Displaying 20 results from an estimated 1000 matches similar to: "Help to extract results from lme.object"
2006 Oct 02
2
Help with lrm function in package Design
Hi, there,
I am having trouble using 'lrm' function in package 'Design'. Basically,
the ' . ' after ' ~ ' wouldn't work. Here are some sample codes:
> temp <-
data.frame(a=c(rep(0,3),rep(1,3)),b=rnorm(6),c=c('a','b','c','a','b','c'))
> lrm(a~.,data=temp)
Error in terms.formula(formula, specials =
2004 Jul 16
3
rpart and TREE, can be the same?
Hi, all,
I am wondering if it is possible to set parameters of 'rpart' and 'tree'
such that they will produce the exact same tree? Thanks.
Auston Wei
Statistical Analyst
Department of Biostatistics and Applied Mathematics
The University of Texas MD Anderson Cancer Center
Tel: 713-563-4281
Email: wwei@mdanderson.org
[[alternative HTML version deleted]]
2006 Mar 10
1
error message in cph
Hi, List,
I am using function 'cph' in package 'Design'. I have run into this error
message but could not find documentation after looking for a long time.
Could someone help me out? What kind of problem it is in my data set and
how to fix it?
Thanks a lot!
Auston
Error in fitter(X, Y, strata = Strata, offset = offset, weights = weights,
:NA/NaN/Inf in foreign function
2005 Sep 20
2
why this postscript didn't work?
Hi, List,
I used the following codes to generate ps plots but foo.ps contains
nothing. Would someone please point out what is wrong with my codes?
Thanks a million!
postscript('foo.ps')
par(mfrow=c(2,1))
par(mfg=c(1,1))
hist(rnorm(100),col='blue')
par(mfrow=c(2,2))
par(mfg=c(2,1))
hist(rnorm(50),col='blue')
par(mfg=c(2,2))
hist(rnorm(60),col='blue')
dev.off()
2011 Jan 19
2
VarCorr
I have a loop that I would like to use to extract the "stddev" for
each itteration so I can average the "stddev" for all the runs. It
would be helpful to know how to extract the "stddev" for each run from
the VarCorr. Thanks
MCruns<-1000
sighatlvec<-rep(NA,MCruns)
sighatbvec<-rep(NA,MCruns)
sighatevec<-rep(NA,MCruns)
for(mc in 1:MCruns)
{
2011 Jun 08
1
using stimulate(model) for parametric bootstrapping in lmer repeatabilities
Hi all,
I am currently doing a consistency analysis using an lmer model and
trying to use parametric bootstrapping for the confidence intervals.
My model is like this:
model<-lmer(y~A+B+(1|C/D)+(1|E),binomial)
where E is the individual level for consistency analysis, A-D are
other fixed and random effects that I have to control for.
Following Nakagawa and Scheilzeth I can work out the
2005 Sep 01
2
VarCorr function for assigning random effects: was Question
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
2001 Nov 14
2
lme: how to extract the variance components?
Dear all,
Here is the question:
For example, using the "petrol" data offered with R.
pet3.lme<-lme(Y~SG+VP+V10+EP,random=~1|No,data=petrol)
pet3.lme$sigma gives the residual StdDev.
But I can't figure out how to extract the "(intercept) StdDev",
although it is in the print out if I do "summary(pet3.lme)".
In
2003 Jul 14
1
methods help and glmmPQL
Dear All,
I would like to ask you to help me with my memeory. I remember using some
function that would list all the possible methods I could apply to an
object. Say, if I had an object of
class=lme,
it would tell me that that I could do stuff like
qqnorm(myobjct), or VarCorr(myobject). In general, a very complete list.
I though this list of all possible methods would pop out by typing
2003 Feb 13
1
fixed and random effects in lme
Hi All,
I would like to ask a question on fixed and random effecti in lme. I am
fiddlying around Mick Crawley dataset "rats" :
http://www.bio.ic.ac.uk/research/mjcraw/statcomp/data/
The advantage is that most work is already done in Crawley's book (page 361
onwards) so I can check what I am doing.
