Re: [MORPHMET] Adjusting permutted p-values in a DFA for morphometric analysis

that (cross-validated) classification rates in discriminant analysis and multivariate tests for difference in means, although somehow related, can still be thought to serve two different purposes so I personally don't think one should be abandoned in favour of the other Best, Carmelo -- Carmelo

Re: [MORPHMET] Tests on allometry pattern of several groups

be more time consuming. I hope this helps. Best, Carmelo -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via its

Re: [MORPHMET] high-throughput 2D scanning using photo-scanner

on the approach. H. -- 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. -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz

Re: [MORPHMET] MANOVA and shape data

. Again, maybe resampling-based approaches might be a better choice (while, as Andrea Cardini was suggesting in some previous post, also recognizing the limitations of one's analysis). I hope this helps, Carmelo -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz

Re: [MORPHMET] Warped Grids in MorphoJ

an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage

Re: [MORPHMET] Ontogenetic changes in morphology

...@morphometrics.org. -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org

Re: [MORPHMET] MANOVA and shape data

Dear all, as an addendum to my previous message on tests for multivariate normality, I've just noticed that a new R package for this (MVN by Korkmaz et al 2014 - http://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf ) is out. Best, Carmelo -- Carmelo Fruciano Marie

Re: [MORPHMET] Testing for sexual dimorphism

Dear Alex, I imagine most people would consider MAN(C)OVA and/or permutation tests for difference in multivariate means as the typical approach. Obviously, the choice of methods might also depend on the design and research question. There is a chance that with 10 observations per sex you

Re: [MORPHMET] Extracting Individual Mahalanobis Distances

it, send an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Marie Curie Fellow - University of Konstanz - Konstanz, Germany Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via

Re: [MORPHMET] 2D Capture Protocol for mostly 2D specimens

opinion, the most important part is having some sort of scale in the picture, possibly not too far from the specimen. Well, that's my two cents, I hope this helps... Best, Carmelo -- Carmelo Fruciano Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http

Re: [MORPHMET] save trace of linear measurement on photo image

! Caroline D. Judy, PhD candidate Louisiana State University -- 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. -- Carmelo Fruciano Marie Curie

Re: [MORPHMET] comparison of RV values

things. Best, Carmelo -- Carmelo Fruciano Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails

Re: [MORPHMET] How to include new specimens in TPSdig and information on EDMA software

. thanks in advance cheers Miguel -- 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. -- Carmelo Fruciano Honorary Fellow - University

Re: [MORPHMET] question Elliptic Fourier Descriptors

Dear Jens, you might want to consider working with multivariate analyses (i.e. using all PCs and not a single one) and, as it has been suggested, using (multivariate) linear models rather than dividing scores by your size measure. Best, Carmelo -- Carmelo Fruciano Honorary Fellow

Re: [MORPHMET] how create nexux file for phylogeny in MorphoJ

d stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage a

Re: [MORPHMET] Appending TPS files

file called all.TPS. Other solutions (importing in R, combining and then exporting) might be more elegant, though... Best, Carmelo -- Carmelo Fruciano Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research/ -- MORPHMET may be ac

Re: [MORPHMET] testing for allometry in tpsRegr

Elahep ha scritto: Hi morphometricians, I have a data set consists of 7 landmarks and 7 semi-landmarks on the carapace of a crab and I want to control my data for the effect of allometry with tpsRegr. I am not sure which dataset should I use as dependent variable

Re: [MORPHMET] Importing Data from Landmark Editor into MorphoJ

Dear Jay, the text file, as in the link you provided and copied to a text editor, contained a mixture of double spaces and tabs. For instance, already in the first line you have a tab between the ID and the first coordinate but two spaces between the first and the second coordinate.

Re: [MORPHMET] Sliding Semilandmarks

hanges the results of your superimposition. A post/discussion that may be interesting to you can be found at Stephan Schlager's blog: http://zarquon42b.github.io/2014/11/07/ProcDSliding/ Best, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Br

Re: [MORPHMET] Doubts about Error Measurement

elp. Liu Dear Liu, Perhaps the best way to report this would be to say that 3.63% of the total sum of squares is accounted for by/due to a certain term (digitization, preparation)? Best, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane,

Re: [MORPHMET] Using photographs from distinct sources to GM analyses

eiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/research

Re: [MORPHMET] Crowdsourced GM Bibliography

ge at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Postdoc

Re: [MORPHMET] Doubts about Error Measurement

mp; Byrnes 1990? In advance, thanks a lot for the help. Liu Dear Liu, Perhaps the best way to report this would be to say that 3.63% of the total sum of squares is accounted for by/due to a certain term (digitization, preparation)? Best, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Quee

Re: [MORPHMET] Form Space?

