Dear Ashly and morphomet community Many thanks for your email was indeed very good to me, I'm sorry to not reply in time I had a very bad problem of health and I was out of the work for at least 3 weeks and I'm back slowly, and I will ask for a bit of more help, I'm still a bit confused, but I'm trying to get the differences more clear, and opening new questions... Maybe some can help me if is possible and for sure will help another with the same question (other colleagues have the same)
Ashly, or maybe another morphometrician is ok to me explain the magnitude of FA in an article looking into the MS of the Procrustes ANOVA for example the MS of IndxSide (that represent FA) of Population 1 (with pesticide) with the MS of IndxSide of the Population 2 (without Pesticide) and the Control one... and use it to said if the MS is higher in one this should have more FA than the other, I don't know if was good explained and will be OK in an article... Others said that maybe the Regression of Shape and FA Scores also could explain the relationship with FA where higher numbers of FA Score could represent shape with more presence of asymmetry. And some one can please in a simple word explain the differences when we use the Procrustes Distances and Mahalanobis Distances please when we evaluate shape differences. Many thanks again for all your helps I will be very looking forward your reply to finally be very clear with this question how see this magnitude, and for sure as Ahsly mentioned as well there is some way in geomorph with the function bilat.symmetry Many thanks in advance GF El jue., 11 jun. 2020 a las 12:14, Ashly Romero (<[email protected]>) escribió: > Hi Graham, > > > > While I don’t know the ins and outs of the Procrustes FA Scores or > Mahalanobis FA Scores exactly, I have had these same questions. I’ve copied > what the MorphoJ User Guide from Klingenberg’s website says below. It can > be found here: > https://morphometrics.uk/MorphoJ_guide/frameset.htm?index.htm I’ll also > attach the Klingenberg and Monteiro (2005) paper because there is one > paragraph in it where it describes the calculation of the FA Score in > MorphoJ. > > > > “If the data have object symmetry or if a Side effect was included in the > analysis, the output dataset also contains individual scores that quantify > the amount of fluctuating asymmetry of shape for each individual > (Klingenberg and Monteiro 2005). These scores quantify the individual > asymmetries of shape (as deviations from the mean asymmetry) either in > units of Procrustes distance (absolute shape differences) or by using > Mahalanobis distances (scaled relative to the variation of asymmetry in the > sample).” > > > > Here is the paragraph from the article cited that describes the > calculation… > > > > “An equivalent calculation of these distances can be done easily with > standard statistics software using the following procedure: (1) carry out a > principal component analysis (using the covariance matrix) of the data, for > instance the signed right-left differences of landmark positions, and > compute the principal component scores for each observation; (2) > standardize the scores for each principal component to variance 1.0; (3) > sum up the squares of these standardized principal component scores for > every observation; and (4) compute the square root of the resulting sum for > each observation. If the analysis is based on partial warps scores and the > uniform components of shape variation, all the variables should be included > in this procedure, but if the coordinates of Procrustes-superimposed > landmarks or Procrustes residuals are used, the last four (for two- > dimensional data) or seven (for three-dimensional data) principal > components should be omitted from steps (2) to (4) because they have zero > variances (up to rounding errors).” > > > > I’ve seen in the Morphmet and Geomorph group archives that people have > said it’s possible to calculate FA scores from the FA.component output in > the bilat.symmetry function in the Geomorph package, but I haven’t figured > out exactly how to do that yet. > > > > If you’re looking at the difference in FA between a sample exposed to > pesticide and one that isn’t, I’m not sure that regressing FA scores on > shape is the best way to do that. You may want to re-evaluate what that > would actually be telling you. > > > > I’m sure others will be able to add to this, but I thought I’d respond > with what I’ve found so far on this topic. > > > > All the best, > > Ashly > > > > --- > > Ashly Romero, MA > > PhD Candidate, Biological Anthropology > > University of Arkansas > > Email: [email protected] > > > > *From: *<[email protected]> on behalf of Graham Freitas < > [email protected]> > *Date: *Wednesday, June 10, 2020 at 9:30 PM > *To: *"[email protected]" <[email protected]> > *Subject: *[MORPHMET2] Question about Kingenberg Procrustes ANOVA in > MorphoJ or Another Method Please > > > > Dear Morphomet Community > > > > I have read an article of the Dr. Kingenberg of the journal Symmetry 2015 > of Fluctuating Asymmetry with a very complete overview of the methodology > > > > I understand that the Software MorphoJ is very easy to use and I have > been trying to work in Fluctuating Asymmetry with it in GM. > > > > I wanted to ask the other researcher in the community if anyone have some > idea and can help. > > > > I am confused with the procedure in MorphoJ of the calculation of the > *intensity > of Fluctuating Asymmetry * > > > > I read some articles that they use a regression of Shape with FA Scores, > using the dataset provided of the Procrustes ANOVA... and there are two > type FA Scores: Procrustes FA Scores and Mahalanobis FA Scores... > > > > My question: Can I use this in a regression with the symmetric > component or shape (shape vs Procrustes FA Scores) to represent the > intensity of FA? > > > > Is this data really showing intensity? Is that real Fluctuating > Asymmetry? Please I need a simple answer to see if I'm misunderstanding it > > > > When I saw a Regression of Shape vs Procrustes FA Scores and points are > located in higher values of Shape FA Scores, Its ok said that this > individuals have higher Fluctuating Asymmetry? > > > > I have a feeling that this "Procrustes FA Scores" is Procustes distance > between left and right side of the structure or I'm wrong... > > > > Your expert comments will be very valuable for me and also for another > student that is working with MorphoJ in this topic. > > > > If not there is another way to calculate the intensity of Fluctuating > Asymmetry in Geometric Morphometrics? I wanted to evaluate for example > population exposed to pesticide and not exposed and see the intensity > reflect or not developmental instability or is only an artefact of the > methodology and we have to act with caution. > > > > Many thanks in advance > > GF > > -- > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/morphmet2/CACxe6NYwYx-hdTtZ9NfYBJX--yLSzGGN%3DhTHjt51LZ9W3tC3Ww%40mail.gmail.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_msgid_morphmet2_CACxe6NYwYx-2DhdTtZ9NfYBJX-2D-2DyLSzGGN-253DhTHjt51LZ9W3tC3Ww-2540mail.gmail.com-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dfooter&d=DwMFaQ&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=JIeyUBPXb9HgXICMwkXS3gVcUgYhbMR0l8IpgZ8DqeU&m=-M0sfbJlYG4WoxdqST6QRspzjNEhg2pu7PHV5TqVzHI&s=8EcKBvF52D9AIJj-AL_9hjVjhSvIFlhZPgzUVKSMq4s&e=> > . > > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. 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