Displaying 7 results from an estimated 7 matches for "orthofem".
2007 Nov 09
1
Confidence Intervals for Random Effect BLUP's
...I cobbled
together using Orthodont data.frame as an example. There was some
discussion of how to properly access lmer slots and bVar, but I'm not
sure I understood. Is the approach shown below correct?
Rick B.
# Orthodont is from nlme (can't have both nlme and lme4 loaded at same
time!)
# OrthoFem<-Orthodont[Orthodont$Sex=="Female",]
# http://tolstoy.newcastle.edu.au/R/help/06/03/23758.html
library(lme4)
fm1OrthF. <- lmer(distance~age+(age|Subject), data=OrthoFem)
lmer(distance~age+(age|Subject), data=OrthoFem)@bVar$Subject[2,2,]*
(attr(VarCorr(lmer(distance~age+(age|
Su...
2006 Jun 05
1
Extracting Variance components
I can ask my question using and example from Chapter 1 of Pinheiro & Bates.
> # 1.4 An Analysis of Covariance Model
>
> OrthoFem <- Orthodont[ Orthodont$Sex == "Female", ]
> fm1OrthF <-
+ lme( distance ~ age, data = OrthoFem, random = ~ 1 | Subject )
> summary( fm1OrthF )
Linear mixed-effects model fit by REML
Data: OrthoFem
AIC BIC logLik
149.2183 156.169 -70.60916
Random effec...
2007 Jun 25
1
degrees of freedom in lme
...ta=Machines))
numDF denDF F-value p-value
(Intercept) 1 36 773.5709 <.0001
Machine 2 10 20.5762 3e-04
No problem here: the results are essentially the same, which is expected. Now
I turn to an ANCOVA with a random grouping factor.
> data(Orthodont)
> OrthoFem <- Orthodont[Orthodont$Sex=="Female",];
> summary(aov(distance~age+Error(Subject/age),data=OrthoFem))
Error: Subject
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 10 177.227 17.723
Error: Subject:age
Df Sum Sq Mean Sq F value Pr(>F)
age 1 50.592...
2006 Mar 21
1
Scaling behavior ov bVar from lmer models
Hi all,
To follow up on an older thread, it was suggested that the following
would produce confidence intervals for the estimated BLUPs from a linear
mixed effect model:
OrthoFem<-Orthodont[Orthodont$Sex=="Female",]
fm1OrthF. <- lmer(distance~age+(age|Subject), data=OrthoFem)
fm1.s <- coef(fm1OrthF.)$Subject
fm1.s.var <- fm1OrthF. at bVar$Subject
fm1.s0.s <- sqrt(fm1.s.var[1,1,])
fm1.s0.a <- sqrt(fm1.s.var[2,2,])
fm1.s[,1]+outer(fm1.s0.s, c(-2,0...
2005 Jul 12
1
nlme plot
...2.3.
What's wrong?
TIA.
Rod.
---------------------------------------------------------
>library(nlme)
> names( Orthodont )
[1] "distance" "age" "Subject" "Sex"
> levels( Orthodont$Sex )
[1] "Male" "Female"
> OrthoFem <- Orthodont[ Orthodont$Sex == "Female", ]
>
> fm1OrthF <- lme( distance ~ age, data = OrthoFem, random = ~ 1 | Subject )
> fm2OrthF <- update( fm1OrthF, random = ~ age | Subject )
> orthLRTsim <- simulate.lme( fm1OrthF, fm2OrthF, nsim = 1000 )
> plot( orthLRTs...
2006 Nov 28
2
Problem with pairs() in nlme
Dear r-helpers,
After successfully running
require(nlme)
vfr.lmL <- lmList(
estimate ~ (slant + respType + visField + hand)^2 | subject, vfr
)
pairs(vfr.lmL, id = 0.01, adj = -0.5) # Pinheiro & Bates (p. 141)
produces the following error:
Error in sprintf(gettext(fmt, domain = domain), ...) :
object "form" not found
Any guesses as to what I may have done wrong?
2005 Dec 22
2
bVar slot of lmer objects and standard errors
Hello,
I am looking for a way to obtain standard errors for emprirical Bayes estimates of a model fitted with lmer (like the ones plotted on page 14 of the document available at http://www.eric.ed.gov/ERICDocs/data/ericdocs2/content_storage_01/0000000b/80/2b/b3/94.pdf). Harold Doran mentioned (http://tolstoy.newcastle.edu.au/~rking/R/help/05/08/10638.html) that the posterior modes' variances