[R-sig-ME] increasing nAGQ causes error

Fri May 29 18:55:48 CEST 2009

Dr. Bolker,

Thanks for your prompt reply.  I created a subset of my dataset (attached). 
This subset contains 14 of the 22 cities in the full dataset, and one 
covariate (% impervious surfaces [IMP]).  I had convergence issues before 
standardizing covariates, so I used:

subset2$IMPS<-(subset2$IMP-mean(subset2$IMP))/(sqrt(var(subset2$IMP)))

Fitting all 3 covariates takes quite a long time, and I get the same error 
when using just one of them:

> test2<-glmer(USED~1+IMPS+(1+IMPS|CITY),family=binomial,data=subset2,nAGQ=8)
> test2
Error in asMethod(object) : matrix is not symmetric [1,2]

Perhaps it's noteworthy that I did not receive the error when using a 
smaller subset with only the first 8 cities (in alphabetical order).

I look forward to your response.  Thanks again...

-Grant

----- Original Message ----- 
From: "Ben Bolker" <bolker at ufl.edu>
To: "Grant T. Stokke" <gts127 at psu.edu>
Cc: <r-sig-mixed-models at r-project.org>
Sent: Friday, May 29, 2009 12:11 PM
Subject: Re: [R-sig-ME] increasing nAGQ causes error

>  This sounds worth digging into, but it's hard to dig
> into without a reproducible example.  I don't get the
> problem with the GLMM example in the lme4 package:
>
> example(lmer)
> update(gm1,nAGQ=8)
> update(gm1,nAGQ=10)
>
> etc.
>
>  Can you post your data set, or a subset or simulated
> data set that gives the same problem, somewhere?
>
>  Ben Bolker
>
> Grant T. Stokke wrote:
>> Hello All,
>>
>> I'm new to R and new to this mailing list, so I hope I've presented
>> the proper info in this post.  I'm using GLMMs to model the selection
>> of urban roosting locations by crows.  My dataset consists of 22
>> cities, with each city containing 1000 unused locations and from 83
>> to 2000 used locations.  I have three covariates for each used or
>> unused location which I've standardized across all observations: %
>> canopy (CANS), % impervious surfaces (IMPS), and nighttime light
>> level (LTS).  Using the default setting nAGQ=1, my full model is
>> fitted without error:
>>
>>> CIL_CIL<-glmer(USED~1+CANS+IMPS+LTS+(1+CANS+IMPS+LTS|CITY),family=binomial,data=sitescale)
>>>  CIL_CIL
>> Generalized linear mixed model fit by the Laplace approximation
>> Formula: USED ~ 1 + CANS + IMPS + LTS + (1 + CANS + IMPS + LTS |
>> CITY) Data: sitescale AIC   BIC logLik deviance 15122 15237  -7547
>> 15094 Random effects: Groups Name        Variance   Std.Dev. Corr
>>  CITY   (Intercept) 321.698184 17.93595 CANS          0.073271
>> 0.27069  0.026 IMPS          0.661947  0.81360  0.080 -0.698 LTS
>> 455.829122 21.35016 -0.988  0.031 -0.132 Number of obs: 27128,
>> groups: CITY, 22
>>
>> Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept)
>> -16.21878    4.01227  -4.042 5.29e-05 *** CANS          0.07881
>> 0.07162   1.100 0.271147 IMPS          0.63137    0.17750   3.557
>> 0.000375 *** LTS          19.50827    4.78822   4.074 4.62e-05 ***
>> --- Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>>
>> Correlation of Fixed Effects: (Intr) CANS   IMPS CANS  0.020
>>  IMPS  0.074 -0.500 LTS  -0.989  0.025 -0.124
>>
>> When I increase nAGQ to 8, however, I get the following error:
>>
>>> CIL_CIL.nAGQ8<-glmer(USED~1+CANS+IMPS+LTS+(1+CANS+IMPS+LTS|CITY),family=binomial,data=sitescale,nAGQ=8)
>>>  CIL_CIL.nAGQ8
>> Error in asMethod(object) : matrix is not symmetric [1,2]
>>
>> I get the same error message with other values for nAGQ (I tried nAGQ
>> = 2, 3, 5, and 50).  Is there anything I can do to fit the model
>> using nAGQ > 1 without error?  Thanks in advance for your help!
>>
>> -Grant Stokke
>>
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17) i386-pc-mingw32
>>
>> locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages: [1] stats     graphics  grDevices utils
>> datasets  methods   base
>>
>> other attached packages: [1] mgcv_1.5-5         lme4_0.999375-30
>> Matrix_0.999375-26 lattice_0.17-22
>>
>> loaded via a namespace (and not attached): [1] grid_2.9.0
>> nlme_3.1-90 tools_2.9.0
>>> CIL_CIL.nAGQ8
>> Error in asMethod(object) : matrix is not symmetric [1,2]
>>> traceback()
>> 18: .Call(dense_to_symmetric, from, "U", TRUE) 17: asMethod(object)
>> 16: as(from, "symmetricMatrix") 15: .class1(object) 14: as(as(from,
>> "symmetricMatrix"), "dMatrix") 13: .class1(object) 12: as(as(as(from,
>> "symmetricMatrix"), "dMatrix"), "denseMatrix") 11: .class1(object)
>> 10: as(as(as(as(from, "symmetricMatrix"), "dMatrix"), "denseMatrix"),
>>  "dpoMatrix") 9: asMethod(object) 8: as(sigma(object)^2 *
>> chol2inv(object at RX, size = object at dims["p"]), "dpoMatrix") 7:
>> vcov(object) 6: vcov(object) 5: summary(x) 4: summary(x) 3:
>> printMer(object) 2: function (object) standardGeneric("show")(<S4
>> object of class "mer">) 1: function (object)
>> standardGeneric("show")(<S4 object of class "mer">)
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
> -- 
> Ben Bolker
> Associate professor, Biology Dep't, Univ. of Florida
> bolker at ufl.edu / www.zoology.ufl.edu/bolker
> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
> 
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: subset2.txt
URL: <https://stat.ethz.ch/pipermail/r-sig-mixed-models/attachments/20090529/eb8d7c90/attachment.txt>