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Fred Bookstein
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or which is my mistake?
Thank you very much!
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a, Y., & Klingenberg, C. P. (2011). Beyond bilateral symmetry:
geometric morphometric methods for any type of symmetry. *BMC evolutionary
biology*, *11*(1), 280.
Best wishes!
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Ian,
The command summary(manova(..)) will perform a parametric manova. However,
for the datafile you sent, that operation will not be possible because the
number of variables relative to sample size (note, you posted a similar
issue about a month ago to Morphmet).
The alternative is to use
Thank you very much!
Best,
Agnese Lanzetti
agnese.lanze...@hotmail.it
Ph.D. candidate
Joint Doctoral Program in Evolutionary Biology
San Diego State University
University of California, Riverside
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,x5,y5,x6,y6,x7,y7,x8,y8,x9,y9,x10,y10,x11,y11,x12,y12,x13,y13,x14,y14,x15,y15,x16,y16,x17,y17,x18,y18,x20,y20,x21,y21,x22,y22,x23,y23,x24,y24,x25,y25,x26,y26,x27,y27,x28,y28,x29,y29,x30,y30,x31,y31)~
as.factor(Species),data=data1)
SAV<-summary.aov(Raf.manova1)
print(SAV)
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in Jim
Rohlf's lab in Stony Brook, the current work in Paris and his Workshop here
in Berlin (https://www.physalia-courses.org/courses-workshops/course22/)
Here is the link: https://www.physalia-courses.org/news/n14/
Happy reading!
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ory
strategies. Ecology of Freshwater Fish. DOI to follow
Phenotypic and resource use partitioning amongst sympatric lacustrine brown
trout, Salmo trutta. Biological Journal of the Linnean Society. DOI
10.1093/biolinnean/bly032
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Are there any upcoming US-based workshops that would be appropriate for new
graduate students looking to learn geometric morphometrics (both R-based and
non-R based)?
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I have a phylogeny and 3-D morphometric data and I want to calculate trait
disparity between sister species and their PC scores. Is there a package or
script that can do this in R?
Thanks,
Nick
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Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/
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x30,y30,x31,y31)~as.factor(group),data=data1)
>
> summary(Raf.manova1)
>
> summary(Raf.manova1,test = "Pillal")
>
> summary(Raf.manova1, test = "wilks")
>
> summary(Raf.manova1, test = "Hotelling-Lawley")
>
> summary(Raf.manova1, test = "Roy
6,x27,y27,x28,y28,x29,y29,x30,y30,x31,y31)~as.factor(group),data=data1)
summary(Raf.manova1)
summary(Raf.manova1,test = "Pillal")
summary(Raf.manova1, test = "wilks")
summary(Raf.manova1, test = "Hotelling-Lawley")
summary(Raf.manova1, test = "Roy")
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to R (2009).
9. Mixed effects models and extensions in ecology with R (2009).
10. Analysing Ecological Data (2007).
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keeping y the same, but since the midplane
> x coordinates are not at 0 this obviously doesn't work.
>
> Any advice or code would be greatly appreciated!
>
> Thanks,
> Christy
>
> --
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> ---
> Y
if there is an easy way to do this. I naively tried multiplying the
x coordinate dimensions *-1 and keeping y the same, but since the midplane
x coordinates are not at 0 this obviously doesn't work.
Any advice or code would be greatly appreciated!
Thanks,
Christy
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t; indique y no comunique su contenido a terceros, procediendo a su
> destrucción.
>
>
>
> Antes de imprimir este correo piense si es realmente
> necesario.
> El medioambiente es cosa de todos.
>
>
>
>
>
>
>
>
> --
> MORPHMET may be acces
medioambiente es cosa de todos.
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t; ESTIMATE YOUR GLOBAL FOOTPRINT:
> http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
>
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> ---
> You received this message because you are subscribed to the Google Groups
>
-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
ESTIMATE YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
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twice, on specimen by specimen basis (like #2) and then by
specimen's average aligned coordinates
Which approach seems most logical?
n
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prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/
6 Hope Park Crescent
Edinburgh
EH8 9NA
+44 (0) 7966500340
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/r/how-to-create-an-array-in-r/
I hope this helps.
Carmelo
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==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/
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87
>
> 2767108126331581213920471693
> 175315351159184110672151
> 100924371071
>
> 295692829361692211223601
have come up
with nothing.I have tried both long and wide format and have had the same
result. any help is much appreciated.
