[R-sig-ME] glmmPQL crashes on inclusion of corSpatial object
Thierry Onkelinx
thierry.onkelinx at inbo.be
Mon Jul 25 13:36:17 CEST 2016
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 op 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 op 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]]
>>>
>>> _______________________________________________
>>> R-sig-mixed-models op r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>
>>
> _______________________________________________
> R-sig-mixed-models op r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
[[alternative HTML version deleted]]
More information about the R-sig-mixed-models
mailing list