. You can see an example of these plots in one of my own papers (Fruciano et al 2012 - Environmental Biology of Fishes) and, really, in many others, where it is used to produce exploratory plots. I hope this helps. Best, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland Universit

Re: [MORPHMET] Deformation Grids

at you describe are the deformation grids that you obtain using the "Discriminant Function..." module, which display the deformation between two group means (further info in MorphoJ user guide). Cheers, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland Universi

Re: [MORPHMET] the problem with CVA... or is it?

n. Pairwise comparisons of species/group means are another alternative, depending on the number of groups and, most importantly, the point you want to make. I hope this helps, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honor

Re: [MORPHMET] Re: the problem with CVA... or is it?

Best, Carmelo P.S. Here, the issue is not demonizing CVA but, rather, understanding what is it for and using it for the right purposes. -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honorary Fellow - University of Catania - Catania, Ital

[MORPHMET] New publications

Dear Colleagues, I'd like to notify you about a few recent publications of mine with morphometric content. Thanks for your attention and best wishes, Carmelo Fruciano Fruciano, C.*, Franchini, P.*, Kovacova, V., Elmer, K., Henning, F., Meyer, A. 2016. Genetic linkage of adaptive traits

Re: [MORPHMET] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honorary Fellow - University of Catania - Catania, Italy e-mail c.fruci...@unict.it http://www.fruciano.it/

Re: brief comment on non-significance Re: [MORPHMET] procD.allometry with group inclusion

p://www.footprintnetwork.org/en/index.php/GFN/page/calculators/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails

Re: [MORPHMET] geiger rescale error

e/calculators/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@mor

Re: [MORPHMET] Merge MorphoJ files

always work. But I guess it's easy enough to give it a try using an advanced text editor (such as Notepad++). I hope this helps, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honorary Fellow - University of Catania - Catania, I

Re: [MORPHMET] MorphoJ Text File Formatting

a file in TPS format but you had left the default "text" selected, instead of switching to TPS under "File Types" on the "Create new dataset" menu. I hope this helps. Best, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Techn

Re: [MORPHMET] curve analysis

e the Procrustes fit in MorphoJ includes reflection. You can find a description of this in the MorphoJ user guide. I hope this helps, Carmelo -- Carmelo Fruciano Postdoctoral Fellow - Queensland University of Technology - Brisbane, Australia Honorary Fellow - University of Catania - Catania,

Re: [MORPHMET] Interpreting PCA results

Dear Mahediran, to my understanding from David's phrasing, it is just a way to visualize shape variation along a given PC axis (as the value at 0 is the mean). One could use some other criterion (for instance the maximum and minimum scores along that given PC). But, of course, all the other

Re: [MORPHMET] Save aligned in TPSRelW

Dear Pere, there are various workarounds to that. For instance, one can convert the original tps file to an nts file and then copy the line with the labels from the original nts to the tps with aligned specimens. Another option, which is useful when one has the names in the file names and

Re: [MORPHMET] Re: Interpreting PCA results

Dear Morphmet list, first, thank you all for the very interesting and stimulating posts. In my humble opinion, not being PCA a "predictive" tool, it can be easily misused as such. Personally, I most frequently use PCA to have a quick look at what my data looks like. In other words, to look at

Re: [MORPHMET] Question on TPS and lack of scale

Dear Ely, the coordinates will be expressed as their pixel position. Clearly, in many/most cases (e.g., different magnification in different pictures) the size information you can extract from these configurations of landmarks is not usable unless you manage to get that information in some

[MORPHMET] New publication - measurement error

Dear all, perhaps this new publication of mine (on measurement error) could be of interest to some people in the list. http://onlinelibrary.wiley.com/doi/10.1002/ece3.3256/full Best, Carmelo == Carmelo Fruciano School of Earth, Environmental & Biological Sciences Queens

