Patrick Johann Schratz
2016-Jul-24 13:10 UTC
[R] glmmPQL crashes on inclusion of corSpatial object
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, correl = 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]]
Patrick Johann Schratz <patrick.schratz <at> gmail.com> writes:> > 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] >By the way, this has been cross-posted both to StackOverflow and to r-sig-mixed-models at r-project.org. Cross-posting between R lists is explicitly deprecated; cross-posting between R lists and StackOverflow is not *explicitly* deprecated anywhere, but is probably a bad idea (tends to waste the time of answerers who don't know the question has been commented on and/or answered already elsewhere). Try to pick the single best venue and stick to it. Ben Bolker