[R] VarCorr function for assigning random effects: was Question
Doran, Harold
HDoran at air.org
Thu Sep 1 18:00:24 CEST 2005
You are correct, VarCorr IS compatible with lmer. It must be what you state below. I should have saved the message but VarCorr() complained that I was not dealing with an lme() object. I had multiple packages (nlme, Matrix, mlmRev, among others) in the search path.
On 9/1/05, Doran, Harold <HDoran at air.org> wrote:
> If you are indeed using lme and not lmer then the needed function is
> VarCorr(). However, 2 recommendations. First, this is a busy list and
> better emails subject headers get better attention. Second, I would
> recommend using lmer as it is much faster. However, VarCorr seems to
> be incompatible with lmer and I do not know of another function to
> work with lmer.
I hope that VarCorr is compatible with lmer. It is intended to be
> library(lme4)
Loading required package: Matrix
Loading required package: lattice
> example(VarCorr)
VarCrr> (fm2 <- lmer(Reaction ~ Days + (1 | Subject) + (0 +
Days | Subject), sleepstudy))
Linear mixed-effects model fit by REML
Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
Data: sleepstudy
AIC BIC logLik MLdeviance REMLdeviance
1753.669 1769.634 -871.8346 1752.047 1743.669
Random effects:
Groups Name Variance Std.Dev.
Subject (Intercept) 627.571 25.0514
Subject Days 35.858 5.9881
Residual 653.584 25.5653
# of obs: 180, groups: Subject, 18; Subject, 18
Fixed effects:
Estimate Std. Error DF t value Pr(>|t|)
(Intercept) 251.4051 6.8854 178 36.5128 < 2.2e-16 ***
Days 10.4673 1.5596 178 6.7117 2.480e-10 ***
---
Signif. codes: 0 $-1òø***òù 0.001 òø**òù 0.01 òø*òù 0.05 òø.òù 0.1 òø òù 1
VarCrr> VarCorr(fm2)
Groups Name Variance Std.Dev.
Subject (Intercept) 627.571 25.0514
Subject Days 35.858 5.9881
Residual 653.584 25.5653
What may have occurred is that you had the nlme package loaded after the lme4 (actually the important package is Matrix which gets loaded by lme4) package was loaded. The VarCorr generic in nlme would mask the VarCorr generic in the Matrix package.
>
> Hence, a better email subject header will attract the attention of
> others *much* smarter than me!
>
> I hope this helps,
> Harold
>
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Mahmoud Torabi
> Sent: Wednesday, August 31, 2005 9:51 PM
> To: R-help at stat.math.ethz.ch
> Cc: mtorabi at math.carleton.ca
> Subject: [R] Question
>
> Dear Sir/Madam
>
> I would be pleased if anybody can help me. I'm using linear mixed
> model
> (lme) function.I'm doing some simulation in my research and need to be
> assigned variance components values during of my program.
> Specifically, when I use lme function, I can get some information by
> use summary() and I can assign some valuse like variance of fixed
> parameters and variance of random error term by using for example
> varFix and sigma.But I don't know how I can assign for variance of random effect.
> I know in SPLUS we have command var.ran, how about R ?
The development version of the Matrix package, available at
https://svn.r-project.org/R-packages/trunk/Matrix
and soon to be Matrix_0.98-6 has a "simulate" method for lmer objects that may be of interest to you.
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