Re: [R] How can one make stepAIC and lme

Prof Brian Ripley Tue, 13 May 2008 09:06:18 -0700

You are using subset() as a function -- lme has a subset argument, andsubset() has non-standard semantics.

The dataset you are using is subset(D1,age!=14): it is that which you needto make sure is visible. You didn't make D1 visible, just its columns.


On Tue, 13 May 2008, Jorunn Slagstad wrote:

Hi again,

I've tried using with() inside my function in the following manner:

library(nlme)
library(MASS)
PredRes<-function(D1)
{
with(D1, {lmemod<-lme(distance~age*Sex, random=~1|Subject,
data=subset(D1,age!=14), method="ML")
themod<-stepAIC(lmemod,dir="both")
summary(themod)
prs=predict(themod,newdata=subset(D1,age==14))
obs<-subset(D1,age==14)$distance
print(mean(obs-prs))
} )
}

but the error message still reads:

PredRes(Orthodont)

Start:  AIC=345.12
distance ~ age * Sex

Error in subset(D1, age != 14) : object "D1" not found

Does this mean that the only option for making a function of this type
work is to use the "<<-" operator?
--
Regards
Jorunn



2008/5/9 Prof Brian Ripley <[EMAIL PROTECTED]>:

It's a known scoping issue in lme -- you are doing this from a function.
 Make sure your dataset is visible -- e.g. use with().



 On Fri, 9 May 2008, Jorunn Slagstad wrote:

Dear R-help

I'm working on a large dataset which I have divided into 20 subsets based

on similar features. Each subset consists of observations from different
locations and I wish to use the location as a random effect.

For each group I want to select regressors by a stepwise procedure and

include a random effect on the intercept. I use stepAIC() and lme(). (The
lmer()-function doesn't work with the stepAIC()-function.)


Since I have many groups, and I wish to do the same thing for each group,

I have constructed a function which takes the dataset as input variable and
gives a prediction result (here mean absolute error) as output.


This is an example using the Orthodont dataset:

library(MASS)
library(nlme)
PredRes<-function(D1)
{
lmemod=lme(distance~age*Sex, random=~1|Subject,

data=subset(D1,age!=14),method="ML")

themod=stepAIC(lmemod,dir="both")
prs=predict(themod,newdata=subset(D1,age==14))
obs<-subset(D1,age==14)$distance
print(mean(obs-prs))
}

Using this function with D1=Orthodont gives:

PredRes(Orthodont)

Start:  AIC=345.12
distance ~ age * Sex

Error in subset(D1, age != 14) : object "D1" not found

The code works when I take Orthodont in directly:

lmemod=lme(distance~age*Sex, random=~1|Subject,

data=subset(Orthodont,age!=14),method="ML")

themod=stepAIC(lmemod,dir="both")

Start:  AIC=345.12
distance ~ age * Sex

        Df    AIC
- age:Sex  1 344.49
<none>       345.12

Step:  AIC=344.49
distance ~ age + Sex

        Df    AIC
<none>       344.49
+ age:Sex  1 345.12
- Sex      1 348.70
- age      1 371.77

prs=predict(themod,newdata=subset(Orthodont,age==14))
obs<-subset(Orthodont,age==14)$distance
print(mean(obs-prs))

[1] 0.2962963

How can I make this code work with dataset av input variable in a

function?


I'm using R version:

Version:
platform = x86_64-unknown-linux-gnu
arch = x86_64
os = linux-gnu
system = x86_64, linux-gnu
status =
major = 2
minor = 6.0
year = 2007
month = 10
day = 03
svn rev = 43063
language = R
version.string = R version 2.6.0 (2007-10-03)

Locale:

LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C


Search Path:
.GlobalEnv, package:MASS, package:nlme, package:stats, package:graphics,

package:grDevices, package:utils, package:datasets, package:methods,
Autoloads, package:base


By the way the R version 2.7.0 Patched (2008-05-08 r45647) gives the same

error message.


--
Regards
Jorunn Slagstad

______________________________________________
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.


 --
 Brian D. Ripley,                  [EMAIL PROTECTED]
 Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
 University of Oxford,             Tel:  +44 1865 272861 (self)
 1 South Parks Road,                     +44 1865 272866 (PA)
 Oxford OX1 3TG, UK                Fax:  +44 1865 272595



 ______________________________________________
 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.


--
Brian D. Ripley,                  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

______________________________________________
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] How can one make stepAIC and lme

Reply via email to