Re: [R] finding global variables in a function containing formulae
> -Original Message-
> From: William Dunlap
> Sent: Saturday, November 03, 2012 11:23 AM
> To: 'Hafen, Ryan P'; Bert Gunter
> Cc: r-help@r-project.org
> Subject: RE: [R] finding global variables in a function containing formulae
>
> findGlobals must be explicitly ignoring calls to the ~ function.
> You could poke through the source code of codetools and find
> where this is happening.
I looked through some old notes and found you could
disable the special handler for "~" by removing it from
the environment codetools:::collectUsageHandlers:
> findGlobals(function(y)lm(y~x)) # doesn't note 'x' as a global reference
[1] "~" "lm"
> tildeHandler <- codetools:::collectUsageHandlers[["~"]]
> remove("~", envir=codetools:::collectUsageHandlers)
> findGlobals(function(y)lm(y~x)) # notes 'x'
[1] "~" "lm" "x"
> # reinstall "~" handler to get original behavior
> # or detach("package:codetools", unload=TRUE) and reattach
> assign("~", tildeHandler, envir=codetools:::collectUsageHandlers)
> findGlobals(function(y)lm(y~x)) # does not note 'x'
[1] "~" "lm"
You still have the false alarm problem.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
>
> 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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> > Behalf
> > Of Hafen, Ryan P
> > Sent: Friday, November 02, 2012 4:28 PM
> > To: Bert Gunter
> > Cc: r-help@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" 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
> > >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)
> > >> }
>
Re: [R] finding global variables in a function containing formulae
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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf
> Of Hafen, Ryan P
> Sent: Friday, November 02, 2012 4:28 PM
> To: Bert Gunter
> Cc: r-help@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" 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
> >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)$variables
> >> # [1] "xGlobal" "yGlobal"
> >>
> >> I would like to find that plotFn1 also uses globals xGlobal and
> >>yGlobal. Any suggestions on how I might do this?
> >>
> >> __
> >> R-help@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >>http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> >--
> >
> >Bert Gunter
> >Genentech Nonclinical Biostatistics
> >
> >Internal Contact Info:
> >Phone: 467-7374
> >Website:
> >http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-bio
> >statistics/pdb-ncb-home.htm
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] finding global variables in a function containing formulae
On Thu, Nov 1, 2012 at 2:04 PM, Hafen, Ryan P wrote:
> I need to find all global variables being used in a function and
> findGlobals() in the codetools package works quite nicely. However, I am not
> able to find variables that are used in formulae. Simply avoiding formulae
> in functions is not an option because I do not have control over what
> functions this will be applied to.
>
> Here is an example to illustrate:
>
> library(codetools)
>
> xGlobal <- rnorm(10)
> yGlobal <- rnorm(10)
>
> plotFn1 <- function() {
>plot(yGlobal ~ xGlobal)
> }
>
> plotFn2 <- function() {
>y <- yGlobal
>x <- xGlobal
>plot(y ~ x)
> }
>
> plotFn3 <- function() {
>plot(xGlobal, yGlobal)
> }
>
> findGlobals(plotFn1, merge=FALSE)$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?
If this is only being applied to your own functions then we can have a
convention when writing them to help it in which we "declare" such
variables so that findGlobals can locate them:
plotFn1 <- function() {
xGlobal; yGlobal
plot(yGlobal ~ xGlobal)
}
findGlobals(plotFn1)
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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)$variables
}
findGlobalVars(plotFn1)
I would like findGlobalVars() to be able to find variables in formulae
that might be present in f.
On 11/1/12 1:19 PM, "Bert Gunter" wrote:
>Does
>
>?all.vars
>##as in
>> all.vars(y~x)
>[1] "y" "x"
>
>help?
>
>-- Bert
>
>On Thu, Nov 1, 2012 at 11:04 AM, Hafen, Ryan P
>wrote:
>> I need to find all global variables being used in a function and
>>findGlobals() in the codetools package works quite nicely. However, I
>>am not able to find variables that are used in formulae. Simply
>>avoiding formulae in functions is not an option because I do not have
>>control over what functions this will be applied to.
>>
>> Here is an example to illustrate:
>>
>> library(codetools)
>>
>> xGlobal <- rnorm(10)
>> yGlobal <- rnorm(10)
>>
>> plotFn1 <- function() {
>>plot(yGlobal ~ xGlobal)
>> }
>>
>> plotFn2 <- function() {
>>y <- yGlobal
>>x <- xGlobal
>>plot(y ~ x)
>> }
>>
>> plotFn3 <- function() {
>>plot(xGlobal, yGlobal)
>> }
>>
>> findGlobals(plotFn1, merge=FALSE)$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@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@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.
Re: [R] finding global variables in a function containing formulae
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 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)$variables
> # [1] "xGlobal" "yGlobal"
>
> I would like to find that plotFn1 also uses globals xGlobal and yGlobal. Any
> suggestions on how I might do this?
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] finding global variables in a function containing formulae
I need to find all global variables being used in a function and findGlobals()
in the codetools package works quite nicely. However, I am not able to find
variables that are used in formulae. Simply avoiding formulae in functions is
not an option because I do not have control over what functions this will be
applied to.
Here is an example to illustrate:
library(codetools)
xGlobal <- rnorm(10)
yGlobal <- rnorm(10)
plotFn1 <- function() {
plot(yGlobal ~ xGlobal)
}
plotFn2 <- function() {
y <- yGlobal
x <- xGlobal
plot(y ~ x)
}
plotFn3 <- function() {
plot(xGlobal, yGlobal)
}
findGlobals(plotFn1, merge=FALSE)$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@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.
