[R] Cholmod warning when fitting a poisson GLMM

Thu, 01 Jul 2010 08:28:53 -0700 

Hi, 

I am getting a warning message when I am fitting a generalized mixed model 
(mod_2) and I don't understand why because when I add just an interaction 
factor the model works perfectly (mod_1).

Does anyone know what it happpens ?

Thanks,

Aïda
 



> mod_1<-lmer(sur15~soeviv15_4plus+frviv15_4plus+frat_15death+dad_class_new+soeviv15_4plus:dad_class_new
>  +frviv15_4plus:dad_class_new+ 
> aine+ageatmumdeath+(1|newparish)+(1|mumID)+(1|cohorte),
+ weights=prop_off_tracked_to_age_15,family=poisson, 
data=basepreindust2_sur15,RMEL=F)

> mod_1
Generalized linear mixed model fit by the Laplace approximation
Formula: sur15 ~ soeviv15_4plus + frviv15_4plus + frat_15death + dad_class_new 
+  soeviv15_4plus:dad_class_new + frviv15_4plus:dad_class_new + aine + 
ageatmumdeath + (1 | newparish) + (1 | mumID) + (1 |cohorte)
   Data: basepreindust2_sur15
  AIC  BIC logLik deviance
 2333 2416  -1151     2303
Random effects:
 Groups    Name        Variance  Std.Dev.
 mumID     (Intercept) 0.0470305 0.216865
 newparish (Intercept) 0.0027002 0.051964
 cohorte   (Intercept) 0.0011787 0.034332
Number of obs: 1924, groups: mumID, 1293; newparish, 5; cohorte, 3

Fixed effects:
                                Estimate Std. 
Error z value Pr(>|z|)   
(Intercept)                    1.3013435  0.0570543  
22.809  < 2e-16 ***
soeviv15_4plus                -0.0608455  0.0191099  -3.184  
0.00145 **
frviv15_4plus                 -0.0075483  0.0191727  -0.394  
0.69380   
frat_15death                   0.0007571  0.0073176   
0.103  0.91760   
dad_class_new3                -0.0983394  0.0404488  -2.431  
0.01505 * 
dad_class_new4                -0.1401969  0.0744017  -1.884  
0.05952 . 
aine1                          0.0139884  
0.0389805   0.359  0.71970   
ageatmumdeath                  0.0019492  0.0009732   
2.003  0.04519 * 
soeviv15_4plus:dad_class_new3  0.0839922  0.0277758   3.024  0.00250 **
soeviv15_4plus:dad_class_new4  0.1014875  0.0560405   1.811  0.07015 . 
frviv15_4plus:dad_class_new3   0.0020857  0.0287243   0.073  0.94212   
frviv15_4plus:dad_class_new4  -0.0211242  0.0616165  -0.343  0.73172   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ 
’ 1

Correlation of Fixed Effects:
            (Intr) sv15_4 fr15_4 frt_15 dd_c_3 dd_c_4 aine1  agtmmd 
s15_4:__3 s15_4:__4 f15_4:__3
sovv15_4pls 
-0.237                                                                              
frvv15_4pls -0.253 
-0.139                                                                       
frat_15deth -0.237 -0.154 
-0.218                                                                
dd_clss_nw3 -0.303  0.214  0.270  
0.072                                                         
dd_clss_nw4 -0.228  0.117  0.145  0.072  
0.247                                                  
aine1       -0.155  0.247  0.264 -0.153 -0.039 
-0.028                                           
ageatmumdth -0.511  0.128  0.123 -0.273 -0.028  0.049 
-0.049                                    
svv15_4:__3  0.091 -0.608  0.182 -0.044 -0.402 -0.084  0.041  
0.043                             
svv15_4:__4  0.061 -0.299  0.095 -0.029 -0.086 -0.481  0.039  0.001  
0.214                      
frv15_4:__3  0.129  0.158 -0.592  0.024 -0.460 -0.107  0.022 -0.009 
-0.219    -0.052            
frv15_4:__4  0.058  0.077 -0.274  0.015 -0.088 -0.470  0.023 -0.006 
-0.050    -0.047     0.186


