From Thierry.ONKELINX at inbo.be  Thu Apr  3 12:09:16 2014
From: Thierry.ONKELINX at inbo.be (ONKELINX, Thierry)
Date: Thu, 3 Apr 2014 10:09:16 +0000
Subject: [Rd] summary of lme4.0 model in package
Message-ID: <AA818EAD2576BC488B4F623941DA7427F3A21CF9@inbomail.inbo.be>

Dear all,

My package has Depends: lme4.0 in the DESCRIPTION. I need to extract the fixed effect of a model and their standard errors. I use coef(summary(model)) inside a function to do that. Model is the output of a call to glmer() from the lme4.0 package.

coef(summary(model)) throws an error: $ operator is invalid for atomic vectors

I have tracked it down to a problem with summary(model) because str(summary(model)) gives this

Classes 'summaryDefault', 'table'  Named chr [1:3] "1" "mer" "S4"
  ..- attr(*, "names")= chr [1:3] "Length" "Class" "Mode"

But it should return

Formal class 'summary.mer' [package "lme4.0"] with 42 slots
  ..@ methTitle: chr "Generalized linear mixed model fit by the Laplace approximation"
  ..@ logLik   :Class 'logLik' : -2265 (df=12)
--- output snipped ---

What puzzles me is that the function gives the error when called from the package, but works fine when I source the code of the function manually.

#this fails
MyPackage:MyFunction(model)
#this works
source("MyPackage/R/MyFunction.R")
MyFunction(model)

Any idea on what is going wrong and how to fix this?

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252    LC_MONETARY=Dutch_Belgium.1252
[4] LC_NUMERIC=C                   LC_TIME=Dutch_Belgium.1252

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

other attached packages:
[1] sendmailR_1.1-2   base64enc_0.1-1   ABV_0.2-21        lme4.0_0.999999-4 lattice_0.20-28   Matrix_1.1-3

loaded via a namespace (and not attached):
 [1] AFLP_0.4.0-66       colorspace_1.2-4    dichromat_2.0-0     digest_0.6.4        Epi_1.1.63
 [6] fortunes_1.5-2      ggplot2_0.9.3.1.99  grid_3.0.2          gridExtra_0.9.1     gtable_0.1.2
[11] labeling_0.2        lme4_1.1-5          lubridate_1.3.3     MASS_7.3-30         memoise_0.1
[16] mgcv_1.7-28         minqa_1.2.3         multcomp_1.3-2      munsell_0.4.2       mvtnorm_0.9-9997
[21] nlme_3.1-115        permute_0.8-3       plyr_1.8.1          proto_0.3-10        RColorBrewer_1.0-5
[26] Rcpp_0.11.1         RcppEigen_0.3.2.1.1 reshape_0.8.4       reshape2_1.2.2      RODBC_1.3-10
[31] sandwich_2.3-0      scales_0.2.3        seqinr_3.0-9        signal_0.7-3        splines_3.0.2
[36] stats4_3.0.2        stringr_0.6.2       survival_2.37-7     TH.data_1.0-3       tools_3.0.2
[41] vegan_2.1-41        watervogels_0.5-51  xtable_1.7-3        zoo_1.7-11


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 at 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


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[Rd] summary of lme4.0 model in package
ONKELINX, Thierry