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

Mon Jul 25 14:19:46 CEST 2016

  This example crashes for me too under Ubuntu 14.04 (virtual), r-devel,
with

fit5 <- glmmPQL(fo, random = ~1 | date, data = d,
+                 correl = correl, family = binomial)
iteration 1
*** Error in `/usr/local/lib/R/bin/exec/R': corrupted double-linked
list: 0x0000000007bef0d0 ***

  This was asked on Stack Overflow as well:

http://stackoverflow.com/questions/38509095/glmmpql-crashes-on-inclusion-of-corspatial-object

 I was going to suggest INLA as well.  I was working up to providing a
worked example, but it's non-trivial to set up (understatement): see
e.g.
https://www.math.ntnu.no/inla/r-inla.org/tutorials/spde/spde-tutorial.pdf

  Another non-trivial approach:
https://github.com/bbolker/mixedmodels-misc/blob/master/notes/corr_braindump.rmd
(use lme4's modular structure to incorporate nlme-based corStruct
information within models) -- this would be less efficient since it
would involve computing the Cholesky decomposition of a 1000x1000 matrix
at each step (and, indeed, might crash in the same place that glmmPQL
did), where INLA uses some very very clever computational tricks ...

On 16-07-25 07:36 AM, Thierry Onkelinx wrote:
> Dear Patrick,
> 
> It seems like the correlation structure makes the model unstable. I get
> convergence when setting fixed = TRUE, but the estimate are very unstable.
> 
> I'd suggest to have a look at the INLA package which allows to fit
> spatially correlated random intercepts. It's described in "Spatial and
> Spatio-Temporal Bayesian models with R-INLA" (Blangiardo & Cameletti, 2015)
> 
> Best regards,
> 
> 
> 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
> 
> 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
> 
> 2016-07-25 12:38 GMT+02:00 Patrick Johann Schratz <patrick.schratz at gmail.com
>> :
> 
>> 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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>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>>
>>>
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