Re: [MORPHMET] Doubt Scaling photos

Hi Anderson, I concur with Murat about the usefulness of having actually multiple specimens. Analyses on a single specimen, although in principle attractive (as one "isolates" error from biological variation), are not necessarily informative on a practical level. Also there are two problems,

Re: [MORPHMET] p value always identical

Dear Callie, I am not sure I fully understand your question. Perhaps you could provide details as to how your 20 projectile points are transformed into data, how the pairwise rotation of two configurations was applied to your 20 projectile points, and what is the aim of the test. Now, let's

Re: [MORPHMET] Re: Trouble with 2-D morphomeric analysis in geomorph

id is to create some indexing variables for specimen and landmark and used them to restructure the data. I hope this helps, Carmelo -- ====== Carmelo Fruciano Institute of Biology Ecole Normale Superieure - Paris CNRS http://www.fruciano.it/research/ ##

Re: [MORPHMET] digit.curves

/r/how-to-create-an-array-in-r/ I hope this helps. Carmelo -- == Carmelo Fruciano Institute of Biology Ecole Normale Superieure - Paris CNRS http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this mess

Re: [MORPHMET] How to obtain measurements from 3D scans

. This paper suggest an approach you can use to quantify how well your 2D data approximate the 3D data. As you would have both, it could be a good way to check whether the projection you are choosing gives you appropriate results. I hope this helps, Carmelo -- == Carmelo

Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto: Hi Carmelo, Thank you for your answer. My project tests for the influence of kairomones of a predator fish on the morphology of Salamander larvae during its development. To do this, I take pictures every other week of larvae spawned from six

Re: Re: [MORPHMET] Digitizing landmarks on live larvae

Dear Avi, elaborating further also based on Jim's answer, some open questions/considerations that you might entertain are: - if you intend to use sliding semilandmarks (which in general sounds like a good idea), how are certain points such as 1,39,41,55 going to be slid? (i.e., relative to

Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

e should keep? Thank you, Avi On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote: Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto: > Hi Carmelo, > Thank you for your answer. > My project tests for the influence of kairomones of a

Re: [MORPHMET] digitizing very variable leaves

Hi Tina, The software Shape by Iwata & Ukai is an user friendly option for performing elliptic Fourier analysis. https://academic.oup.com/jhered/article/93/5/384/2187412 http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/ Elliptic Fourier analysis is also implemented in NTSYSpc, which is also

Re: ***SPAM*** [MORPHMET] Extract Classifier from ID string

Dear Bekkym I'm assuming you actually have a problem with the specimen names in the file you imported in MorphoJ. It's hard to know what exactly the problem is with the information you provide, but I will point out that a trick which may or may not apply to your specific case is to convert

Re: ***SPAM*** [MORPHMET] Extract Classifier from ID string

Hi Nelly, you're welcome, and sorry for calling you with some other name. Best, Carmelo On 22/03/2018 15:06, Nelly Ndungu wrote: Thanks Carmelo, This trick has worked, thanks alot. Kind Regards, Nelly Ndungu On Thu, Mar 22, 2018 at 4:50 PM, Carmelo Fruciano <c.fruci...@unict

Re: [MORPHMET] A question regarding "target shape"

. I hope this helps. Best, Carmelo -- ====== Carmelo Fruciano Institute of Biology Ecole Normale Superieure - Paris CNRS http://www.fruciano.it/research/ El miércoles, 31 de octubre de 2018, 13:51:07 (UTC-6), K. James Soda escribió: Dear Mr. Ardón, Good question. Wh

Re: [MORPHMET] A question regarding "target shape"

tric morphometric studies of size and shape. Zoomorphology In general, as said above, it's very hard to give straightforward answers to your question. I hope this still helps, though. Carmelo == Carmelo Fruciano Institute of Biology Ecole Normale Superieure - Paris CNRS http://www.fruc

Re: [MORPHMET] Problem to export data from Landmak editor to MorphoJ

Thank you very much! -- ====== Carmelo Fruciano Institute of Biology Ecole Normale Superieure - Paris CNRS http://www.fruciano.it/research/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Gro

Re: [MORPHMET] morph disparity

of orthogonal axes). Then - provided that I don't know enough about your system/question/analysis and this is just a general opinion - I would just stick to multivariate measures of variation. I hope this helps. Carmelo -- == Carmelo Fruciano Institute of Biology Ecole Normale