From: Spencer Graves <spencer.graves_at_pdf.com>

Date: Thu 08 Jul 2004 - 06:02:11 EST

> VC[1,2]

Error in VC[1, 2] : incorrect number of dimensions

R-help@stat.math.ethz.ch mailing list

https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jul 08 06:06:44 2004

Date: Thu 08 Jul 2004 - 06:02:11 EST

I just tried it in both lme4 and nlme. I got it in nlme but not lme4. I'm sure lme4 is better in many ways, but I could not figure out how to get what you want in lme4.

Specifically, I tried the following:

DF <- data.frame(x=rep(letters[1:2], 2), y=rep(1:2, 2)+0.01*(1:4))
fit <- lme(y~1, random=~1|x, data=DF)

VC <- VarCorr(fit)

VC

VC[1,2]

When I did this in library(nlme), I got the following:

> VC

x = pdLogChol(1)

Variance StdDev

(Intercept) 0.5101563004 0.71425227

Residual 0.0001999596 0.01414071

> VC[1,2]

[1] "0.71425227"

However, when I did it in library(lme4), I got something different:

> VC

Groups Name Variance Std.Dev. x (Intercept) 0.50995 0.71411 Residual 2e-04 0.014142

> VC[1,2]

Error in VC[1, 2] : incorrect number of dimensions

I was concerned by the differences in the estimates in this case, so I ported this problem to S-Plus 6.2. There I got the "lme4" answers from both "lme" and "varcomp".

hope this helps. spencer graves

Stephen Ellner wrote:

>Spencer Graves wrote:

*>
**>
**>
**>> Have you considered "VarCorr"? I've used it with "lme", and the
**>>documentation in package lme4 suggests it should work with GLMM, which
**>>might also do what you want from glmmPQL.
**>>
**>>
**>
**>Thanks for the pointer (I was not aware that nlme and lme4 had different
**>versions of lme), but I'm still stuck at the same place using lme4:> VarCorr(fit)
**> Groups Name Variance Std.Dev.
**> yeart (Intercept) 0.040896 0.20223
**> Residual 0.091125 0.30187
**>
**>The number I need to extract and store is the .20223, but all the
**>components I can find in VarCorr(fit) are something else.
**>
**>u=VarCorr(fit); slotNames(u)
**>[1] "scale" "reSumry" "useScale"
**>
**>
**>>u@scale
**>>
**>>
**>[1] 0.3018693
**>
**>
**>>u@reSumry
**>>
**>>
**>$yeart
**>An object of class "corrmatrix"
**> (Intercept)
**>(Intercept) 1
**>Slot "stdDev":
**>(Intercept)
**> 0.6699156
**>
**>
**>>u@useScale
**>>
**>>
**>[1] TRUE
**>
**>In glmmML the estimate is returned as the $sigma component
**>of the model, but I also need the same info from 'family=gaussian'
**>models.
**>
**>
**>Stephen P. Ellner (spe2@cornell.edu)
**>Department of Ecology and Evolutionary Biology
**>Corson Hall, Cornell University, Ithaca NY 14853-2701
**>Phone (607) 254-4221 FAX (607) 255-8088
**>
**>______________________________________________
**>R-help@stat.math.ethz.ch mailing list
**>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
**>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
**>
**>
*

R-help@stat.math.ethz.ch mailing list

https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jul 08 06:06:44 2004

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