[R] Getting residual term out of lmer summary table
aline.frank at wsl.ch
aline.frank at wsl.ch
Tue Nov 12 06:01:30 CET 2013
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?
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