[R-sig-ME] Could not get a lmer or glmer summary

[Eric Edeline]

Dear David,

here is the Str(m11):

 > m11<-lmer(Logl ~ 1|Species, data=Data)
 > str(m11)
Formal class 'mer' [package "lme4"] with 34 slots
  ..@ env     :<environment: 0xc077a5c>
  ..@ nlmodel : language I(x)
  ..@ frame   :'data.frame':    92093 obs. of  2 variables:
  .. ..$ Logl   : num [1:92093] 3.72 4.35 4.83 4.56 5.5 ...
  .. ..$ Species: Factor w/ 50 levels "ABH","ABL","ANG",..: 20 18 32 29 
48 3 21 2 31 24 ...
  .. ..- attr(*, "terms")=Classes 'terms', 'formula' length 3 Logl ~ 1
  .. .. .. ..- attr(*, "variables")= language list(Logl)
  .. .. .. ..- attr(*, "factors")= int(0)
  .. .. .. ..- attr(*, "term.labels")= chr(0)
  .. .. .. ..- attr(*, "order")= int(0)
  .. .. .. ..- attr(*, "intercept")= int 1
  .. .. .. ..- attr(*, "response")= int 1
  .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
  .. .. .. ..- attr(*, "predvars")= language list(Logl)
  .. .. .. ..- attr(*, "dataClasses")= Named chr "numeric"
  .. .. .. .. ..- attr(*, "names")= chr "Logl"
  ..@ call    : language lmer(formula = Logl ~ 1 | Species, data = Data)
  ..@ flist   :'data.frame':    92093 obs. of  1 variable:
  .. ..$ Species: Factor w/ 50 levels "ABH","ABL","ANG",..: 20 18 32 29 
48 3 21 2 31 24 ...
  .. ..- attr(*, "assign")= int 1
  ..@ X       : num [1:92093, 1] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..- attr(*, "assign")= int 0
  ..@ Xst     :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int(0)
  .. .. ..@ p       : int 0
  .. .. ..@ Dim     : int [1:2] 0 0
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : NULL
  .. .. .. ..$ : NULL
  .. .. ..@ x       : num(0)
  .. .. ..@ factors : list()
  ..@ Zt      :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:92093] 19 17 31 28 47 2 20 1 30 23 ...
  .. .. ..@ p       : int [1:92094] 0 1 2 3 4 5 6 7 8 9 ...
  .. .. ..@ Dim     : int [1:2] 50 92093
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : NULL
  .. .. .. ..$ : NULL
  .. .. ..@ x       : num [1:92093] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..@ factors : list()
  ..@ pWt     : num(0)
  ..@ offset  : num(0)
  ..@ y       : num [1:92093] 3.72 4.35 4.83 4.56 5.5 ...
  ..@ Gp      : int [1:2] 0 50
  ..@ dims    : Named int [1:18] 1 92093 1 50 1 1 0 1 2 5 ...
  .. ..- attr(*, "names")= chr [1:18] "nt" "n" "p" "q" ...
  ..@ ST      :List of 1
  .. ..$ : num [1, 1] 1.41
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr "(Intercept)"
  .. .. .. ..$ : chr "(Intercept)"
  ..@ V       : num[0 , 0 ]
  ..@ A       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int [1:92093] 19 17 31 28 47 2 20 1 30 23 ...
  .. .. ..@ p       : int [1:92094] 0 1 2 3 4 5 6 7 8 9 ...
  .. .. ..@ Dim     : int [1:2] 50 92093
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : chr [1:50] "ABH" "ABL" "ANG" "APR" ...
  .. .. .. ..$ : NULL
  .. .. ..@ x       : num [1:92093] 1.41 1.41 1.41 1.41 1.41 ...
  .. .. ..@ factors : list()
  ..@ Cm      :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. ..@ i       : int(0)
  .. .. ..@ p       : int 0
  .. .. ..@ Dim     : int [1:2] 0 0
  .. .. ..@ Dimnames:List of 2
  .. .. .. ..$ : NULL
  .. .. .. ..$ : NULL
  .. .. ..@ x       : num(0)
  .. .. ..@ factors : list()
  ..@ Cx      : num(0)
  ..@ L       :Formal class 'dCHMsimpl' [package "Matrix"] with 10 slots
  .. .. ..@ x       : num [1:50] 19.48 84.97 95.87 4.35 10.7 ...
  .. .. ..@ p       : int [1:51] 0 1 2 3 4 5 6 7 8 9 ...
  .. .. ..@ i       : int [1:50] 0 1 2 3 4 5 6 7 8 9 ...
  .. .. ..@ nz      : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..@ nxt     : int [1:52] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..@ prv     : int [1:52] 51 0 1 2 3 4 5 6 7 8 ...
  .. .. ..@ colcount: int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..@ perm    : int [1:50] 0 1 2 3 4 5 6 7 8 9 ...
  .. .. ..@ type    : int [1:4] 2 1 0 1
  .. .. ..@ Dim     : int [1:2] 50 50
  ..@ deviance: Named num [1:13] 9.97e+04 9.97e+04 3.61e+02 3.22 
4.15e-01 ...
  .. ..- attr(*, "names")= chr [1:13] "ML" "REML" "ldL2" "ldRX2" ...
  ..@ fixef   : Named num 4.79
  .. ..- attr(*, "names")= chr "(Intercept)"
  ..@ ranef   : num [1:50] -0.9126 -0.4434 1.3085 -0.0774 0.2951 ...
  ..@ u       : num [1:50] -0.6463 -0.3141 0.9267 -0.0548 0.209 ...
  ..@ eta     : num [1:92093] 3.68 4.22 4.82 4.26 5.1 ...
  ..@ mu      : num [1:92093] 3.68 4.22 4.82 4.26 5.1 ...
  ..@ muEta   : num(0)
  ..@ var     : num(0)
  ..@ resid   : num [1:92093] 0.03999 0.12217 0.00859 0.30464 0.40331 ...
  ..@ sqrtXWt : num[0 , 1]
  ..@ sqrtrWt : num(0)
  ..@ RZX     : num [1:50, 1] 13.77 60.2 67.92 2.92 7.52 ...
  ..@ RX      : num [1, 1] 5
  ..@ ghx     : num(0)
  ..@ ghw     : num(0)


David Duffy wrote:
> On Wed, 24 Mar 2010, Eric Edeline wrote:
>
>> I am having troubles with getting a summary for lmer and glmer models 
>> that otherwise (apparently) converged properly (i can for instance 
>> extract ranefs). Could anyone point to me the mistake?
>
> Could you show us str(m11) ?
>

-- 
Eric Edeline
Assistant Professor
UMR 7618 BIOEMCO
Ecole Normale Supérieure
46 rue d'Ulm
75230 Paris cedex 05
France

Tel: +33 (0)1 44 32 38 84
Fax: +33 (0)1 44 32 38 85

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