Re: [R] Constructing groupedData objects in nlme - a little problem
Hi Dieter, I never really used groupedData objects at all. I can imagine that if you become even more immersed in nlme and lattice, groupedData could reduce your typing, and sometimes simplify your life, but it was not a hurdle I chose willingly. Hank On Jun 4, 2008, at 1:15 PM, Dieter Menne wrote: Toby Marthews lsce.ipsl.fr> writes: 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): ... ...but, as you can see, the coefficients I get at the end this time are completely different and I don't know why. Somehow, I am not creating the structure properly even though the formula and data values are all correct. Hank is right. On the other hand your well-defined query points to a problem using groupedData. I do a lot of my work with nlme and love it, but I admit that I only started to understand it after I totally stopped using groupedData. Which makes reading Pinheiro/Bates sometimes difficult, because many examples give the impression that these must be done with groupedData. Everything can be done by explicitly saying what should be analyzed in lme and friends, there is no need to rely on groupedData. Note that in lme4 that partially re-designs nlme, there is no such thing as groupedData. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.cas.muohio.edu/ecology http://www.muohio.edu/botany/ "If the stars should appear one night in a thousand years, how would men believe and adore." -Ralph Waldo Emerson, writer and philosopher (1803-1882) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing groupedData objects in nlme - a little problem
Toby Marthews lsce.ipsl.fr> writes: > > 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): ... > > ...but, as you can see, the coefficients I get at the end this time are > completely different and I don't know why. Somehow, I am not creating the > structure properly even though the formula and data values are all > correct. > Hank is right. On the other hand your well-defined query points to a problem using groupedData. I do a lot of my work with nlme and love it, but I admit that I only started to understand it after I totally stopped using groupedData. Which makes reading Pinheiro/Bates sometimes difficult, because many examples give the impression that these must be done with groupedData. Everything can be done by explicitly saying what should be analyzed in lme and friends, there is no need to rely on groupedData. Note that in lme4 that partially re-designs nlme, there is no such thing as groupedData. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing groupedData objects in nlme - a little problem
HI Toby,
I think that the problem is that you have not specified using Rail and
travel in the model statement, but rather are still using x1 and x2.
It also does not realize that you want x1 to be a factor. Try
x1=factor(c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6))
x2=c(55,53,54,26,37,32,78,91,85,92,100,96,49,51,50,80,85,83)
eg1=data.frame(x1,x2);
colnames(eg1)=c("Rail","travel");
eg1gd=groupedData(travel~1|Rail,data=eg1)
print(eg1gd)
x11();
print(plot(eg1gd))
femodel=lm(x2~x1-1,data=eg1gd)
femodel=lm(travel~Rail-1,data=eg1gd)
summary(femodel)
Cheers,
Hank
On Jun 4, 2008, at 10:01 AM, Toby Marthews wrote:
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$coefficients)
Result:
x12 x15 x11 x16 x13 x14
31.7 50.0 54.0 82.7 84.7 96.0
...which works fine. This uses a built-in groupedData object called
"Rail"
that is part of the nlme library.
I am trying to 'recreate' this groupedData object. Here's what I've
done:
x1=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6);
x2=c(55,53,54,26,37,32,78,91,85,92,100,96,49,51,50,80,85,83)
eg1=data.frame(x1,x2);
colnames(eg1)=c("Rail","travel");
eg1gd=groupedData(travel~1|Rail,data=eg1)
print(eg1gd)
x11();
print(plot(eg1gd))
femodel=lm(x2~x1-1,data=eg1gd)
print(femodel$coefficients)
Result:
x1
16.49817
...but, as you can see, the coefficients I get at the end this time
are
completely different and I don't know why. Somehow, I am not
creating the
structure properly even though the formula and data values are all
correct.
Can anyone help? I've looked at the ?groupedData man page, but it
has no
solution to this.
Thanks very much for any advice,
Toby
Pinheiro JC & Bates DM (2000). Mixed-Effects Models in S and S-PLUS
(1st
ed.). Springer, New York.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056
Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.cas.muohio.edu/~stevenmh/
http://www.cas.muohio.edu/ecology
http://www.muohio.edu/botany/
"If the stars should appear one night in a thousand years, how would men
believe and adore." -Ralph Waldo Emerson, writer and philosopher
(1803-1882)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] 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$coefficients)
Result:
x12 x15 x11 x16 x13 x14
31.7 50.0 54.0 82.7 84.7 96.0
...which works fine. This uses a built-in groupedData object called "Rail"
that is part of the nlme library.
I am trying to 'recreate' this groupedData object. Here's what I've done:
x1=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6);x2=c(55,53,54,26,37,32,78,91,85,92,100,96,49,51,50,80,85,83)
eg1=data.frame(x1,x2);colnames(eg1)=c("Rail","travel");eg1gd=groupedData(travel~1|Rail,data=eg1)
print(eg1gd)
x11();print(plot(eg1gd))
femodel=lm(x2~x1-1,data=eg1gd)
print(femodel$coefficients)
Result:
x1
16.49817
...but, as you can see, the coefficients I get at the end this time are
completely different and I don't know why. Somehow, I am not creating the
structure properly even though the formula and data values are all
correct.
Can anyone help? I've looked at the ?groupedData man page, but it has no
solution to this.
Thanks very much for any advice,
Toby
Pinheiro JC & Bates DM (2000). Mixed-Effects Models in S and S-PLUS (1st
ed.). Springer, New York.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
