Dear all,
I am experiencing problems when trying to fit the following GLMM with
library lme4:
m5=with(DF3,lmer(n.spp~log(hs.arrastre+1)+zona+prof+SSTA+zona*log(hs.arrastre+1)+zona*SSTA+zona*prof+
(1|aņo) +(1|grado),weight=n.lances,family="poisson"))
The response variable are counts (number of species), and there are four
explanatory variables with fixed effects: three continuous variables (SSTA,
arrastre, prof) and one is a three-level factor (zona). There are two
crossed (uncorrelated random effects): (1|aņo) with aņo having 24 levels;
the other random effect (1|grado) has by coincidence also 24 levels. The DF
has 419 rows and no missing values.
The numbers of cases for each of the random effects are unbalanced but not
zero:
> with(DF2, table(aņo))
1984 1985 1987 1988 1989 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
2001 2002 2003 2005 2006 2007 2008 2009 2010
3 4 3 29 12 23 8 8 40 31
9 12 12 6 14 32 7 8 28 31
35 26 26 12
> with(DF2, table(grado))
333 342 343 344 345 352 353 354 355 356 363 364 365 366 374 375 376 385 386
387 395 396 397 398
7 35 22 18 9 22 31 25 18 17 28 32 10 6
22 26 11 13 18 13 9 9 12 6
> with(DF2, table(grado, aņo)) is very sparse, which is why I am trying to
fit uncorrelated random effects.
I have used the very same dataset, with the same model structure) for other
analyses with response variables having Gaussian distribution and have had
no problems at all.
I invariably obtain the error message:
Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1.
In addition: Warning messages:
1: In mer_finalize(ans) :
Cholmod warning 'not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 432
2: In mer_finalize(ans) :
Cholmod warning 'not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 432
I have absolutely no idea how to interpret this message or resolve the
error.
After trying to fit the same model with library glmmAMDB, I obtain another
(equally cryptical) error message:
Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
number of items to replace is not a multiple of replacement length
In addition: Warning messages:
1: In glmmadmb(n.spp ~ log(hs.arrastre + 1) + zona + prof + SSTA + :
NAs removed in constructing fixed-effect model frame: you should probably
remove them manually, e.g. with na.omit()
2: In II[, ii] + REmat$codes[[i]] :
longer object length is not a multiple of shorter object length:
I have tried many of the control options of either library (i.e. changing
the # of iterations, of evaluations, etc) but the error messages remain
unchanged.
I would really appreciate if any of you could possible spare some minutes
and suggest some alternative.
Many thanks in advance,
Cheers
Pablo
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