Displaying 20 results from an estimated 6000 matches similar to: "lme4 groupedData is missing"
2005 Aug 12
1
Problem with lme4
Hi,
I cannot seem to get lme4 to work. I have installed the lme4 and Matrix
package with apt-get. and both can be found in /usr/lib/R/site-library.
When I tried an example for lmer, R could not find the function lmer(),
> library(lme4)
Attaching package: 'lme4'
The following object(s) are masked from package:nlme :
getCovariateFormula getResponseFormula
2008 Jun 04
2
Constructing groupedData objects in nlme - a little problem
Dear R-help,
I am trying to create groupedData objects using the nlme library. I'm
missing something basic, I know:
Here is the first example in ch.1 of Pinheiro & Bates (2000):
library(nlme)
x2=Rail$travel;x1=Rail$Rail;eg1=data.frame(x1,x2);eg1gd=Rail
print(eg1gd)
x11();print(plot(eg1gd))
femodel=lm(x2~x1-1,data=eg1gd)
print(femodel$coefficients)
Result:
x12 x15 x11
2009 Jul 02
1
Problem with groupedData and lme
Dear R-users,
I'm currently having trouble with the implementation of a groupedData
object in the lme() function.
Executing the following function
> applyScalingSimp <- function(input.population)
> {
> ## GA is a time value
> varInOrder <- c("GA","weight","grouping","sex")
> modelVar <-
2005 Mar 01
3
packages masking other objects
hello all,
I am trying to use the function getCovariateFormula(nlme) in conjunction with the library lme4. When I load both packages I get the following message and the getCovariateFormula function no longer works:
library(nlme)
library(lme4)
Attaching package 'lme4':
The following object(s) are masked from package:nlme :
contr.SAS getCovariateFormula
2003 May 30
2
color in plot title: title(sub="something", col=4)
Is there a way to specify the color of the main title, the subtitle, or
the axis labels? I mean, for instance, something like
title(main="cougar", col=2)
For me, the above command produces the color black; that is, the "col"
argument has no effect.
I'm on a Windows 2000 machine with
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system
2008 Jul 17
2
nested calls, variable scope
Below is an example of a problem I encounter repeatedly when I write functions. A call works at the command line, but it does not work inside a function, even when I have made sure that all required variables are available within the function. The only way I know to solve it is to make the required variable global, which of course is dangerous. What is the elegant or appropriate way to solve
2018 Mar 22
0
How do I include a factor in a groupedData object? Meaning and use of inner and outer parameters
Dear John
You are only allowed to have the primary covariate on the left hand side
of the vertical bar. Other covariates go in inner or outer.
Michael
On 22/03/2018 12:59, Sorkin, John wrote:
> Windows 10 64-bit, R-Studio, R version 3.4.3
>
>
> Several questions relating to groupedData:
>
> (1) I am trying to create a groupedData object that can be used to run an analysis
2006 Dec 07
2
groupedData Error Using outer=TRUE
I'm using groupedData from nlme. I set up a groupedData data.frame with
outer=~group1. When I try to plot with outer=TRUE, I get "subscript out
of bounds." This happens most of the time. When it works, I get
spaghetti-type plots for comparing groups. But I don't understand why it
doesn't usually work.
> longa.mod.1.gd <- groupedData(mod1.logit~time|
2018 Mar 22
3
How do I include a factor in a groupedData object? Meaning and use of inner and outer parameters
Windows 10 64-bit, R-Studio, R version 3.4.3
Several questions relating to groupedData:
(1) I am trying to create a groupedData object that can be used to run an analysis that I have been able to urn using lmer. When I include the interaction terms in the groupedData opbject I get an error message stating that + is not meaningful for factors. How do I include factors in my model? See code and
2000 Jul 24
1
How to use groupedData() within a function?
Dear Group:
I have been trying to write an R function within which the function
groupedData() would be used.
