Closed PhilGossieaux closed 6 years ago
Phil,
Because each data design is slightly different, a far better approach is for you to first consult the primary literature on how one estimates measurement error, and then adapt those approaches and equations for your particular system.
A good reference is: Arnqvist and Martensson. 1998. Measurement error in geometric morphometics: empirical strategies to assess and reduce its impact on measures of shape. Acta Zoologica 44:73-96
Dean
Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University www.public.iastate.edu/~dcadams/http://www.public.iastate.edu/~dcadams/ phone: 515-294-3834
From: PhilGossieaux notifications@github.com Sent: Wednesday, August 1, 2018 4:04 PM To: geomorphR/geomorph geomorph@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [geomorphR/geomorph] Calculate repeatability (#18)
Hello everyone,
I would like to evaluate my landmarks repeatability but I am not sure that I am doing it correctly. I am trying to follow the method detailed here https://www.r-bloggers.com/tips-tricks-8-examining-replicate-error/
In my study, I want to digitize each individual (ind) twice, thus I will have 2 sets of landmarks (rep) per individual.
I should first perform a gpa and a Procrustes ANOVA. Is it correct that my ANOVA formula is written as: procD.lm(shape ~ ind+ind:rep, data=gdf) or should it be procD.lm(shape ~ ind*rep, data=gdf)?
Then, once I have the ANOVA table, is it right that the formula I am supposed to use is this one (with n the number of replicates): ((MS(ind) – MS(ind:rep))/n ) / (MS(ind)+MS(ind:rep)))? Since the denominator is supposed to be the total MS, shouldn't I also include the MS of the residuals?
The data set mosquito has a slightly different structure since they have 2 replicates of each side of each individual. I have only 2 levels in my data (ind and rep) and there is 3 in the mosquito data (ind, side and rep) but for the sake of the example, I would like to use this data and only use 2 levels of data hierarchy (ind and rep).
data(mosquito)
Y.gpa <- gpagen(mosquito$wingshape)
gdf <- geomorph.data.frame(wingshape = Y.gpa$coords, ind=mosquito$ind, rep=mosquito$replicate)
anova.table <- procD.lm(wingshape ~ ind+ind:rep, data=gdf)
I obtain: MS(ind) = 0.0116542 MS(ind:rep) = 0.0046112 MS(residuals) = 0.0039679
Then to calculate repeatability here, should I use (assuming here incorrectly that I have 2 replicates): ((0.0116542 - 0.0046112)/2)/(0.0116542+0.0046112)
The result would be 0.2165025.
I feel that there is something incorrect in the way I estimate repeatability. What I am doing wrong?
Thanks a lot.
Phil
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Thanks a lot Dean. So according to the formula provided in the article, I should use R = [MS(among individuals)-MS(within individuals)/n] / [MS(within individuals)+(MS(among individuals)-MS(within individuals)/n)]
Does it seem correct to you if my ANOVA formula is procD.lm(shape ~ ind+ind:rep)
And then I ignore the residuals and use R = [MS(ind)-MS(ind:rep)/n] / [MS(ind)+(MS(ind)-MS(ind:rep)/n)]
Does this make sense?
Thanks a lot!
Phil
Not quite. As stated just prior to their equations, for their design a one-way anova was used. The factorial approach is for other data designs.
This is why I mentioned matching the data design with the analysis is important:
Dean
Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University www.public.iastate.edu/~dcadams/http://www.public.iastate.edu/~dcadams/ phone: 515-294-3834
From: PhilGossieaux notifications@github.com Sent: Thursday, August 2, 2018 8:58 AM To: geomorphR/geomorph geomorph@noreply.github.com Cc: Adams, Dean [EEOBS] dcadams@iastate.edu; Comment comment@noreply.github.com Subject: Re: [geomorphR/geomorph] Calculate repeatability (#18)
Thanks a lot Dean. So according to the formula provided in the article, I should use R = [MS(among individuals)-MS(within individuals)/n] / [MS(within individuals)+(MS(among individuals)-MS(within individuals)/n)]
Does it seem correct to you if my ANOVA formula is procD.lm(shape ~ ind+ind:rep)
And then I ignore the residuals and use R = [MS(ind)-MS(ind:rep)/n] / [MS(ind)+(MS(ind)-MS(ind:rep)/n)]
Does this make sense?
Thanks a lot!
Phil
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Thanks a lot for your answer Dean, I will look into it.
Cheers
Phil
Hello everyone,
I would like to evaluate my landmarks repeatability but I am not sure that I am doing it correctly. I am trying to follow the method detailed here https://www.r-bloggers.com/tips-tricks-8-examining-replicate-error/ but I want to make sure that I am doing it properly.
In my study, I want to digitize each individual (ind) twice, thus I will have 2 sets of landmarks (rep) per individual.
I should first perform a gpa and a Procrustes ANOVA. Is it correct that my ANOVA formula is written as: procD.lm(shape ~ ind+ind:rep, data=gdf) or should it be procD.lm(shape ~ ind*rep, data=gdf)?
Then, once I have the ANOVA table, is it right that the formula I am supposed to use is this one (with n the number of replicates): ((MS(ind) – MS(ind:rep))/n ) / (MS(ind)+MS(ind:rep)))? Since the denominator is supposed to be the total MS, shouldn't I also include the MS of the residuals?
The data set mosquito has a slightly different structure since they have 2 replicates of each side of each individual. I have only 2 levels in my data (ind and rep) and there is 3 in the mosquito data (ind, side and rep) but for the sake of the example, I would like to use this data and only use 2 levels of data hierarchy (ind and rep).
I obtain: MS(ind) = 0.0116542 MS(ind:rep) = 0.0046112 MS(residuals) = 0.0039679
Then to calculate repeatability here, should I use (assuming here incorrectly that I have 2 replicates): ((0.0116542 - 0.0046112)/2)/(0.0116542+0.0046112)
The result would be 0.2165025.
I feel that there is something incorrect in the way I estimate repeatability. What I am doing wrong?
Thanks a lot.
Phil