I am tryg to reproduce the nested analysis on page 368:
2001 Oct 09
1
PROC MIXED user trying to use (n)lme...
Dear R-users
Coming from a proc mixed (SAS) background I am trying to get into
the use of (n)lme.
In this connection, I have some (presumably stupid) questions
which I am sure someone out there can answer:
1) With proc mixed it is easy to get a hold on the estimated
variance parameters as they can be put out into a SAS data set.
How do I do the same with lme-objects? For example, I can see the
2006 May 08
1
Repeatability and lme
Dear R-help list members
I gathered longitudinal data on fish behaviour which I try to analyse using
a multi level model for change. Mostly, I am following Singer & Willett
(2003), who provide also the S/R code for their examples in the book (e.g.
http://www.ats.ucla.edu/stat/Splus/examples/alda/ch4.htm). Of course I am
interested in change over time, but I am also very much interested in
2004 Jul 06
2
lme: extract variance estimate
For a Monte Carlo study I need to extract from an lme model
the estimated standard deviation of a random effect
and store it in a vector. If I do a print() or summary()
on the model, the number I need is displayed in the Console
[it's the 0.1590195 in the output below]
>print(fit)
>Linear mixed-effects model fit by maximum likelihood
> Data: datag2
> Log-likelihood:
2007 Jan 20
1
aov y lme
Dear R user,
I am trying to reproduce the results in Montgomery D.C (2001, chap 13,
example 13-1).
Briefly, there are three suppliers, four batches nested within suppliers
and three determinations of purity (response variable) on each batch. It is
a two stage nested design, where suppliers are fixed and batches are random.
y_ijk=mu+tau_i+beta_j(nested in tau_i)+epsilon_ijk
Here are the
2006 Apr 25
1
lme: how to compare random effects in two subsets of data
Dear R-gurus,
I have an interpretation problem regarding lme models.
I am currently working on dog locomotion, particularly on some variation
factors.
I try to figure out which limb out of 2 generated more dispersed data.
I record a value called Peak, around 20 times for each limb with a record.
I repeat the records during a single day, and on several days.
I tried to build two models, one
2006 Jul 28
3
random effects with lmer() and lme(), three random factors
Hi, all,
I have a question about random effects model. I am dealing with a
three-factor experiment dataset. The response variable y is modeled
against three factors: Samples, Operators, and Runs. The experimental
design is as follow:
4 samples were randomly chosen from a large pool of test samples. Each
of the 4 samples was analyzed by 4 operators, randomly selected from a
group of
2007 Jul 31
1
Extracting random parameters from summary lme and lmer
LS,
I'm estimating multilevel regression models, using the lme-function
from the nlme-package. Let's say that I estimated a model and stored
it inside the object named 'model'. The summary of that model is
shown below:
Using summary(model)$tTable , I receive the following output:
> summary(model)$tTable
Value Std.Error DF t-value
2003 May 20
1
Extracting elements from an reStruct
Sorry if this is obvious, but my S skills aren't great and I haven't been
able to find it documented anywhere.
I want to write a new function for use with lme objects; the function will
simply calculate an ICC (aka "rho") for each level of a mixed-effects
model. What I need for this is pretty simple:
(c(var1..varn, residual)) / sum(c(var1..varn, residual))
where var1..varn
2004 Sep 21
2
Bootstrap ICC estimate with nested data
I would appreciate some thoughts on using the bootstrap functions in the
library "bootstrap" to estimate confidence intervals of ICC values
calculated in lme.
In lme, the ICC is calculated as tau/(tau+sigma-squared). So, for instance
the ICC in the following example is 0.116:
> tmod<-lme(CINISMO~1,random=~1|IDGRUP,data=TDAT)
> VarCorr(tmod)
IDGRUP = pdLogChol(1)
2004 Feb 17
1
extracting standard error from lme output
Dear R experts,
I want to extract standard error from the output of lme, but I found
fix.effects() does not include SE of the coefficients. Many thanks in
advance.
Best regards,
Yu-Kang
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