Hi,

well, as for the contrasts - it turned out that they were actually dropped
from the model but I realized that after some time ;) as there was no error
message. In fact I tried to fit several contrasts and they turned out not to
be orthogonal, which I didn't notice in the first place. So this one solved
- my fault ;)

This tabular form I asked about was a special "wish" from one reviewer who
could not believe that MCMCglmm returns just a simple regression-like
summary and produces no ordinary ANOVA table (with relevant SSs, MSs and F
ratios). It took some time to explain to him that it's actually the same
(and this regression-like output contains far more information) but he gave
up. I'd heard about this problem before and some people tried reproducing
such tables using marginal means and overall mean to produce relevant SSs;
with complex random effects' structures and unbalanced numbers of
measurements it becomes non-trivial and I agree it should not be done.

Cheers,
sz.

On 29 January 2011 15:56, Jarrod Hadfield <j.hadfield@ed.ac.uk> wrote:

> Hi,
>
> Some versions ago there was a problem if contrasts were specified where the
> sum of the contrasts for a factor was zero. This had been fixed in version
> 2.05. In addition, is it possible that some contrast cannot be estimated and
> are dropped? You should get a warning message when this happens. You can
> estimate the contrast by specifying singular.ok= TRUE in the call to
> MCMCglmm, but be careful  - all the information is coming from the prior.
>
> Not sure what is meant by the second question. Do you mean you would like
> to obtain some summary measure or summary p-value for all effects of the
> same type? In short, I have not implemented a method for this, but
> occasionally I use Wald tests to get something that resembles a p-value.
> This is almost certainly not technically valid, but on a practical basis it
> seems to give good answers for the few cases I've tried.
>
> Cheers,
>
> Jarrod
>
>
>
> Quoting Szymek Drobniak <geralttee@gmail.com>:
>
>  Hello everyone again,
>>
>> it seems this evening is reach in MCMCglmm-based thinking, sorry for
>> overloading the list with too much MCMCstuff. My question is - does
>> MCMCglmm
>> recognize "contrasts" attribute of data-frames correctly? I've tried
>> fitting
>> models to frames with defined contrasts but - at least sometimes it seems
>> it's not working (output does not contain all constrasts I've specified).
>> Have anyone tried this? And second question, loosely related to previous
>> one
>> - is it any way to transform MCMCglmm output (with coeficient for all-1
>> levels of the fixed effect) into simple anova output (with one row for
>> each
>> fixed effect)?
>>
>> Cheers,
>> sz.
>>
>> --
>> Szymon Drobniak || Population Ecology Group
>> *Institute of Environmental Sciences, Jagiellonian University
>> ul. Gronostajowa 7, 30-387 Kraków, POLAND
>> *tel.: +48 12 664 52 19 fax: +48 12 664 69 12
>>
>> www.eko.uj.edu.pl/drobniak
>>
>>        [[alternative HTML version deleted]]
>>
>>
>>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>


-- 
Szymon Drobniak || Population Ecology Group
*Institute of Environmental Sciences, Jagiellonian University
ul. Gronostajowa 7, 30-387 Kraków, POLAND
*tel.: +48 12 664 52 19 fax: +48 12 664 69 12

www.eko.uj.edu.pl/drobniak

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