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"
10672151
> 100924371071
>
> 295692829361692211223601300
> 1784 1304101617008882084
> 8322480872
>
>
>
>
>
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n(Y,curves=slidermatrix)
summary(Y.gpa)
plot(Y.gpa)
Y.gpa <- gpagen(Y,curves=slidermatrix,ProcD=FALSE )
summary(Y.gpa)
plot(Y.gpa)
a<-(Y.gpa$coords)
plotTangentSpace(a)
slider matrix:
beforeslide after
567
781
> plot(Y.gpa)
> a<-(Y.gpa$coords)
> plotTangentSpace(a)
>
>
>
>
> slider matrix:
>
> before slideafter
> 567
> 781
> 123
> 345
> 18 7
> 7
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X-Googl
YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
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http://www.morphometrics.org<http://www.morphometrics.org/>
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178413041016
1700888 2084832 2480 872
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est features. I think they recently implemented copy/paste landmark
> names and then undo if you accidentally moved a position of a landmark.
>
>
>
> M
>
>
>
> *From:* davide tamagnini
> *Sent:* Monday, July 30, 2018 7:08 AM
> *To:* MORPHMET
> *Subject:* [M
. I've double checked the numbers--my tree and matrices all
have the same number of taxa and matching names--and made sure I'm using
the current versions of morpho and R.
Has anyone else encountered this problem or have any ideas what I might be
doing wrong?
Many thanks,
Lawrence
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d 3D geometric morphometrics of sliding semilandmarks to highly
variable soft tissue (lungs) and we obtained very interesting results
on sexual dimorphism.
Cheers from Madrid,
Nicole
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space or in any direction of interest within the PC
> space.
>
>
>
> _ _ _ _ _ _ _ _ _
>
> F. James Rohlf, Distinguished Prof. Emeritus
>
> [image: univautosig]
>
> Depts. of Anthropology and of Ecology & Evolution
>
>
>
>
>
> *From:* Yi
regards
Sole
Soledad De Esteban-Trivigno
Institut Català de Paleontologia Miquel Crusafont (ICP)
Campus de la Universitat Autònoma de Barcelona
Cerdanyola del Vallès (Barcelona). Spain
www.icp.cat
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You
.
_ _ _ _ _ _ _ _ _
F. James Rohlf, Distinguished Prof. Emeritus
Depts. of Anthropology and of Ecology & Evolution
From: Yinan Hu <yinanhu...@gmail.com>
Sent: Friday, May 18, 2018 2:19 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] How to project shape
projection (i.e. using the mean difference of PC1 score
>> and PC2 score) doesn't feel right to me as I don't think PC scores are
>> directly comparable between different PCs. Or am I wrong?
>> Any suggestions would be greatly appreciated.
>>
>> Many thanks for your time
score) doesn't feel right to me as I don't think PC scores are
> directly comparable between different PCs. Or am I wrong?
> Any suggestions would be greatly appreciated.
>
> Many thanks for your time.
>
> --
> MORPHMET may be accessed via its webpage at http://www.morph
effects, using the command, though i inserted int.first = false, somehow
>>> it’s not working often shows error
>>>
>>> *Paint3factor<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data
>>> = Paintgeo3fac, iter = 99, RRPP = FALSE, print.progres
gt;>> it’s not working often shows error
>>>
>>> Paint3factor<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data =
>>> Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first =
>>> FALSE)
>>>
>>>
>>>
&
score) doesn't feel right to me as I don't think PC scores are directly
comparable between different PCs. Or am I wrong?
Any suggestions would be greatly appreciated.
Many thanks for your time.
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02467
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email: katrin.schae...@univie.ac.at
http://www.anthropology.at
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from changing, + to *, inserting int.first, any other stuff to be
>> added?
>>
>> Please help me :(
>>
>> Thanks in Advance!
>>
>> Truly
>>
>> Mahen
>>
>>
>> --
>> ***
>> M Mahendi
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834
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ON)
> Anaikatti (PO), Coimbatore - 641108, TamilNadu, India
> Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901
> Fax: 0422-2657088
> http://www.sacon.in/staff/dr-m-mahendiran/
> <http://www.sacon.in/staff/dr-m-mahendiran/>
>
> P Please consider the envir
20901
Fax: 0422-2657088
http://www.sacon.in/staff/dr-m-mahendiran/
P Please consider the environment before printing this email
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"M
Dear colleagues,
This course might be of interest for some people in morphmet list: “Mapping
Trait Evolution”, June 4th-8th, 2018.
Instructor: Dr. Jeroen Smaers (Stony Brook University, USA).
PROGRAM:
Monday. (R packages: ape, Geiger).
