glmmPQL crashes on inclusion of corSpatial object
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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