[R] finding global variables in a function containing formulae

[William Dunlap]

findGlobals must be explicitly ignoring calls to the ~ function.
You could poke through the source code of codetools and find
where this is happening.

Or, if you have the source code for the package you are investigating,
use sed to change all "~" to "%TILDE%" and then use findGlobals on
the resulting source code.  The messages will be a bit garbled but
should give you a start.  E.g., compare the following two, in which y
is defined in the function but x is not:
   > findGlobals(function(y)lm(y~x))
  [1] "~"  "lm"
  > findGlobals(function(y)lm(y %TILDE% x))
  [1] "lm"      "%TILDE%" "x"

You will get false alarms, since in a call like lm(y~x+z, data=dat) findGlobals
cannot know if dat includes columns called 'x', 'y', and 'z' and the above
approach errs on the side of reporting the potential problem.

You could use code in codetools to analyze S code instead of source code
to globally replace all calls to "~" with calls to "%TILDE%" but that is more
work than using sed on the source code. 

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
> Of Hafen, Ryan P
> Sent: Friday, November 02, 2012 4:28 PM
> To: Bert Gunter
> Cc: r-help at r-project.org
> Subject: Re: [R] finding global variables in a function containing formulae
> 
> Thanks.  That works if I a have the formula expression handy.  But suppose
> I want a function, findGlobalVars() that takes a function as an argument
> and finds globals in it, where I have absolutely no idea what is in the
> supplied function:
> 
> findGlobalVars <- function(f) {
>    require(codetools)
>    findGlobals(f, merge=FALSE)$variables
> }
> 
> 
> findGlobalVars(plotFn1)
> 
> I would like findGlobalVars() to be able to find variables in formulae
> that might be present in f.
> 
> 
> 
> 
> On 11/1/12 1:19 PM, "Bert Gunter" <gunter.berton at gene.com> wrote:
> 
> >Does
> >
> >?all.vars
> >##as in
> >> all.vars(y~x)
> >[1] "y" "x"
> >
> >help?
> >
> >-- Bert
> >
> >On Thu, Nov 1, 2012 at 11:04 AM, Hafen, Ryan P <Ryan.Hafen at pnnl.gov>
> >wrote:
> >> I need to find all global variables being used in a function and
> >>findGlobals() in the codetools package works quite nicely.  However, I
> >>am not able to find variables that are used in formulae.  Simply
> >>avoiding formulae in functions is not an option because I do not have
> >>control over what functions this will be applied to.
> >>
> >> Here is an example to illustrate:
> >>
> >> library(codetools)
> >>
> >> xGlobal <- rnorm(10)
> >> yGlobal <- rnorm(10)
> >>
> >> plotFn1 <- function() {
> >>    plot(yGlobal ~ xGlobal)
> >> }
> >>
> >> plotFn2 <- function() {
> >>    y <- yGlobal
> >>    x <- xGlobal
> >>    plot(y ~ x)
> >> }
> >>
> >> plotFn3 <- function() {
> >>    plot(xGlobal, yGlobal)
> >> }
> >>
> >> findGlobals(plotFn1, merge=FALSE)$variables
> >> # character(0)
> >> findGlobals(plotFn2, merge=FALSE)$variables
> >> # [1] "xGlobal" "yGlobal"
> >> findGlobals(plotFn3, merge=FALSE)$variables
> >> # [1] "xGlobal" "yGlobal"
> >>
> >> I would like to find that plotFn1 also uses globals xGlobal and
> >>yGlobal.  Any suggestions on how I might do this?
> >>
> >> ______________________________________________
> >> R-help at 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.
> >
> >
> >
> >--
> >
> >Bert Gunter
> >Genentech Nonclinical Biostatistics
> >
> >Internal Contact Info:
> >Phone: 467-7374
> >Website:
> >http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-bio
> >statistics/pdb-ncb-home.htm
> 
> ______________________________________________
> R-help at 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.