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understanding error with "profile" method of lme4a

3 messages · Darren Norris, Ben Bolker, Douglas Bates

Original
Darren Norris
# 
Can anyone suggest how to resolve the following error - 
I can't see anything in the presentations ( http://lme4.r-forge.r-project.org/slides/2011-03-16-Amsterdam/ ) to suggest what I am doing wrong:

data is available here:
http://cid-f0a9fa3480208398.office.live.com/self.aspx/lmeData/DarrensSpace.RData

library("lme4a")
pr1<-profile(fmer2f<-lmer(yall~yearSeason+sun+total_precip_trip+mean_temp_trip+surveyArea+obscat+hour_period+(1|yearMonth),REML=FALSE,data=df.p))

#Erro em x[ndat + (1L:deg) - deg] :
  #somente 0's podem ser usados junto com subscritos negativos
#Calls: profile ... interpSpline.formula -> interpSpline -> interpSpline.default

Tanslation: only 0's can be used together with negative subscripts.

Many thanks (session info below),
Darren

R version 2.12.2 (2011-02-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=pt_BR.UTF-8          LC_NUMERIC=C
 [3] LC_TIME=pt_BR.UTF-8           LC_COLLATE=pt_BR.UTF-8
 [5] LC_MONETARY=pt_BR.UTF-8       LC_MESSAGES=pt_BR.UTF-8
 [7] LC_PAPER=pt_BR.UTF-8          LC_NAME=pt_BR.UTF-8
 [9] LC_ADDRESS=pt_BR.UTF-8        LC_TELEPHONE=pt_BR.UTF-8
[11] LC_MEASUREMENT=pt_BR.UTF-8    LC_IDENTIFICATION=pt_BR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4a_0.999375-65  MatrixModels_0.2-1 minqa_1.1.15       Rcpp_0.9.2
[5] Matrix_0.999375-48 lattice_0.19-17    rkward_0.5.4

loaded via a namespace (and not attached):
[1] codetools_0.2-8  grid_2.12.2      lme4_0.999375-39 nlme_3.1-98
[5] splines_2.12.2   stats4_2.12.2    tools_2.12.2
2 days later
Ben Bolker
# 
Darren Norris <doon75 at ...> writes:
to suggest what I am doing wrong:
self.aspx/lmeData/DarrensSpace.RData
total_precip_trip+mean_temp_trip+surveyArea+
obscat+hour_period+(1|yearMonth),REML=FALSE,data=df.p))
interpSpline -> interpSpline.default
Thanks for the reproducible example.		 	   		  

  It looks like I have the same package versions as you (except
Rcpp_0.9.2.1 -- and a different locale) -- but I get a different
error message:

Error in na.fail.default(data.frame(x = as.numeric(obj1),
   y = as.numeric(obj2))) : 
  missing values in object
In addition: Warning message:
In sqrt(ores$fval - base) : NaNs produced

  Looking at summary(fmer2f), it seems that your estimate for
the random effect variance is zero. In principle profiling still
ought to work, but I can imagine that could cause problems.

  Will try to see what's going on here and whether things can
be made more robust.  (The first thing will probably be to make
up a small simulated example where the RE variance estimate comes
out to zero, to see if the guess is correct/whether it's a universal
problem in this case.)

  I would also recommend spending some more time looking at your
data and at the fit to see that everything seems to make sense
(outliers, blocks with extreme values, very strong parameter
correlations, etc.)  That won't fix the problem, but having
numerical difficulties is sometimes an indicator that the data
are wonky (and sometimes not).

  Ben Bolker
2 days later
Douglas Bates
#
On Mon, Apr 4, 2011 at 11:10 AM, Ben Bolker <bbolker at gmail.com> wrote:
Indeed it does.  I haven't been able to work out how to handle that case.
The Dyestuff2 data set, which is simulated data, provides such an
example.  Box and Tiao wrote that they assume such data occur in
practice - it's just that they are never published because they fail
to show an effect.