On 2 May 2012, at 11:08, Samantha Patrick wrote:
Hi
Firstly I sent this message last week but can find no evidence that it actually sent.
However, if this is a double posting I am very sorry.
I am currently working with repeated measures for individuals and I am
trying to quantify individual repeatability. Normally, for continuous
distributions, I would use a mixed model and calculate the variance
explained by individual divided by the total variance. However my individual scores
are ordinal and I have been using the clmm function in the Ordinal package:
example of data:
ID Bird Sex scoremax year
622 BS8831 M 2 2008
623 BS8831 M 1 2010
624 BS8831 M 1 2011
625 BS9065 M 1 2010
626 BS9065 M 3 2011
627 BS19724 F 4 2010
628 BS19724 F 5 2010
629 BS21302 F 1 2010
630 BS25376 F 1 2011
631 BS9184 F 2 2009
632 BS19989 M 3 2011
633 BS21617 M 4 2008
634 BS21617 M 2 2009
635 BS21617 M 1 2010
where scoremax ranges from 1-5, and there are 1188 birds and 1638
observations.
scoremax<-as.factor(scoremax)
does
scoremax = as.ordered(scoremax)
make any difference in your results?
I ask this because as.factor() does not, strictly speaking, create an ordered factor.
BW
F
bird<-as.factor(bird)
year<-as.factor(year)
fmm1<- clmm(scoremax~year+ (1|bird), link = c("probit"), Hess =TRUE)
summary(fmm1)
but this only gives the variance estimate for bird, with no residual
estimate. Some investigations reveal that using an ordinal regression
in MCMCglmm will also not estimate the residual variance, and it seems
you need to constrain this value. I have been unable to find any posts
about repeatability in ordinal data.
My questions I guess are:
Is using a mixed model appropriate for calculating the repeatability of
ordinal data (and if not does anyone know any other methods)?
If it is, does anyone have any hints on how to calculate the residual variance,
to enable repeatability estimates to be calculated.
Many Thanks
Sam
--
Dr Samantha Patrick
Post Doctoral Fellow
Centre d'Etudes Biologiques de Chiz? - CNRS
79360 Villiers-en-Bois
France
T:+33 549 097 846
M:+33 675 603 451
Skype: sammy_patrick
http://www.cebc.cnrs.fr/Fidentite/patrick/patrick.htm
http://www.researchgate.net/profile/Samantha_Patrick/