R help - Nov 2013 - Getting residual term out of lmer summary table

Hello

I'm working with mixed effects models using lmer() and have some problems to
get all variance components of the model's random effects. I can get the
variance of the random effect out of the summary and use it for further
calculations, but not the variance component of the residual term. Could
somebody help me with that problem? Thanks a lot! Below an example.

Aline



## EXAMPLE
#----------

require(lme4)

## Simulate data for the example
set.seed(6)
x1 <- runif(n=100, min=10, max=100) ## a continuos variable
x2 <- runif(n=100, min=10, max=100) ## a continuos variable

treat <- rep(letters[1:4], times=25) ## a fixed factor with 4 levels
treat.effect <- 20*rep(1:4, times=25) 

group.label <- rep(LETTERS[1:5], each=20)  ## the random effect
group.effect <- 10*rep(1:5, each=20)       ## there are 5 groups

## Response variable:
y <- 2*x1 + (-5)*x2 + treat.effect + group.effect + rnorm(100)

## Dataframe
d.ex <- data.frame(y, x1, x2, "Group"=group.label, treat)

## Apply model
mod1 <- lmer(y~x1+x2+treat+x1:treat+ (1|Group), data=d.ex)
output <- summary(mod1); output # ok, there is the variance component of the
random effect group and the residual term

## Now I'd like to get the variance components of the random effect
"Group" and of the residual term "Residual" in order
# to do further calculations with these numbers
output$varcor[1] ## reveals the variance of the random effect "Group"
output$varcor[2] ## does not reveal the residual term! what other command do I
need to use then?

<aline.frank <at> wsl.ch> writes:
> 
> Hello
 
> I'm working with mixed effects models using lmer() and have some
> problems to get all variance components of the model's random
> effects. I can get the variance of the random effect out of the
> summary and use it for further calculations, but not the variance
> component of the residual term. Could somebody help me with that
> problem? Thanks a lot! Below an example.
  There's an r-sig-mixed-models at r-project.org mailing list that
is specifically for mixed-models (especially lme4) questions.
 
> Aline
 
> ## EXAMPLE
> #----------
> 
require(lme4)

## Simulate data for the example
set.seed(6)
x1 <- runif(n=100, min=10, max=100) ## a continuos variable
x2 <- runif(n=100, min=10, max=100) ## a continuos variable

treat <- rep(letters[1:4], times=25) ## a fixed factor with 4 levels
treat.effect <- 20*rep(1:4, times=25) 

group.label <- rep(LETTERS[1:5], each=20)  ## the random effect
group.effect <- 10*rep(1:5, each=20)       ## there are 5 groups

## Response variable:
y <- 2*x1 + (-5)*x2 + treat.effect + group.effect + rnorm(100)

## Dataframe
d.ex <- data.frame(y, x1, x2, "Group"=group.label, treat)

## Apply model
mod1 <- lmer(y~x1+x2+treat+x1:treat+ (1|Group), data=d.ex)
output <- summary(mod1); output
## # ok, there is the variance component of the random effect group and the
residual term
> 
## Now I'd like to get the variance components of the random effect
"Group"
and of the residual term
"Residual" in order 
## to do further calculations with these numbers
output$varcor[1] ## reveals the variance of the random effect "Group"
output$varcor[2] ## does not reveal the residual term! what other command do
I need to use then?

VarCorr(mod1)  ## prints standard dev by default in latest lme4
## print both var and std dev
print(VarCorr(mod1),comp=c("Variance","Std.Dev."))
unlist(VarCorr(mod1))  ## group variance (as raw number)
sigma(mod1)   ## std. dev. of residual variance