[R] nested calls, variable scope

[Jacob Wegelin]

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 this?

# The call to ns works at the command line:

junk<-ns(DAT$Age, knots=74)

# The call to lmer works at the command line, with the call to ns nested within 
it:

junk2<-lmer(formula=Finished ~ Sex01 + ns(DAT$Age, knots= 74 ) + MinCC + PzC + (1 | NAME 
) + (1 | Year), data=myDATonly, family="binomial")

But now I want to do this within a function such as the following:

myfn
function(myknot=74) {
        library(lme4)
        library(splines)
        cat("myknot=", myknot, "\n")
        myMER<-lmer(formula=Finished ~ Sex01 + ns(DAT$Age, knots= myknot) + MinCC + PzC + 
(1 | NAME ) + (1 | Year), data=myDATonly, family="binomial")
}

myfn(74)
myknot= 74 
Error in ns(DAT$Age, knots = myknot) : object "myknot" not found

# The bad way to do it: revise myfn to make myknot a global variable:
myfn
function(myknot=74) {
        library(lme4)
        library(splines)
        cat("myknot=", myknot, "\n")
        myknot<<-myknot
        myMER<-lmer(formula=Finished ~ Sex01 + ns(DAT$Age, knots= myknot
) + MinCC + PzC + (1 | NAME ) + (1 | Year), data=myDATonly,
family="binomial")
}

z<-myfn(74)
myknot= 74

# Runs fine but puts a global variable into .GlobalEnv.


sessionInfo()
R version 2.6.2 (2008-02-08) 
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   stats     graphics  grDevices datasets  utils     methods
base

other attached packages:
[1] lme4_0.999375-13  Matrix_0.999375-9 lattice_0.17-6

loaded via a namespace (and not attached):
[1] boot_1.2-32 grid_2.6.2 


Thanks for any insight.

Jacob A. Wegelin
[EMAIL PROTECTED] 
Assistant Professor
Department of Biostatistics
Virginia Commonwealth University
730 East Broad Street Room 3006
P. O. Box 980032
Richmond VA 23298-0032
U.S.A. 
http://www.people.vcu.edu/~jwegelin

______________________________________________
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.