The following is a sample program:
#######################
sid<-rep(1:6,times=2)
time<-c(1:12)
trt<-rep(letters[1:3],times=4)
tem<-data.frame(sid,time,trt)
test1.fun<- function(dat=dat)
{
groupedData(time ~ trt|sid, data=dat)
}
test1.fun(dat=tem)
2007 Dec 27
2
groupedData function not found
Hello,
I'm trying to use the groupedData function and R is giving me the message: Error: can not find function "groupedData"
The code is coming from a textbook so I think it should be correct:
pigs<-data.frame(cbind(pig.time,pig.id,pig.wt))
pig.growth<-groupedData(pig.wt~pig.time|pig.id,data=pigs)
I have added the package "nlme" and to confirm that it was installed
2009 Jul 14
1
Problem with GroupedData
Hi,
I have an original data frame with 8 columns of variables, which are stored in 'data1' frame.
data1 <- read.csv("E:\\PHD GLASGOW UNIVERSITY\\Data\\R\\Colin\\Cailness21.csv")
attach(data1)
names(data1)
[1] "Date" "d" "m" "y" "Time"
[6] "Depth" "Temp"
2005 Mar 17
2
Repeated Measures, groupedData and lme
Hello
I am trying to fit a REML to some soil mineral data which has been
collected over the time period 1999 - 2004. I want to know if the 19
different treatments imposed, differ in terms of their soil mineral
content. A tree model of the data has shown differences between the
treatments can be attributed to the Magnesium, Potassium and organic
matter content of the soil, with Magnesium being the
2008 Jul 19
1
wroung groupedData despite reading Bates and Pinheiro 3 times
Hi everyone. I am trying to add a formula to my data using the groupedData
function.
My experiment consists of randomized block design using fruits, vegetation
and time as factors. The idea is to see if fruits, vegetation and time
explain the abundance of mice. I am using tree density as a covariate.
So I tried to fit the following structure to my data.
>
2001 Nov 19
1
scope of data in groupedData
I'm trying to write a function that has a dataframe as
an argument. Within the function, I call groupedData
to create a grouped-data object from the dataframe
argument. However, the groupedData function doesn't
seem to see the data. I'm guessing it's getting the
argument name rather than its value, but I'm not
positive.
My system: R 1.3.1 on WinNT 4.0 (Pentium II), nlme
2005 Nov 03
1
Specify Z matrix with lmer function
Is there a way to specify a Z matrix using the lmer function, where the
model is written as y = X*Beta + Z*u + e?
I am trying to reproduce smoothing methods illustrated in the paper
"Smoothing with Mixed Model Software" my Long Ngo and M.P. Wand.
published in the /Journal of Statistical Software/ in 2004 using the
lme4 and Matrix packages. The code and data sets used can be found at
2002 Oct 30
1
groupedData
Dear all,
I tried to create a groupedData object, where the grouping factor
is not ordered.
Here ist the code:
library(nlme)
test<-groupedData(conc~Time|Subject,order.groups=F,data=as.data.frame(Theoph))
> getGroups(test)
Levels: 6 < 7 < 8 < 11 < 3 < 2 < 4 < 9 < 12 < 10 < 1 < 5
I still get an ordered factor. As always thanks for your help
peter
2010 Sep 10
1
lme, groupedData, random intercept and slope
Windows Vista
R 2.10.1
Does the following use of groupedData and lme produce an analysis with both random intercept and slope, or only random slope?
zz<-groupedData(y~time | Subject,data=data.frame(data),
labels = list( x = "Time",
y = "y" ),
units = list( x = "(yr)", y = "(mm)")
)
plot(zz)
2004 Aug 03
2
lme fitted correlation of random effects: where is it?
The print method for lme *prints out* the fitted correlation matrix for
the random effects. Is there any way to get these values as an object in
R? I have examined the components of the lme object (called "junk" in the
example below) and the components of summary(junk) without finding these
numbers.
(How I did this: I dumped the entire lme object to a text file and then
used egrep to
2007 Mar 04
1
plot groupedData in nlme
Hi,
Does anyone know how to make the color of the lines all black when
plotting groupedData with an outer factor:
For example,
library(nlme)
plot(Dialyzer, outer=~QB, key=F)
This generated colored curves in R.2.4.1. How to make all the curves black ?
(or how to alter the color (type) of lines for the nlme groupedData
plotting function in general?)
Thanks
Qiong