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
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--
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
______________________________________________
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