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. 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 ? Thanks alot. M.Torabi ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
VarCorr function for assigning random effects: was Question
2 messages · Doran, Harold, Douglas Bates
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 $-1????***???? 0.001 ????**???? 0.01 ????*???? 0.05 ????.???? 0.1 ???? ???? 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.