Two issues:


1)       Using the exclude.influence  function is supposed to change the model output.  I amnot getting the change:

> M4 <- lmer(dY ~ A+B+(1|C/D/E), data=hole_analysis9, na.action=na.omit, contrasts=TRUE)
> summary(M4)
Linear mixed model fit by REML
Formula: dY ~ A + B + (1 | C/D/E)
   Data: hole_analysis9
    AIC    BIC logLik deviance REMLdev
-26592 -26535  13305   -26682  -26610
Random effects:
Groups                   Name        Variance   Std.Dev.
 E:(D:C) (Intercept) 2.6160e-05 5.1146e-03
D:C           (Intercept) 8.4577e-06 2.9082e-03
C                   (Intercept) 1.0919e-13 3.3044e-07
Residual                             1.1449e-04 1.0700e-02
Number of obs: 4335, groups: E:(D:C), 240; D:C, 40; C, 8

Fixed effects:
               Estimate Std. Error t value
(Intercept)   8.521e-03  1.307e-03   6.520
A          1.809e-05  1.333e-06  13.565
B[T.LR] -1.891e-03  1.840e-03  -1.028
B[T.RF] -1.160e-02  1.919e-03  -6.043
B[T.RR] -1.538e-02  1.899e-03  -8.096

Correlation of Fixed Effects:
            (Intr) A   B[T.L B[T.RF
A         0.352
B[T.LR] -0.622  0.000
B[T.RF] -0.749 -0.433  0.424
B[T.RR] -0.774 -0.487  0.428   0.621

> diag_1 <- estex(M4,"C")
> ME.cook(diag_1,plot=TRUE)
         [,1]
1 0.855810442
2 0.161766304
3 0.059605705
4 0.007075155
5 0.785242878
6 0.027034719
7 1.879700208
8 0.009450442

Level 7 stands out:

> M4_a <- exclude.influence(M4,"C","7",gf="all")
> summary(M4_a)
Linear mixed model fit by REML
Formula: dY ~ A + B + (1 | C/D/E)
   Data: ..1
    AIC    BIC logLik deviance REMLdev
-23273 -23217  11646   -23361  -23291
Random effects:
Groups                   Name        Variance   Std.Dev.
 E:(D:C) (Intercept) 1.6850e-05 4.1049e-03
D:C (Intercept) 1.3042e-05 3.6114e-03
C                   (Intercept) 4.8884e-14 2.2110e-07
Residual                             1.0656e-04 1.0323e-02
Number of obs: 3747, groups: E:(D:C), 210; D:C, 35; C, 7

Fixed effects:
               Estimate Std. Error t value
(Intercept)   1.000e-02  1.419e-03   7.051
A          2.241e-05  1.425e-06  15.726
B[T.LR] -1.869e-03  1.997e-03  -0.936
B[T.RF] -1.314e-02  2.437e-03  -5.393
B[T.RR] -1.835e-02  2.058e-03  -8.917

Correlation of Fixed Effects:
            (Intr) A   B[T.L B[T.RF
A         0.351
B[T.LR] -0.623 -0.002
B[T.RF] -0.626 -0.329  0.363
B[T.RR] -0.774 -0.484  0.430   0.511

The Manual for Influence.ME says that I should have had a new model after the exclude statement along these lines:

dY ~ intercept.alt + C.7+A + B + (0+intercept.alt| C/D/E) - 1

but obviously I did not get that.  Why?


2)       When I try to take repeat the process to look for additional Cook's D values to exclude I get an error:

> diag_3 <- estex(M4_a,"C")
Error in alt.fixed[i, ] <- as.matrix(fixef(model.updated)[altered.no.estex]) :
  number of items to replace is not a multiple of replacement length


3)       Why can I see only the top level of grouping?
> grouping.levels(M4,"C")
[1] "1" "2" "3" "4" "5" "6" "7" "8"
> grouping.levels(M4,"D")
NULL
> grouping.levels(M4,"C:D")
NULL
> grouping.levels(M4,"C/D")
NULL

Joe C. Hightower,  CQE, CRE
Renton Quality Engineering
425-965-5884 (Desk)
425-753-4882 (Cell)


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