[R-sig-ME] glmer / MuMin : Error in asMethod(object) : not a positive definite matrix

[Ben Bolker]

    Pretty hard to debug without a reproducible example (and an 8-day 
run time isn't going to help ...)

   The error message comes ultimately from the Matrix package (the error 
message is found in the "dspMatrix" → "dppMatrix" and "dsyMatrix" → 
"dpoMatrix" coercion methods).  If you run traceback() **immediately** 
after getting the error message, we might get a little bit more information.

   What are the warnings?

  If you've got multiple cores, using pdredge() might decrease your 
run-time.

   I don't know how to tell dredge() to use a try()-clause or equivalent 
to skip over models that have problems.



On 8/28/20 8:40 AM, Guillaume Adeux wrote:
> Hello everyone,
> 
> I am currently exploring the relationship between weed biomass during the
> fallow period and cover crop productivity (in interaction with tillage
> type, nitrogen fertilization, and cover crop species, as imposed by the
> 3-way factorial experimental design).
> This results in a highly complex model which I wish to reduce to achieve
> parsimony.
> Hence, I fitted the full model with glmer as:
> 
> mod_full_CC=glmer(dry_bio_weeds_m2+0.001~
> *block+year*scale(dry_bio_cover_m2)*tillage*N*CC*
> +(1|block:tillage)+(1|block:tillage:N)+(1|block:tillage:N:CC)+(1|block:year)+(1|block:year:tillage)+(1|block:year:tillage:N)+(1|block:year:tillage:N:CC),family=gaussian(link="log"),control=glmerControl(optimizer="nloptwrap",optCtrl=list(algorithm="NLOPT_LN_NELDERMEAD")),data=biomassCC_wo_Cbis)
> 
> and fed it to MuMin::dredge() as:
> 
> options(na.action = "na.fail")
> dred_CC=dredge(mod_full_CC,rank="AICc",fixed=c("block","year"))
> 
> However, I am unable to retrieve my "dred_CC" (after 8 days, arf) object
> because dredge() stops after returning:
> *Error in asMethod(object) : not a positive definite matrix*
> Is this due to a specific problem with one given model? If that's the case,
> how can I tell the function to simply skip it?
> To be completely transparent, it also states "In addition: There were 50 or
> more warnings (use warnings() to see the first 50)" but I don't believe the
> problem comes from there.
> 
> I would greatly greatly appreciate it if someone could lend a hand.
> Thanks for your time.
> 
> Guillaume ADEUX
> 
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> 
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