. So, for instance, CV1 values for each specimen, and the same
 for CV2. In the results tab, I can only find data relevant to my landmarks
 and canonical variates coefficients relating to lanmarks.

 I would love to figure out a way to export my CV1 and CV2 values for
 each specimen to then plot that against other parameters that may be
 effecting shape at those 2 or more canonical variate axes. Has anyone run
 into this problem, and found a solution?

 Question 2. Discriminant Analysis:
 Again, 6 sites with 22 samples, but this time I was only able to compare
 2 sites at a time. Has anyone ever been able to run 1 site against all
 remaining sites? It would be great to get an idea of how my sites compare
 to all others, rather than to just one other at a time. I suspect I have to
 play with my classifier variables, but I am not sure how to go about that.
 At this point, I have made 1 classifier variable that allows me to
 distinguish the different sites.

 If any of you have run into this or simply know how to do this, please
 let me know. I am also happy to give more detail on my study if that would
 help?

 Thank you in advance!
 Gabi

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

 To unsubscribe from this group and stop receiving emails from it, send
 an email to morphmet+u...@morphometrics.org.


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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


-- 
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To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] surface semilandmarks

2015-01-10 Thread Emma Sherratt
Dear Ariadne,

I believe that we have a solution for you with geomorph
http://cran.r-project.org/web/packages/geomorph/ in the R environment. In
geomorph, we have several functions to digitize semilandmarks over 3D
surfaces and curves. Why don't you email to me your femora digitizing
regime and we can discuss how to work with these files.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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




On 9 January 2015 at 23:29, Ariadne Schulz ariadne.sch...@gmail.com wrote:

 Dear All,
 I've got about 160 3D scans of human femora and roughly the same of humeri
 and before I go off and collect more, I want to collect surface and curve
 semilandmarks. I've tried a few methods and looked at some of the papers
 out there and I think EVAN toolbox is the way to go, but it takes a lot of
 meticulous work and staring at a computer screen. I did try Landmark
 Editor, but I'm not convinced that the patches really work on the diaphysis
 (they seem to go beneath the surface) and the flexible patch doesn't seem
 to export points. Does anyone here know a better method, have a suggestion
 or know how to create curve objects that can be imported into EVAN? I can
 pretty much use any and all suggestions.

 Best Regards,
 Ari

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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.


-- 
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to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] arrayspecs in geomorph giving error message

2014-12-30 Thread Emma Sherratt
 -0.2906006 -0.00547907 -0.4337808 0.03663254
 34 -0.2894727  0.00027348 -0.4324036 0.03879201
 35 -0.2900338 -0.00101017 -0.4352513 0.02773395
 36 -0.2911340  0.00317057 -0.4371728 0.03853357
 37 -0.2887806 -0.00350296 -0.4380146 0.04047513
 38 -0.2940667 -0.00058660 -0.4469157 0.03693919
 39 -0.2958324 -0.00273129 -0.4413747 0.03341547
 40 -0.2903865 -0.00050731 -0.4378892 0.03405760
 41 -0.2987432 -0.00461726 -0.4219447 0.04669297
 42 -0.266 -0.00759683 -0.4294421 0.03253387
 43 -0.2948869 -0.00501487 -0.4362682 0.03903118

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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org
 javascript:_e(%7B%7D,'cvml','morphmet%2bunsubscr...@morphometrics.org');
 .



-- 

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L118 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5038
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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

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

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


[MORPHMET] Re: Error with read.ply in geomorph

2014-12-15 Thread Emma Sherratt
Hi David,

Turns out my answer went to only you and not this group.

I believe that your ply file has duplicated vertices and so it is not able 
to match up the vertex coordinates to the triangles.

Please send me the file so that I can examine it.

Emma

On Monday, 15 December 2014 11:53:17 UTC+11, dckatz wrote:

 Hello,

 When I try to read a 3D surface file (ply ascii format) into geomorph, I 
 get the following error: 

 Error in dim(points) - c(ncolpts, npoints) : 
   dims [product 6426920] do not match the length of object [5784228]

 For what it's worth, length of object is *exactly *90% of dims.

 Does anyone have an idea where this problem is coming from and how to fix 
 it? Note that the model opens without difficulty as a binary ply in 
 Geomagic. 

 Thanks.

 David Katz

 -- 
 David Katz
 Doctoral Candidate
 Department of Anthropology--Evolutionary Wing
 University of California, Davis
 Young Hall 204
  

-- 
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to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] Error with read.ply in geomorph

2014-12-15 Thread Emma Sherratt
Dear David and Stefan,

The issue was that the PLY file of David has textures, which our read.ply 
function currently does not support. Resaving the file without the texture 
information made the file readable.

FYI Stefan, the original file read fine with your vsgImport function, but 
only when readcolor=FALSE. When TRUE, it crashed R.

Emma

On Tuesday, 16 December 2014 05:34:00 UTC+11, Stefan Schlager wrote:

  Hi David,
 You can use either vcgImport from Rvcg or file2mesh from Morpho (which is 
 basically the same) to import all kinds of meshes (stl, obj, ply) binary 
 and ascii into an object of class mesh3d

 Best
 Stefan

 On 15/12/14 01:52, David Katz wrote:
  
 Hello, 

  When I try to read a 3D surface file (ply ascii format) into geomorph, I 
 get the following error: 

  Error in dim(points) - c(ncolpts, npoints) :  
   dims [product 6426920] do not match the length of object [5784228]

  For what it's worth, length of object is *exactly *90% of dims.
  
  Does anyone have an idea where this problem is coming from and how to 
 fix it? Note that the model opens without difficulty as a binary ply in 
 Geomagic. 

  Thanks.

 David Katz

  -- 
 David Katz
 Doctoral Candidate
 Department of Anthropology--Evolutionary Wing
 University of California, Davis
 Young Hall 204
   -- 
 MORPHMET may be accessed via its webpage at http://www.morphometrics.org
 To unsubscribe from this group and stop receiving emails from it, send an 
 email to morphmet+u...@morphometrics.org javascript:.


  

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Re: [MORPHMET] Default orientation of 3D plots in geomorph

2014-12-15 Thread Emma Sherratt
Roger,

I would suggest that you can re-orient the Procrustes coordinates to match
the position you would prefer and then this will be the default in all
analyses.

However I'd like to get to the bottom of why you are seeing this. What
version of Geomorph and were you using PrinAxes=T in gpagen?

Contact me directly, then we can post a summary here later.

Emma

On Thursday, December 11, 2014, Roger Close roger.cl...@gmail.com wrote:

 Hi all,

 In my experience the 3D plots generated by geomorph (e.g., by
 plotAllSpecimens) are not oriented the 'right way up'. I would expect the x
 axis to be horizontal, y to be vertical and z to correspond to depth (into
 the image).

 However—at least with my data—geomorph always draws 3D plots with the z
 axis oriented vertically and the y axis going into the image. I'd like to
 change the default orientation so I can automatically generate movies
 without having to manually move the plots.

 Does anyone know how I can change the default orientation?

 Cheers,
 Roger

 ---
 Roger Close, Postdoctoral Research Associate
 Department of Earth Sciences, Oxford University
 South Parks Road
 Oxford OX1 3AN
 United Kingdom

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

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org
 javascript:_e(%7B%7D,'cvml','morphmet%2bunsubscr...@morphometrics.org');
 .



-- 

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L118 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5038
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

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

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

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

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.