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.onkel...@inbo.be
www.inbo.be
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experiment died of.
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that a reasonable answer can be extracted from a given body of data.
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