[R] How do I modify an exported function in a locked environment?

[Duncan Murdoch]

On 7/20/2006 3:49 PM, Steven McKinney wrote:
> 
> Running R.app on Mac OS X 10.4
> 
>> version
>                _                         
> platform       powerpc-apple-darwin8.6.0 
> arch           powerpc                   
> os             darwin8.6.0               
> system         powerpc, darwin8.6.0      
> status                                   
> major          2                         
> minor          3.1                       
> year           2006                      
> month          06                        
> day            01                        
> svn rev        38247                     
> language       R                         
> version.string Version 2.3.1 (2006-06-01)
>> 
> 
> 
> I am trying to learn how to modify functions
> in a locked environment.
> 
> For an example, suppose I'm using the package "zoo".
> 
> zoo contains function "rollmean.default"
> 
>> rollmean.default
> function (x, k, na.pad = FALSE, align = c("center", "left", "right"), 
>     ...) 
> {
>     x <- unclass(x)
>     n <- length(x)
>     y <- x[k:n] - x[c(1, 1:(n - k))]
>     y[1] <- sum(x[1:k])
>     rval <- cumsum(y)/k
>     if (na.pad) {
>         rval <- switch(match.arg(align), left = {
>             c(rval, rep(NA, k - 1))
>         }, center = {
>             c(rep(NA, floor((k - 1)/2)), rval, rep(NA, ceiling((k - 
>                 1)/2)))
>         }, right = {
>             c(rep(NA, k - 1), rval)
>         })
>     }
>     return(rval)
> }
> <environment: namespace:zoo>
> 
> Suppose for whatever reason I want output to be
> in percent, so I'd like to modify the result to be
> rval <- 100 * cumsum(y)/k
> 
> I cannot just copy the function and change it, as the namespace
> mechanism ensures the rollmean.default in 'zoo' continues to be used.
> 
> If I use
> fixInNamespace("rollmean.default", ns = "zoo")
> I can edit the rval <- cumsum(y)/k line to read
> rval <- 100 * cumsum(y)/k
> save the file and exit the R.app GUI editor.
> 
> But this does not update the exported copy of the
> function (the documentation for fixInNamespace says
> this is the case) - how do I accomplish this last step?
> 
> If I list the function after editing, I see the original
> copy.  But if I reinvoke the editor via fixInNamespace(),
> I do see my modification.
> Where is my copy residing?  How do I push it out
> to replace the exported copy?
> 
> Is this the proper way to modify a package function?
> Are there other ways?  I've searched webpages, R news,
> help files and have been unable to find out how to
> get this process fully completed.

You could modify the zoo source and recompile it, or you could write 
your own function that calls the one in zoo and modifies the result.

I don't think you should modify zoo without really careful thought:  you 
should assume that the package has been tested the way it was written, 
and may give incorrect results if you go in and change one function 
without considering everything else in the package.

So I'd recommend writing a wrapper, e.g.

myrollmean <- function(x, k, na.pad = FALSE, align = c("center", "left", 
"right"), ...) {
   result <- rollmean(x, k, na.pad, align, ...)
   return(result*100)
}

 >     ...
Duncan Murdoch
> 
> Any guidance appreciated.
> 
> 
> Steven McKinney
> 
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
> 
> email: smckinney at bccrc.ca
> 
> tel: 604-675-8000 x7561
> 
> BCCRC
> Molecular Oncology
> 675 West 10th Ave, Floor 4
> Vancouver B.C. 
> V5Z 1L3
> Canada
> 
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