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Jacob Wegelin

2008-Jul-17 20:54 UTC

[R] nested calls, variable scope

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:
> myfnfunction(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:> myfnfunction(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
jwegelin at vcu.edu 
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

Jacob Wegelin

2008-Jul-17 20:57 UTC

head link

[R] nested calls, variable scope

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:
> myfnfunction(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:> myfnfunction(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
jwegelin@vcu.edu
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

	[[alternative HTML version deleted]]

Jacob Wegelin

2008-Aug-01 17:31 UTC

head link

[R] nested calls, variable scope

Dear Bert:

Thank you for your reply. But the "eval.parent" function does not seem
to
solve the problem. Below is the code. I have tried running it with

eval.parent(myknot)

as well as with integers from 0 through 4, as in

eval.parent(myknot, 4)

Each attempt produces the same error:

Error in eval(expr, p) : object "myknot" not found

I'm replying to the list in case someone can explain this.

Jake

fnJunk <-function(myknot=44 , myMER ) {
#  Fit lmer (mer, lme4) models for WSER project, using spline (ns), and plot
them for newdata.
   library(lme4)
   library(splines)

if(missing(myMER)){
   cat("myknot=", myknot)
   cat("fit another MER??")
   readline()
   myMER<-lmer(formula=Finished ~ Sex01 +
   ns(DAT$Age, knots= eval.parent(myknot, 0) ) +
   MinCC + PzC + (1 | NAME ) + (1 | Year), data=(DAT),
family="binomial")
   }
# more stuff below here
}

On Thu, Jul 17, 2008 at 6:19 PM, Bert Gunter <gunter.berton@gene.com>
wrote:
> As you may be aware, this is a case of FAQ for R 3.31, lexicographic
> scoping. It **can** be tricky, especially in a complex situation like
> yours.
> Typically eval() and/or substitute are what you need in such situations, to
> force evaluation in the appropriate environment. So try changing your
>
> ns(Dat$Age,knots=myknot)
>
> ## to
>
> ns(Dat$Age,knots=eval.parent(myknot))
>
> If that doesn't work, await wiser advice.
>
> Cheers,
>
> Bert Gunter
> Genentech
>
> -----Original Message-----
> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> On
> Behalf Of Jacob Wegelin
> Sent: Thursday, July 17, 2008 1:58 PM
> To: r-help@stat.math.ethz.ch
> Subject: [R] nested calls, variable scope
>
> 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
> jwegelin@vcu.edu
> 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
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>
>
	[[alternative HTML version deleted]]

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