Morning: Phylogenetic data
rg/courses-workshops/course20/
Here is the full list of our courses and Workshops:
https://www.physalia-courses.org/courses-workshops/
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/10.1101/310789
Best wishes,
Yoland Savriama
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de la Universitat Autònoma de Barcelona
Cerdanyola del Vallès (Barcelona). Spain
www.icp.cat
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Thanks a lot for your replies, I managed to install it!
Best wishes,
Renaud.
Le jeudi 3 mai 2018 12:55:08 UTC+2, Renaud Lebrun a écrit :
>
> Dear Morphmet users,
> would someone still have an installer of Landmark editor
> <http://graphics.idav.ucdavis.edu/research/EvoMorph>
I have recently installed Morphologika v2.5 on a new Windows 10 computer.
It crashes when I try to load in new data (.txt) file. I've tried
re-installing and various compatibility modes. Does anyone have any
suggestions as to what I might be missing?
Thanks,
Rachel Menegaz
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-9d66-0050568000ff
For more Information contact: Caro Kapp
IPM Initiative
Department of Conservation Ecology and Entomology
Stellenbosch University
E-mail: ck...@sun.ac.za
Tel: 021-808 9600
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6712; doi: https://doi.org/10.1101/306712
Best wishes,
Yoland Savriama
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t, can I unbend it using the pigment
> in R (any of the GMM packages or else)? How exactly does the unbending tool
> works: does it unbend fixed and semi LM according to the distance beween
> the pigment curve and a straight line that goes through all pigment curve
> semi-LM's? I'm n
according to the distance beween
the pigment curve and a straight line that goes through all pigment curve
semi-LM's? I'm not sure I got this.
Thanks,
Avi
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)
Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr
Jonathan Potts
www.prstatistics.com/course/movement-ecology-move01/
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Dear MorphMet users,
I write you to present you a software I develop and use for my own research
needs, MorphoDig (available at http://morphomuseum.com/morphodig , and the
sources at https://github.com/morphomuseum/MorphoDig ).
Currently, MorphoDig is mainly a 3D mesh editor, and can serve
re details and application see:
http://personalwesen.univie.ac.at/jobs-recruiting/professuren/detail-seite/news/theoretical-evolutionary-biology/?no_cache=1=d6099e9c6a5bf9ed84f0a773cc6ea192
Please note that the application deadline is 15 April 2018.
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this, but the structure of the problem
>> is more or less the same: Derive a model, test it, if it results in
>> sensible predictions, then apply to your unknowns.
>>
>>
>>
>> Hope this helps some…
>>
>> M
>>
>>
>>
>>
>>
re are other ways than LD to do this, but the structure of the problem
> is more or less the same: Derive a model, test it, if it results in
> sensible predictions, then apply to your unknowns.
>
>
>
> Hope this helps some…
>
> M
>
>
>
>
>
>
>
>
>
>
&g
From: Dr.Abdelnasser Ibrahim <dr.nasse...@gmail.com>
Sent: Monday, April 2, 2018 4:11 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] How can I test the project for identification of unknown
crania?
Dear all,
I'm a Ph.D. student and I'm working with 3D CT scan geometric morphometric
an
.
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?
Thanks for the help,
Karl Fetter
Ph.D. Candidate
Keller Lab
Department of Plant Biology
University of Vermont
k...@uvm.edu
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. Emeritus Dept.
Anthropology and Ecology & Evolution Stonybrook University
Original message From: Sarah Friedman <sarahtfr...@gmail.com>
Date: 3/29/18 8:08 AM (GMT-10:00) To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Re: Multivariate PICs?
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which is a better method
> for studying the variability- using photographs or scans of the specimens.
> The approach would be quite traditional- assigning landmark points, and
> further analysis, etc. All kinds of suggestions are welcome. Thanks!
>
> --
> MORPHMET may be accessed via i
; specimens. The approach would be quite traditional- assigning landmark
>> points, and further analysis, etc. All kinds of suggestions are welcome.
>> Thanks!
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
>> You
, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
-Original Message-
From: Sarah Friedman <sarahtfr...@gmail.com>
Sent: Monday, March 19, 2018 2:24 PM
To: MORPHMET <morphmet@morphometrics.org
the contrasts are
calculated. Does anybody know if the independent contrasts are calculated using
the method described in McPeek (1994), the Euclidean distances between
contrasts on each branch, or another method?
Thanks,
Sarah
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. Thanks!
