[R-sig-ME] Calculating repeatability with ordinal data

[Samantha Patrick]

Hi

Thank you for the tip - I had editted my code!  However, sadly it 
doesn't  solve the problem of how to estimate the residual variance.

Many Thanks

Sam


Le 02/05/2012 12:38, Federico Calboli a écrit :
> 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 Chizé - 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/
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> --
> Federico C. F. Calboli
> Neuroepidemiology and Ageing Research
> Imperial College, St. Mary's Campus
> Norfolk Place, London W2 1PG
>
> Tel +44 (0)20 75941602   Fax +44 (0)20 75943193
>
> f.calboli [.a.t] imperial.ac.uk
> f.calboli [.a.t] gmail.com
>
>
>

-- 

Dr Samantha Patrick
Post Doctoral Fellow
Centre d'Etudes Biologiques de Chizé - 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/