[R-sig-ME] glmmPQL crashes on inclusion of corSpatial object

[Patrick Johann Schratz]

MacbookPro:

 > sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin15.5.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

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

other attached packages:
[1] lme4_1.1-12  Matrix_1.2-6 tibble_1.1   nlme_3.1-128 MASS_7.3-45 
gstat_1.1-3  sp_1.2-3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.6      lattice_0.20-33  intervals_0.15.1 
FNN_1.1          spacetime_1.1-5  zoo_1.7-13       assertthat_0.1 
grid_3.3.1       pacman_0.4.1     minqa_1.2.4      nloptr_1.0.4
[12] xts_0.9-7        splines_3.3.1    tools_3.3.1



Am 25.07.16 um 12:34 schrieb Phillip Alday:
> Hi Patrick,
>
> can you send us your sessionInfo()? Knowing the R version is important, but a few other details matter for debugging this type of problem!
>
> Best,
> Phillip
>
>
>> On 25 Jul 2016, at 19:55, Patrick Johann Schratz <patrick.schratz at gmail.com> wrote:
>>
>> Link to data: <https://www.dropbox.com/s/yi3vf0bmqvydr8h/data.Rd?dl=0>
>> (1170 obs, 9 variables, .Rd file) [plain link in case sth goes wrong
>> with the hyperlink: https://www.dropbox.com/s/yi3vf0bmqvydr8h/data.Rd?dl=0]
>>
>> Simply read it in using `readRDS(file)`.
>>
>> I´m trying to setup a GLMM using the `glmmPQL` function from the `MASS`
>> package including a random effects part and accounting for spatial
>> autocorrelation. However, R (Version: 3.3.1) crashes upon execution.
>>
>>      library(nlme)
>>
>>      # setup model formula
>>      fo <- hail ~ prec_nov_apr + t_min_nov_apr + srad_nov_apr + age
>>
>>      # setup corSpatial object
>>      correl = corSpatial(value = c(10000, 0.1), form = ~ry + rx, nugget
>> = TRUE,
>>                          fixed = FALSE, type = "exponential")
>>      correl = Initialize(correl, data = d)
>>
>>      # fit model
>>      fit5 <- MASS::glmmPQL(fo, random = ~1 | date, data = d,
>>                      correlation = correl, family = binomial)
>>
>> What I tried so far:
>>
>> - reduce number of observation
>> - play with `corSpatial` parameters (range and nugget)
>> - reduce number of fixed predictors
>> - execute code on Windows, Linux (Debian) and Mac R installations
>>
>>
>> While I get no error message on my local pc (RStudio just crashes),
>> running the script on a server returns the following error message:
>>
>> `R: malloc.c:3540: _int_malloc: Assertion (fwd->size & 0x4) == 0'
>> failed. Aborted`
>>
>> Debugging leads me to a "glibc" c++ library problem. I also run valgrind
>> on it. If you need the output, just ask!
>>
>> Help ist highly appreciated!
>> Cheers, Patrick
>>
>> 	[[alternative HTML version deleted]]
>>
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