Displaying 20 results from an estimated 10000 matches similar to: "augPred with lme(...,subset=...)"
2006 Jul 03
1
panel ordering in nlme and augPred plots
Hi,
I'm new at this, I'm very confused, and I think I'm missing something
important here. In our pet example we have this:
> fm <- lme(Orthodont)
> plot(Orthodont)
> plot(augPred(fm, level = 0:1))
which gives us a trellis plot with the females above the males,
starting with "F03", "F04", "F11", "F06", etc. I thought the point of
2005 Sep 29
1
plot.augPred sorted and labelled according second factor
Hi
using this code example:
library(nlme)
fm1 <- lme(Orthodont, random = ~1)
plot(augPred(fm1))
is there any way to have the plots in each cell labelled and ordered
according to Orthodont$Sex? I.e. in addition to the bar with the label for
Orthodont$Subject there is another bar labelling the Sex of the subject?
thanks a lot
christoph
--
2006 Sep 04
1
abline and plot(augPred) help
Dear all
as I did not get any response on my post about abline and
plot(augPred)) I try again. I hope I do not break some posting guide
rules. I would try to contact package maintainer directly but there
is stated to be R-core people, so I feel R-help list shall be OK.
I need to draw straight lines through augPred plotted panels
(vertical or horizontal) at specified point. I know I shall
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
2006 Sep 07
5
augPred plot in nlme library
All,
I'm trying to create an augPred plot in the nlme library, similar to the
plot on
p.43 of Pinheiro & Bates (Mixed Effects Models in S and S-Plus) for
their Pixel data.
My data structure is the same as the example but I still get the error
msg below.
> comp.adj.UKV <- groupedData(adj.UKV ~ Time | Patient_no/Lisinopril,
data = comp.adj.UKV.frm, order.groups = F)
>
2008 Oct 08
1
Observed responses in 'augPred' data frame - Wrong order ?
Dea-R community.
I'd like to draw your attention to an issue I have recently
encountered while doing my current data analysis.
I've got an unexpected (to me) result from the command:
> augPred(lmList(my.object)),
'my.object' being a grouped data frame of class:
> class(my.object)
[1] "nfnGroupedData" "nfGroupedData" "groupedData"
2002 Dec 17
1
lme invocation
Hi Folks,
I'm trying to understand the model specification formalities
for 'lme', and the documentation is leaving me a bit confused.
Specifically, using the example dataset 'Orthodont' in the
'nlme' package, first I use the invocation given in the example
shown by "?lme":
> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
Despite the
2010 Oct 25
1
building lme call via call()
dear all,
I would like to get the lme call without fitting the relevant model.
library(nlme)
data(Orthodont)
fm1 <- lme(distance ~ age, random=list(Subject=~age),data = Orthodont)
To get fm1$call without fitting the model I use call():
my.cc<-call("lme.formula", fixed= distance ~ age, random = list(Subject
= ~age))
However the two calls are not the same (apart from the data
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
2009 Mar 23
1
Extracting SD of random effects from lme object
Hello,
How do I get the standard deviations for the random effects out of the
lme object? I feel like there's probably a simple way of doing this,
but I can't see it. Using the first example from the documentation:
> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
> fm1
Linear mixed-effects model fit by REML
Data: Orthodont
Log-restricted-likelihood:
2008 Aug 28
1
Adjusting for initial status (intercept) in lme growth models
Hi everyone, I have a quick and probably easy question about lme for this
list.
Say, for instance you want to model growth in pituitary distance as a
function of age in the Orthodont dataset.
fm1 = lme(distance ~ I(age-8), random = ~ 1 + I(age-8) | Subject, data =
Orthodont)
You notice that there is substantial variability in the intercepts (initial
distance) for people at 8 years, and that
2005 Apr 25
4
panel ordering in nlme and augPred plots
Dear all
I am trying nlme together with Pinheiro/Bates book. I constructed
grouped data object with suitable plotting layout (according to
some common factor, panels from bottom to top are in increasing
order).
When I do nlme(... some stuff...) I get fitted object which I can plot
with
plot(augPred(fit.nlme6, level=0:1))
but it results in completely different ordering. Is there any way
2006 Nov 09
0
Help with plot(augPred()) plot(comparePred()) in nlme
Dear r-helpers,
When I issue the commands
plot(augPred(mcc.lme, primary = ~ mcc$age, length.out = 2, level = c
(0, 1)))
or
plot(comparePred(mcc1.lis, mcc.lme, primary = ~ mcc$age, length.out =
2), layout = c(4, 3)))
no lines are drawn.
But
fm1 <- lme(Orthodont)
plot(augPred(fm1, level = 0:1, length.out = 2))
does plot lines.
augPred() and comparePredict() seem to be working correctly, as
2019 Jan 17
3
long-standing documentation bug in ?anova.lme
tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And
some names are misspelled in ?lme. I can submit all this stuff as a bug
report if that's preferred.
?anova.lme says:
When only one fitted model object is present, a data frame with
the sums of squares, numerator degrees of freedom, denominator
degrees of freedom, F-values, and P-values
The output of
fm1
1999 Jul 01
1
lme
I am using rw0641.
In my continuing quest to understand repeated measures analysis, I again
return to lme. I exported the Potthoff and Roy data Orthodont.dat from
S-PLUS 4.5 to avoid capture errors and ran the examples in the R help. I
imported the data.frame with
data <- read.table("Orthodont.dat",header=T)
attach(data)
and created the objects
Orthodont.fit1 <-
2003 Mar 04
2
How to extract R{i} from lme object?
Hi, lme() users,
Can some one tell me how to do this.
I model Orthodont with the same G for random
variables, but different R{i}'s for boys and girls, so
that I can get sigma1_square_hat for boys and
sigma2_square_hat for girls.
The model is Y{i}=X{i}beta + Z{i}b + e{i}
b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2
orth.lme <- lme(distance ~ Sex * age, data=Orthodont,
random=~age|Subject,
2011 Jul 07
2
How do I overlay two trellis plots of lme fitted lines produced by plot.augPred?
Hello,
I want to use lme to fit two (or more) models, and then compare the fits
on each individual. I know how to write my own code to do this (for each
individual, plot the raw data, followed by lines() to plot each fitted
curve) but I would like to use plot(augPred(... as it produces a nice
trellis plot. I thought I could do this with par(new=T) but it does not
seem to work.
2010 Oct 18
1
Question about lme (mixed effects regression)
Hello!
If I run this example:
library(nlme)
fm1 <- lme(distance ~ age+Sex, Orthodont, random = ~ age + Sex| Subject)
If I run:
summary(fm1)
then I can see the fixed effects for age and sex (17.7 for intercept,
0.66 for age, and -1.66 for SexFemale)
If I run:
ranef(fm1)
Then it looks like it's producing the random effects for each subgroup
(in this example - each subject). For example,
2009 Jun 01
2
Sweave:Figures from plot (LME output) not getting generated (pdf or eps)
Hi,
I seem to be facing a strange problem when I use Sweave for creating a
LaTeX document of the R lme() output --- The EPS and PDF figure files
get created, but are empty. I have attached a reproducible example
below (taken from the R lme() help example).
------------------------------------------------------------------------------------
\documentclass[a4paper,10pt]{article}
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