Displaying 20 results from an estimated 1000 matches similar to: "standardized random effects with ranef.lme()"
2006 Jul 31
0
standardized residuals (random effects) using nlme and ranef
> To sum up, I can't figure out how MLWin calculates the
> standardized residuals. But I understand that this is not a
> question for the R list.
> Nevertheless, it would help if someone could point me to some
> arguments why not to use them and stick to the results
> obtainable by ranef().
Hi Dirk:
Well, it is interesting that mlWin and lmer generate the same exact
2009 Nov 01
1
package lme4
Hi R Users,
When I use package lme4 for mixed model analysis, I can't distinguish
the significant and insignificant variables from all random independent
variables.
Here is my data and result:
Data:
Rice<-data.frame(Yield=c(8,7,4,9,7,6,9,8,8,8,7,5,9,9,5,7,7,8,8,8,4,8,6,4,8,8,9),
Variety=rep(rep(c("A1","A2","A3"),each=3),3),
2007 Apr 06
2
plotting multilevel / lme lines
Dear expeRts,
I am trying to plot a lme-object {package nlme) in such a way, that
on a selected level the x-axis represents the value on a selected
predictor and the y-axis represents the predicted-outcome variable.
The graphs would than consist of several lines that each represent
one group. I can't find such a plotting function.
I could write such a function myself, based on
2009 Jun 25
2
Problems with subsets in NLME
I am trying to estimate models with subsets using the NLME package. However, I am getting an error in the case below (among others):
> subset <- c(rep(TRUE, 107), FALSE)
> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1, subset=subset)
Error in xj[i] : invalid subscript type 'closure'
> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1,
2009 Feb 02
0
emperical bayes estimates and standard error lme4
Dear all,
I am trying to get the emperical bayes estimates together with their
standard errors out of lme4. Up to now I have used MLwiN to get these
estimates. I have fitted the following - very simple - model, just to
find out how this works.
test<-lmer(y~(1|subject),data,REML=F)
ranef(test,postVar=T)
str(ranef(test,postVar=T)
If I use the formulation of the emperical bayes estimates and
2003 Jan 30
1
as.formula(string) and augPred in lme
Using formulas constructed from strings only
partially works for me in lme:
library(nlme)
data(Orthodont)
fm2<-lme(as.formula("distance~age"),data=Orthodont,random=~1|Subject)
summary(fm2) # works
augPred(fm2) # fails
#Error in inherits(object, "formula") :
#Argument "object" is missing, with no default
I assume that my use of as.formula is wrong, but
2004 Sep 12
1
Discrepency between R and MlwiN
When playing around fitting unconditional growth models using R and MlwiN today, I produced two different sets of estimates that I can't reconcile and wondered if anyone here has an idea:
The data is two-level repeated measures data with measures nested within child. There are two measures per child. I've fit an unconditional growth model as in Singer and Willet (2003) that allows for
2004 Aug 27
2
degrees of freedom (lme4 and nlme)
Hi, I'm having some problems regarding the packages
lme4 and nlme, more specifically in the denominator
degrees of freedom. I used data Orthodont for the two
packages. The commands used are below.
require(nlme)
data(Orthodont)
fm1<-lme(distance~age+ Sex,
data=Orthodont,random=~1|Subject, method="REML")
anova(fm1)
numDF DenDF F-value p-value
(Intercept) 1
2006 Oct 08
2
latex and anova.lme problem
Dear R-helpers,
When I try
> anova(txtE2.lme, txtE2.lme1)
Model df AIC BIC logLik Test L.Ratio p-value
txtE2.lme 1 10 8590 8638 -4285
txtE2.lme1 2 7 8591 8624 -4288 1 vs 2 6.79 0.0789
> latex(anova(txtE2.lme, txtE2.lme1))
Error: object "n.group" not found
I don't even see n.group as one of the arguments of latex()
I checked to see
>
1999 Jun 02
1
lme problem ?
Dear friends. I tried the session below with 10 MB in both vsize and nsize but didn't get the
example work. Is this a problem in LME or in me or both or somewhere else or undefined ?