> mod_2<-lmer(sur15~soeviv15_4plus+frviv15_4plus+frat_15death+dad_class_new 
> +frviv15_4plus:dad_class_new+ 
> aine+ageatmumdeath+(1|newparish)+(1|mumID)+(1|cohorte), 
> weights=prop_off_tracked_to_age_15,family=poisson, 
> data=basepreindust2_sur15,RMEL=F,control = list(msVerbose = 1))

  0:     3767.6598:  1.33869 0.0832467 0.0644826  1.30576 -0.0220911 
-0.0188889 0.00561227 -0.0367862 -0.0735001 0.00785921 0.00209046 0.0218301 
-0.0103924
  1:     3757.7897:  1.33703 0.0832908 0.0645599  1.30563 -0.0222456 
-0.0188829 0.00518377 -0.0368487 -0.0735110 0.00787140 -0.00247635 0.0218423 
-0.0103827
  2:     3745.9984:  1.32280 0.0828516 0.0641048  1.30518 -0.0245513 
-0.0190723 0.00486308 -0.0370936 -0.0735605 0.00842523 0.00231376 0.0219140 
-0.0103036
  3:     3234.0042: 0.977325 0.0741097 0.0555502  1.29274 -0.0734156 
-0.0214680 -0.0100042 -0.0436855 -0.0748839 0.0199044 -0.00206090 0.0242118 
-0.00837900
  4:     3165.8228: 0.927184 0.0736596 0.0552550  1.40622 -0.101104 
0.0337682 -0.0185303 -0.0464208 -0.0952062 0.0185455 -0.00162160 0.0237606 
-0.00121856
  5:     3143.7562: 0.903731 0.0729734 0.0544866  1.40540 -0.0967740 
0.0325119 -0.0165578 -0.0468900 -0.0953327 0.0183130 -0.00648733 0.0233998 
-0.00130747
  6:     3115.6489: 0.898189 0.0727692 0.0546796  1.38913 -0.0885700 
0.0187058 -0.0139194 -0.0467760 -0.0928831 0.0186559 -0.00134163 0.0210460 
-0.00262605
  7:     3082.2905: 0.872730 0.0719408 0.0555959  1.36488 -0.0710244 
-0.00898995 -0.00997794 -0.0467335 -0.0899782 0.0190971 -0.00513307 0.0144395 
-0.00494046
  8:     2895.4929: 0.679086 0.0661372 0.0891088  1.91069 -0.146248 
0.0705396 -0.0664482 -0.0517994 -0.202402 0.0177356 -0.00630075 -0.0654173 
0.0199159
  9:           nan: -0.174440 0.823699 0.851474 -3.66912 0.0283103 
-0.118455 0.193071 -1.35997 0.103926 -0.0112525 -0.262753 -0.414740 -27.2429
 10:           nan: -0.174440 0.823699 0.851474 -3.66912 0.0283103 
-0.118455 0.193071 -1.35997 0.103926 -0.0112525 -0.262753 -0.414740 -27.2429
Message d'avis :
In mer_finalize(ans) :
  Cholmod warning 'not positive definite' at 
file:../Cholesky/t_cholmod_rowfac.c, line 432



>  sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    
LC_MONETARY=French_France.1252 LC_NUMERIC=C                 
[5] LC_TIME=French_France.1252   

attached base packages:
[1] grDevices datasets  splines   graphics  stats     tcltk     
utils     methods   base    

other attached packages:
 [1] Design_2.3-0       MASS_7.3-6         
languageR_1.0      zipfR_0.6-5        coda_0.13-5        
nlme_3.1-96        lme4_0.999375-33   Matrix_0.999375-39
 [9] lattice_0.18-8     svSocket_0.9-48    TinnR_1.0.3        
R2HTML_2.1         Hmisc_3.8-1        survival_2.35-8  

loaded via a namespace (and not attached):
[1] cluster_1.12.3 grid_2.11.1    svMisc_0.9-57  tools_2.11.1 




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