Hi Thierry,

Thanks for your thoughts and suggestions. And yes, the cleaned-up code is
far more easy to read/interpret.

I ran the model again using glmer instead of lmer and it worked.

And for reference, I am using R version 2.15.1 and lme4 version 0.999375-42
which appears to be a little dated.

Thanks again,
  Robert


On Thu, Dec 6, 2012 at 3:49 AM, ONKELINX, Thierry
<Thierry.ONKELINX@inbo.be>wrote:

> Hi Robert,
>
> Try to clean up your code. Use the data argument instead of the $
> notation. And use glmer instead of lmer for generalized models.
> Addingspacesmakesyourcodemuchmorereadable
>
> glmm1 <- glmer(cbind(Probes, fail) ~ Treatment * Species + (1|Bee), data =
> p, family = binomial)
>
> Which version of R and lme4 are you using? The output of sessionInfo() can
> be informative for the developers of lme4.
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: r-sig-mixed-models-bounces@r-project.org [mailto:
> r-sig-mixed-models-bounces@r-project.org] Namens Robert Schaeffer
> Verzonden: woensdag 5 december 2012 22:16
> Aan: r-sig-mixed-models@r-project.org
> Onderwerp: [R-sig-ME] Binomial GLMM - Error (invalid class “mer” object)
>
> Hi All,
>
> I'm relatively new to using GLMMs and am attempting to run an analysis,
> but have encountered an error that I am not sure how to handle.
>
> Error invalidObject(.Object) : invalid class “mer” object: Slot Zt must by
> dims['q']  by dims['n']*dims['s']
>
> I am trying to examine the effect of a treatment on the proportion of
> flowers probed per foraging bout in an inflorescence. There are two
> different pollinator species and each pollinator individual varied in the
> number of bouts performed. The data are structured as follows....
>
>      Bee Plant Flowers           Species Treatment Probes fail
>
> 1     1     1      14    Bombus appositus    Nectar      4  10
>
> 2     1     2      15    Bombus appositus   Control      2  13
>
> 4     1     4      12    Bombus appositus   Control      7    5
>
> 6     1     6      15    Bombus appositus    Nectar      2  13
>
> 7     1     7      10    Bombus appositus   Control      4    6
>
> 12    1    12      15  Bombus appositus   Control    11    4
>
> 13    2     1      14   Bombus flavifrons     Nectar    14    0
>
> 14    2     2      15   Bombus flavifrons    Control      8    7
>
> 15    2     3      15   Bombus flavifrons     Nectar      7    8
>
> 16    2     4      12   Bombus flavifrons    Control      4    8
>
> 17    2     5      16   Bombus flavifrons     Nectar      4  12
>
> 18    2     6      13   Bombus flavifrons    Control      5    8
>
> 19    2     8      14   Bombus flavifrons     Nectar      1  13
>
> 20    2     8      14   Bombus flavifrons     Nectar      5    9
>
> 21    2     9      15   Bombus flavifrons     Nectar      7    8
>
> ......
>
> 465 36    7      10   Bombus flavifrons     Control     1    9
>
> The model structure is as follows:
>
> glmm1<-lmer(cbind(p$Probes,p$fail)~p$Treatment*p$Species+(1|p$Bee), family=
> "binomial")
>
> I included Bee identity as a random term to account for pseudoreplication
> and differences amongst Bees in the number of bouts performed. At least, I
> think this is the correct way to do so. However, I get the error above and
> am not sure how to proceed. Any thoughts or suggestions would be greatly
> appreciated.
>
>
> Cheers,
>
>  Robert Schaeffer
>
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