[R-sig-ME] Ordinal categorical variable as a random effect in MCMCglmm

[Manabu Sakamoto]

Dear Jarrod,

Thanks for your response. Quality is a ranking in the
completeness/missingness of the data; a higher quality data point is scored
higher. This is an attempt to control for potential missing information
from the response variable. The response is a count (hence the family being
Poisson), and the idea is that for each taxon on a phylogeny, there is a
count variable, but that count could potentially be under-estimated based
on the Quality of the data associated with each taxon. But in reality, this
potential under-estimation is unknown and unmeasurable so Quality is just
one attempt to control for this somewhat-known uncertainty.

many thanks,
Manabu

On 3 November 2014 14:22, Jarrod Hadfield <j.hadfield at ed.ac.uk> wrote:

> Dear Manabu,
>
> Could you explain what Quality is? If it is ordered it is hard to see why
> you would be fitting it as random effect? Is this really your response
> variable?
>
> Cheers,
>
> Jarrod
>
>
>
>
> Quoting Manabu Sakamoto <manabu.sakamoto at gmail.com> on Wed, 29 Oct 2014
> 11:16:48 +0000:
>
>  Dear list,
>>
>> I'm using MCMCglmm with some random effects, including a phylogeny and a
>> categorical variable, scored along an ordinal scale, e.g., 1 < 2 < 3 <...
>>
>> If my phylogenetic tip names are stored as a character string Taxon (and
>> there is an associated inverse A object), and my quality codes are stored
>> as an ordered factor variable Quality, then my questions are:
>>
>> 1) Can I specify the random effect formula simply as: random= ~ Taxon +
>> Quality --- i.e., without functions like us() or idh() around Quality?
>> 2) What sort of prior should I assign for Quality? --- For the moment I am
>> using:
>>
>> list(V=1, nu=1, alpha.mu = 0, alpha.V = 25^2)
>>
>>
>> I'd appreciate any advise.
>>
>> Kind regards.
>> Manabu
>> --
>> Manabu Sakamoto, PhD
>> manabu.sakamoto at gmail.com
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>>
>>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>


-- 
Manabu Sakamoto, PhD
manabu.sakamoto at gmail.com

	[[alternative HTML version deleted]]