[R-sig-ME] Another bootMer bug? (after Ben Bolker's fix on Github, Aug 2, 9AM) [CORRECTION]

[Steve Walker]

I don't think this is a bug.  I was able to run it just fine.  Its just 
that a fairly large proportion of the bootstrap samples failed to 
converge.  This is a common situation, as it is just a special case of 
the general fact that not all glmer models are guaranteed to converge.

Cheers,
Steve

On 2013-08-03 11:52 AM, Michael Kubovy wrote:
> **********
> Reproducible example
> **********
> # Point your browser to: https://www.dropbox.com/s/27d780qorp2bbr3/data.txt , and download data.txt
> e1 <- read.table('data.txt', header = TRUE)
> e1$subNum <- factor(e1$subNum)
> e1$sesNum <-factor(e1$sesNum)
> e1$gamma.f <- factor(e1$gamma)
> e1$trial <- e1$trial + 1
> library(car)
> e1$response.f <- Recode(e1$response, " 0 = 'a'; 1 = 'b'; 2 = 'c'; else = 'd'", as.factor.result = TRUE)
> e1$duration <- Recode(e1$dT, " 6 = '100'; else = '300' ", as.factor.result = TRUE)
> names(e1)[10] <- 'bar'
> e1$cbr <- with(e1, c/b)
> e1ba <- e1[e1$response.f == 'a' | e1$response.f == 'b',]
> e1ba$response.f = factor(e1ba$response.f)
> e1ba$which <- factor('b')
> e1ba$aspectRatio <- e1ba$bar
> e1ba$aspectRatio.f <- factor(e1ba$aspectRatio)
> e1ba$aspectRatio.c <- e1ba$aspectRatio - median(e1ba$aspectRatio)
> library(lme4)
> e1ba.mer2 <- glmer(response.f ~ aspectRatio.c + (aspectRatio.c | subNum), family = binomial, data = e1ba)
> mySumm3 <- function(.) {
> 	c(beta=fixef(.))
> }
> boo01 <- bootMer(e1ba.mer2, FUN = mySumm3, nsim = 100, verbose = TRUE, .progress = 'txt')
>
> ###########################
> Here is what I get:
> ###########################
> =    1 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> =    2 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> ==    3 : Named num [1:2] -2.75 -13.22
> - attr(*, "names")= chr [1:2] "beta.(Intercept)" "beta.aspectRatio.c"
> =    4 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> =    5 : Named num [1:2] -2.98 -14.46
> - attr(*, "names")= chr [1:2] "beta.(Intercept)" "beta.aspectRatio.c"
> =    6 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> ==    7 : Named num [1:2] -2.83 -13.75
> - attr(*, "names")= chr [1:2] "beta.(Intercept)" "beta.aspectRatio.c"
> ...
> =   20 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> =   21 : Named num [1:2] -2.87 -13.83
> - attr(*, "names")= chr [1:2] "beta.(Intercept)" "beta.aspectRatio.c"
> =   22 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> ==   23 :List of 3
> $ message : chr "pwrssUpdate did not converge in 30 iterations"
> $ call    : NULL
> $ cppstack: NULL
> - attr(*, "class")= chr [1:4] "std::runtime_error" "C++Error" "error" "condition"
> =   24 : Named num [1:2] -2.77 -13.69
> - attr(*, "names")= chr [1:2] "beta.(Intercept)" "beta.aspectRatio.c"
> ...
> ###########################
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      splines   datasets  utils     stats     graphics  grDevices methods   base
>
> other attached packages:
> [1] boot_1.3-9          scales_0.2.3        effects_2.2-4       colorspace_1.2-2    MuMIn_1.9.5         lme4_0.99999911-8
> [7] RcppEigen_0.3.1.2.1 Rcpp_0.10.4         Matrix_1.0-12       lattice_0.20-15     sos_1.3-5           brew_1.0-6
> [13] ggplot2_0.9.3.1     car_2.0-18          nnet_7.3-7          MASS_7.3-27
>
> loaded via a namespace (and not attached):
> [1] dichromat_2.0-0    digest_0.6.3       gtable_0.1.2       labeling_0.2       minqa_1.2.1        munsell_0.4.2
> [7] nlme_3.1-110       plyr_1.8           proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2     stringr_0.6.2
> [13] tools_3.0.1
>
>
>
> ______________________________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
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