[R-sig-ME] glmer error: contrasts can only be applied to factors of 2 or more levels

[Dan McCloy]

Never mind this one.  As usual, I was making a silly mistake due to
the late hour, and Ben Bolker knew just what to suggest to illuminate
my error.  Indeed, I had mis-typed one of the level names in one of
the factors, yielding only one level represented when it got passed to
glmer and run through na.omit().
-- dan

On Mon, Sep 1, 2014 at 5:19 PM, Dan McCloy <drmccloy at uw.edu> wrote:
> I'm getting the following error, despite the fact that all my fixed
> effects were converted to factors and had their contrast attributes
> set prior to calling glmer.
>
> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>   contrasts can be applied only to factors with 2 or more levels
> Calls: glmer ... model.matrix -> model.matrix.default -> contrasts<-
>
> Here is the model specification:
> glmer(press ~ truth*adj*idn*num + (1|subj), data=wl,
> family=binomial(link="probit"))
>
> Here are the predictors. As you can see, they are all already factors
> and have contrasts set, so I can't figure out why glmer is trying to
> set contrasts anyway, much less why it thinks any of these have fewer
> than two levels:
>
> R> head(wl$truth)
> [1] neither neither neither neither neither neither
> attr(,"contrasts")
>         target foil
> neither      0    0
> target       1    0
> foil         0    1
> Levels: neither target foil
> R> head(wl$adj)
> [1] TRUE TRUE TRUE TRUE TRUE TRUE
> attr(,"contrasts")
>       TRUE
> TRUE     1
> FALSE   -1
> Levels: TRUE FALSE
> R> head(wl$idn)
> [1] FALSE FALSE FALSE FALSE FALSE FALSE
> attr(,"contrasts")
>       TRUE
> TRUE     1
> FALSE   -1
> Levels: TRUE FALSE
> R> head(wl$num)
> [1] six six six six six six
> attr(,"contrasts")
>       three
> three     1
> six      -1
> Levels: three six
>
> Here is the session info:
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] lme4_1.1-7   Rcpp_0.11.2  Matrix_1.1-4
>
> loaded via a namespace (and not attached):
> [1] grid_3.1.1      lattice_0.20-29 MASS_7.3-34     minqa_1.2.3
> nlme_3.1-117    nloptr_1.0.4    splines_3.1.1     tools_3.1.1
>
> Can anybody shed some light on what is going on here, and / or how to
> work around it?  I've run similar models with very similar data on
> slightly older versions of lme4 (but still >1.0) and never run into
> this, so I'm wondering if a bug was introduced in the latest version.
> -- dan
>
> Daniel McCloy
> http://dan.mccloy.info/
> Postdoctoral Research Fellow
> Institute for Learning and Brain Sciences
> University of Washington