On 28 Aug 2020, at 16:37, Ben Bolker <bbolker at gmail.com> wrote:
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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