mlcollyer
commented
6 years ago Phil,
The results are different because you are adding the step of subtracting the consensus to obtain your values. I think you were confused by our help file interchanging the terms "Procrustes coordinates” and "Procrustes residuals”, which are the same thing. Procrustes residuals refers to the fact that individual landmarks undergo a linear transformation by subtracting the configuration centroid (center of gravity) that along with scaling and rotating, put the original landmarks in a new coordinate system. “Residuals” should not convey that the consensus configuration is subtracted from the coordinates. In fact that is not a good thing to do, as it removes the configuration, altogether.
We should probably update our help page to be less ambiguous but please be aware that Y.gpa$coords are Procrustes residuals.
Cheers! Mike
On Jul 23, 2018, at 9:46 AM, PhilGossieaux notifications@github.com wrote:
Hello everyone,
I am currently trying to extract partial warp scores from my data but I am really not sure about the right method to do so in geomorph. I am using the 3.0.6 version.
To better understand how partial warp scores are estimated, I am trying to get the Procrustes residuals. To do so, I first calculated Procrustes residuals by hand (consensus configuration - landmark coordinates). Here is an example with the plethodon data :
data(plethodon) Y.gpa <- gpagen(plethodon$land) # GPA-alignment Y.gpa$consensus - Y.gpa$coords[,,1] # Procrustes residuals for the first individual
Here are the results I obtain :
X Y[1,] -0.0344125269 0.0007795351 [2,] -0.0173644760 -0.0024695930 [3,] -0.0013939463 -0.0121645486 [4,] -0.0054344476 -0.0015275652 [5,] 0.0042459454 0.0009465181 [6,] -0.0085043603 0.0175240242 [7,] 0.0246763774 -0.0015201942 [8,] -0.0117064381 -0.0093034324 [9,] 0.0046035509 -0.0045212382 [10,] 0.0027063193 0.0035193421 [11,] 0.0417190925 -0.0199987873 [12,] 0.0008649097 0.0287359394
Then, I used the $data function of gpagen (returns a data frame with an n x (pk) matrix of Procrustes residuals and centroid size) to verify my results as follows :
Y.gpa$data[1,]
and obtained :
coords.X.1 coords.Y.1 coords.X.2 coords.Y.2 coords.X.3 coords.Y.3 coords.X.4 coords.Y.4 coords.X.5 1 0.1867449 -0.02601616 0.2106543 -0.09257173 -0.03230658 0.005234662 -0.2763898 >-0.08784332 -0.3149726 coords.Y.5 coords.X.6 coords.Y.6 coords.X.7 coords.Y.7 coords.X.8 coords.Y.8 coords.X.9 coords.Y.9 1 -0.05877959 -0.3174958 -0.04960619 -0.3422491 0.04157688 -0.1765378 0.1096506 >0.01698919 0.1033746 coords.X.10 coords.Y.10 coords.X.11 coords.Y.11 coords.X.12 coords.Y.12 Csize 1 0.1867616 0.07142079 0.3104119 0.08151401 0.54839 -0.09795449 15.22692
The results obtained by hand and those obtained with $data are quite different and I do not understand why. Moreover, I plot the difference between consensus shape and the landmark coordinates of individual #1 https://github.com/geomorphR/geomorph/pull/1 (the one I took as an example here) :
plotRefToTarget(Y.gpa$consensus,Y.gpa$coords[,,1],gridPars=gridPar(pt.bg = "green", pt.size = 1), method="vector",mag=3, label=T)
When I compare the plot to my Procrustes residuals, those calculated by hand make much more sense than those obtained with $data.
Can anyone explain me how $data in gpagen calculates Procrustes residuals?
Finally, has anyone a method to calculate partial warp scores in geomorph?
Thanks a lot.
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PhilGossieaux
deanadams
dnavon
Hello everyone,
I am currently trying to extract partial warp scores from my data but I am really not sure about the right method to do so in geomorph. I am using the 3.0.6 version.
To better understand how partial warp scores are estimated, I am trying to get the Procrustes residuals. To do so, I first calculated Procrustes residuals by hand (consensus configuration - landmark coordinates). Here is an example with the plethodon data :
Here are the results I obtain :
Then, I used the
$datafunction ofgpagen(returns a data frame with an n x (pk) matrix of Procrustes residuals and centroid size) to verify my results as follows :and obtained :
The results obtained with
$dataare actually the coordinates of landmarks after the GPA, not the Procrustes residuals.Is this normal and can this impact other estimations made by geomorph?
Also, has anyone a method to calculate partial warp scores in geomorph?
Thanks a lot.