On Jan 4, 2008 6:21 PM, Andrea Previtali <[EMAIL PROTECTED]> wrote:
>
> Sorry, I realized that somehow the message got truncated. Here is the
> remaining part of the SAS output:
>
> Solutions for Fixed Effects:
>
> Effect DIST DW ELI SEX SEAS Estimate Std. Error
> DF t Value Pr > |t|
>
> Intercept -4.6540
> 0.6878 17 -6.77 <.0001
>
> DIST*DW 0 0 1.4641
> 0.4115 3077
> 3.56 0.0004
> DIST*DW 0 1 1.1333
> 0.4028 3077
> 2.81 0.0049
> DIST*DW 1 0 1.3456
> 0.3745
> 3077 3.59 0.0003
> DIST*DW 1 1 0 .
> .
> . .
>
> SEX*ELI 0 0 1.2633
> 0.4155
> 3077 3.04 0.0024
> SEX*ELI 0 1 0.6569
> 0.4140 3077 1.59
> 0.1126
> SEX*ELI 1 0 1.0728
> 0.4364
> 3077 2.46 0.0140
> SEX*ELI 1 1 0
> .
> . . .
>
> WT 0.00758
> 0.01912
> 3077 0.40 0.6918
>
> SEAS 0 0.7839
> 0.1588
> 3077 4.94 <.0001
>
> SEAS 1 0
> .
> . . .
>
> DEN -0.01343
> 0.002588
> 3077 -5.19 <.0001
>
> Type III Tests of Fixed Effects
>
> Effect NUM.DF DEN.DF F Value
> Pr > F
> DIST*DW 3 3077 6.06
> 0.0004
> SEX*ELI 3 3077 6.30
> 0.0003
> WT 1 3077
> 0.16
> 0.6918
> SEAS 1 3077
> 24.37
> <.0001
> DEN 1 3077
> 26.94
> <.0001
At least on my mail reader the copies of the output ended up with
wrapped lines and, apparently, some changes in the spacing. I enclose
two text files, glimmix.txt and glmer.txt, that are my reconstructions
of the originals. Please let me know if I have not reconstructed them
correctly. In particular, i don't think I got the first table of
"Solutions for Fixed Effects:" in the glimmix.txt file correct. It
seems to mix t statistics and F statistics in ways that I don't
understand.
Another thing I don't understand is what the Pseudo-Likelihood is.
Perhaps it is what I would call the penalized weighted residual sum of
squares. The likelihood reported by lmer and based on the binomial
distribution is very different.
If you want to compare coefficients I suggest using
options(contrasts = c("contr.SAS", "contr.poly")
and assure that SEX, DIST, DW and ELI are factors, then call lmer.
This will ensure that the SEX, DIST, DW and ELI terms and their
interactions are represented by contrasts in which the last level is
the reference level (the SAS convention) as opposed to the first level
(the R convention).
Also, you may be confusing the S language formula terms with the SAS
formula terms. In R the asterisk denotes crossing of terms and the :
is used for an interaction. Thus SEX*ELI is equivalent to SEX + ELI +
SEX:ELI in R. In SAS, it is the interaction that is written as
SEX*ELI. I suggest that you change your SAS formula to include main
effects for SEX, ELI, DIST and DW.
Generalized linear mixed model fit using PQL
Formula: SURV ~ SEX * ELI + DW * DIST + SEAS + DEN + WT + (1 | SITE)
Family: binomial(logit link)
AIC BIC logLik deviance
1539 1606 -758.7 1517
Random effects:
Groups Name Variance Std.Dev.
SITE (Intercept) 0.27816 0.52741
number of obs: 3104, groups: SITE, 19
Estimated scale (compare to 1 ) 0.9458749
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.144259 0.458672 -2.495 0.012606
SEX -0.606026 0.167289 -3.623 0.000292 ***
ELI -0.190757 0.219599 -0.869 0.385034
DW -0.328796 0.175882 -1.869 0.061565 .
DIST -0.117745 0.374148 -0.315 0.752989
SEAS -0.784971 0.158748 -4.945 7.62e-07 ***
DEN -0.013381 0.002585 -5.176 2.27e-07 ***
WT 0.007735 0.019115 0.405 0.685732
SEX:ELI -0.466425 0.461596 -1.010 0.312274
DW:DIST -1.015454 0.404683 -2.509 0.012099 *
Model Information
Variance Matrix Blocked By Site
Estimation Technique: Residual PL
Degrees of Freedom Method: Containment
Fit Statistics
-2 Res Log Pseudo-Likelihood: 17868.73
Pseudo-AIC: 17890.73
Pseudo-BIC: 17957.14
Covariance Parameter Estimates
Cov Parm Subject Estimate Std Error
Intercept Site 0.2975 0.1799
Solutions for Fixed Effects
Effect DIST DW ELI SEX SEAS Estimate Std Error DF
t Value Pr> |t|
Intercept -4.6540 0.687 17
-6.77 F
DIST*DW 3 3077
6.06 0.0004
SEX*ELI 3 3077
6.30 0.0003
WT 1 3077
0.16 0.6918
SEAS 1 3077
24.37
Solutions for Fixed Effects:
Effect DIST DW ELI SEX SEAS Estimate Std. Error
DF t Value Pr > |t|
Intercept -4.6540 0.6878
17 -6.77 <.0001
DIST*DW 0 0 1.4641 0.4115
3077 3.56 0.0004
DIST*DW 0 1 1.1333 0.4028
3077 2.81 0.0049
DIST*DW 1 0 1.3456 0.3745
3077 3.59 0.0003
DIST*DW 1 1 0 .
. . .
SEX*ELI 0 0 1.2633 0.4155
3077 3.04 0.0024
SEX*ELI 0 1 0.6569 0.4140
3077 1.59 0.1126
SEX*ELI 1 0 1.0728 0.4364
3077 2.46 0.0140
SEX*ELI 1 1 0 .
. . .
WT 0.00758 0.01912
3077 0.40 0.6918
SEAS 0 0.7839 0.1588
3077 4.94 <.0001
SEAS 1 0 .
. . .
DEN -0.01343 0.002588
3077 -5.19 <.0001
Type III Tests of Fixed Effects
Effect NUM.DF DEN.DF F Value
Pr > F
DIST*DW 3 3077 6.06
0.0004
SEX*ELI 3 3077 6.30
0.0003
WT 1 3077 0.16
0.6918
SEAS 1 3077 24.37
<.0001
DEN 1 3077 26.94
<.0001
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