On 06/12/2012 2:28 PM, Jacob Wegelin wrote:
I want to fit a series of lme() regression models that differ only in the
degrees of freedom of a ns() spline. I want to use a wrapper function to do
this. The models will be of the form
y ~ ns(x, df=splineDF)
where splineDF is passed as an argument to a wrapper function.
This works fine if the regression function is lm(). But with lme(),
I get an error. fitfunction() below demonstrates this.
Why?
Presumably this is a bug in nlme. Formulas have associated
environments. In your example, that would be the local frame of the
fitfunction, and splineDF lives there. It looks as though lme is not
looking in the formula environment for the splineDF value.
Another workaround besides the one you found is to use substitute() to
put the value of splineDF into the formula, i.e.
fitfunction<-function(splineDF=1) {
junk$splineDF <- splineDF
thislm<-lm( y ~ ns(x, df=splineDF), data= junk)
thislm
cat("finished thislm\n")
fixed <- eval(substitute( y ~ ns(x, df=splineDF),
list(splineDF=splineDF)))
thislme<-lme(
fixed= fixed
, random= ~ 1 | idvar
, data= junk)
thislme
}
It's not much better than your kludge in this example, but it might be
more convenient if you want to work with different formulas.
Duncan Murdoch
KLUDGEfit() below provides a clumsy solution. It turns the lme()
command, along with the appropriate value of splineDF, into a text
string and then uses eval(parse(text=mystring)). But is there not a
more elegant solution?
set.seed(5)
junk<-data.frame(x=rnorm(100))
junk$y<-junk$x + rnorm(nrow(junk))
junk$idvar<- factor(sample(LETTERS[1:10], size=nrow(junk), replace=TRUE))
library("nlme")
library(splines)
fitfunction<-function(splineDF=1) {
thislm<-lm( y ~ ns(x, df=splineDF), data= junk)
thislm
cat("finished thislm\n")
thislme<-lme(
fixed= y ~ ns(x, df=splineDF)
, random= ~ 1 | idvar
, data= junk)
thislme
}
fitfunction()
KLUDGEfit<-function(splineDF=2) {
thislm<-lm( y ~ ns(x, df=splineDF), data= junk)
thislm
cat("finished thislm\n")
mystring<-paste(
"thislme<-lme( fixed= y ~ ns(x, df="
, splineDF
, "), random= ~ 1 | idvar , data= junk)"
, sep="")
eval(parse(text=mystring))
thislme
}
KLUDGEfit()
Thanks for any insight
Jacob A. Wegelin
Assistant Professor
Department of Biostatistics
Virginia Commonwealth University
830 E. Main St., Seventh Floor
P. O. Box 980032
Richmond VA 23298-0032
U.S.A.
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and provide commented, minimal, self-contained, reproducible code.