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ds,
Carlo
*Carlo Pecoraro, Ph.D*
Physalia-courses DIRECTOR
i...@physalia-courses.org
http://www.physalia-courses.org/
Twitter: @physacourses
mobile: +49 15771084054
https://groups.google.com/forum/#!forum/physalia-courses
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Institut Català de Paleontologia Miquel Crusafont (ICP)
Campus de la Universitat Autònoma de Barcelona
Cerdanyola del Vallès (Barcelona). Spain
www.icp.cat
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shown below i.e 0,1,2,3.79.
Therefore i could not classify.
How can this be corrected so that i have the full names instead of
numbers in the classifier column.
Kindly assist.
Nelly Ndungu
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he .jpg file.
As shown below i.e 0,1,2,3.79.
Therefore i could not classify.
How can this be corrected so that i have the full names instead
of numbers in the classifier column.
Kindly assist.
Nelly Ndungu
--
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that i have the full names instead of numbers
> in the classifier column.
>
>
> Kindly assist.
> Nelly Ndungu
> --
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> ---
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ds that were in the .jpg file.
> As shown below i.e 0,1,2,3.79.
> Therefore i could not classify.
> How can this be corrected so that i have the full names instead of numbers
> in the classifier column.
>
>
> Kindly assist.
> Nelly Ndungu
>
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so that i have the full names instead of
numbers in the classifier column.
Kindly assist.
Nelly Ndungu
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Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: +386 41 808 366
E: tina.klenov...@um.si<mailto:ime.prii...@um.si>,
www.fnm.um.si<http://www.fnm.uni-mb.si>
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850858
[5] https://www.ncbi.nlm.nih.gov/pubmed/26628903
[6] https://www.ncbi.nlm.nih.gov/pubmed/26120349
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To
R.
>
> Tina
>
>
>
> *From:* Paolo Piras [mailto:paolopir...@gmail.com]
> *Sent:* Thursday, March 15, 2018 2:14 PM
> *To:* Carmelo Fruciano
> *Cc:* MORPHMET
> *Subject:* Re: [MORPHMET] digitizing very variable leaves
>
>
>
> Hi Tina,
>
> if your colleagues are i
ic Fourier analysis is also implemented in NTSYSpc, which is also
> user-friendly.
>
> You probably want to read a bit on the methodology to see if it fits what
> you plan to do and its potential shortcomings.
>
> I hope this helps.
>
> Carmelo
>
>
>
> On 15/
user-friendly.
You probably want to read a bit on the methodology to see if it fits
what you plan to do and its potential shortcomings.
I hope this helps.
Carmelo
On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote:
Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf,
and
species.
In which user friendly program (like MorphoJ ☺) can I analyse outline data and
visualize variability?
Thank you again,
Tina
From: Joanna Lenarczyk [mailto:j.kowal...@botany.pl]
Sent: Thursday, March 15, 2018 10:21 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves
. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University
From: Tina Klenovšek <tina.klenov...@um.si>
Sent: Wednesday, March 14, 2018 12:28 AM
To: f.james.rohlf <f.james.ro...@stonybrook.edu>
Cc: morphmet@morphometrics.org
Subject: RE: [MORPHMET] digitizing very
From: Carmelo Fruciano <c.fruci...@unict.it>
Date: 3/12/18 9:51 PM (GMT-10:00)
To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae
Dear Avi,
I guess it's hard to formulate any rule of thumb.
Some analyses might no
;c.fru...@unict.it >
> Date: 3/12/18 9:51 PM (GMT-10:00)
> To: MORPHMET <morp...@morphometrics.org >
> Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae
>
> Dear Avi,
>
> I guess it's hard to formulate any rule of thumb.
>
> Some analyse
: Wednesday, March 14, 2018 3:59 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves
An assumption of the usual GMM methods is that shape variation is "small". I
think these leaves exceed this quite a bit! Another problem is landmarks. How
to match leaves with a
sage From: Carmelo Fruciano <c.fruci...@unict.it>
Date: 3/12/18 9:51 PM (GMT-10:00) To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae
Dear Avi,
I guess it's hard to formulate any rule of thumb.
ible (less stringent assumptions,
which
obviously doesn't mean assumption-free) and therefore more generally
applicable. But, of course, the approach in tpsUtil can be a great
solution if it's appropriate to your data.
Best,
Carmelo
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MORPHMET may be accessed via its webpage
ints along an hypothetical
> line (which you would remove after the unbending)
> - that your arching is well represented by the chosen function
>
> You are the best judge on whether these assumptions are satisfied in
> your case or not.
> I suggested the Valentin et al. (2008 - J
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