R help - Nov 2012 - 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?

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-biostatistics/pdb-ncb-home.htm

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

On Thu, Nov 1, 2012 at 2:04 PM, 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?
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)

-- 
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GKX Group, GKX Associates Inc.
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