R : Copyright 1999, The R Development Core Team
Version 0.64.0 Patched (May 3, 1999)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type
2005 Mar 14
2
par(new=TRUE) vs par(new=FALSE)
Just out of curiosity (and I hope that my question does not confuse
those who intuitively understood the par(new=TRUE) statement right in
the beginning):
I would like to know whether beginners (learning R) had the same
difficulty as I had: Intuitively I thought that par(new=TRUE) would draw
a new plot (and not into an already existing plot) and that
par(new=FALSE) would not draw a new plot
2005 May 23
3
skewness and kurtosis in e1071 correct?
I wonder whether the functions for skewness and kurtosis in the e1071
package are based on correct formulas.
The functions in the package e1071 are:
# --------------------------------------------
skewness <- function (x, na.rm = FALSE)
{
if (na.rm)
x <- x[!is.na(x)]
sum((x - mean(x))^3)/(length(x) * sd(x)^3)
}
# --------------------------------------------
and
#
2009 Aug 14
1
post hoc test after lme
Hi!
I am quiet new with R and I have some problems to perform a posthoc test
with an lme model.
My model is the following:
>lme1<-lme(eexp~meal+time, random=~1|id,na.action=na.omit)
and then i try to get a post hoc test:
>summary(glht(lme1,linfct=mcp(meal="Tukey)))
but I get a warning message: Erreur dans as.vector(x, mode) : argument
'mode' incorrect
Thank you for your
2004 Dec 31
1
lme: Confusion about Variances
Dear R users!
I used lme to fit a mixed model with random intercept and spatial Gaussian
correlation i.e. I fitted a model of the following form:
Y = X*beta + error
and
error = U + W(t) + Z
where U is the random intercept (normally distributed), W(t) the stationary
Gaussian process and Z also a normally distributed (the residual) rv. Each of
these three random variables have a variance which
2006 Apr 25
1
summary.lme: argument "adjustSigma"
Dear R-list
I have a question concerning the argument "adjustSigma" in the
function "lme" of the package "nlme".
The help page says:
"the residual standard error is multiplied by sqrt(nobs/(nobs -
npar)), converting it to a REML-like estimate."
Having a look into the code I found:
stdFixed <- sqrt(diag(as.matrix(object$varFix)))
if (object$method
2005 Sep 20
1
Problem with read.spss() and as.data.frame(), or: alternative to subset()?
Trying to select a subset of cases (rows of data) I encountered several
problems:
Firstly, because I did not read the help to read.spss() thoroughly
enough, I treated the data read as a data frame. For example,
dr2000 <- read.spss('myfile.sav')
d <- subset(dr2000,RBINZ99 > 0)
and thus received an error message (Object "RBINZ99" not found), because
dr2000 is not a
2012 Mar 20
1
Remove quotes from a string to use in a variable call
Hi,
I have a string that I want to use in a variable call. How can I remove the
quotes and/or the string properties of the string to use it in a variable
call?
Here's an example:
library(lme)
fm2 <- lme(distance ~ age, data = Orthodont, random = ~ 1)
summary(fm2)
I want to update the above regression to include new predictors according to
what is in a string:
predictors <-
2013 Feb 05
1
lmer - BLUP prediction intervals
Dear all
I have a model that looks like this:
m1 <- lmer(Difference ~ 1+ (1|Examiner) + (1|Item), data=englisho.data)
I know it is not possible to estimate random effects but one can
obtain BLUPs of the conditional modes with
re1 <- ranef(m1, postVar=T)
And then dotplot(re1) for the examiner and item levels gives me a nice
prediction interval. But I would like to have the prediction
2006 Aug 13
3
How to reply to a thread if receiving R-help mails in digest form
I receive R-help messages in digest form that makes it difficult to
answer a post. I noticed that my answer is not added to the thread
(instead, a new thread is started) although I use the same subject line
(starting with "Re: ") as the original post. Is there a solution (I
prefer the digest to separate messages for several reasons and don't
want to change my email reader)?
The
2003 Jun 03
3
Update VR_7.1-6
The update of VR by downloading VR_7.1-6.zip and using install.packages
(from local zip files) fails with the following error message:
Error in file(file, "r") : unable to open connection
In addition: Warning message:
cannot open file `VR/DESCRIPTION'
Other packages can be installed without problems, except of dse_2003.4-1
with a similar error message.
Why?
Operating System: