R help - Jul 2006 - How do I modify an exported function in a locked environment?

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.

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

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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.

Please do not post to multiple lists: I have removed R-help.

On Thu, 20 Jul 2006, Steven McKinney wrote:
> Running R.app on Mac OS X 10.4
> 
> I am trying to learn how to modify functions
> in a locked environment.
This is deliberately hard.
> 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?
You need to unlock the binding, then assign in package:zoo.
Something like

unlockBinding("rollmean.default",
as.environment("package:zoo"))
assign("rollmean.default", zoo:::rollmean.default,
pos="package:zoo")

However, it is not usual to export methods, and that is why this case is 
particularly hard.
> 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?
Many would say it was not proper 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.
> Any guidance appreciated.
You may not like the guidance ....

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

As others have mentioned its not really a good idea
to modify the namespace of a package and writing
a wrapper as Duncan suggested is much preferable.

An intermediate approach that
is not as good as the wrapper but better than modifying
the namespace is to copy the objects of interest
to your workspace, change their environments
appropriately and then modify their functionality:

library(zoo)

# copy objects of interest and set their environment

rollmean <- zoo:::rollmean
environment(rollmean) <- .GlobalEnv

rollmean.zoo <- zoo:::rollmean.zoo
environment(rollmean.zoo) <- .GlobalEnv

rollmean.default <- zoo:::rollmean.default
environment(rollmean.default) <- .GlobalEnv

# modify functionality

rollmean.default0 <- rollmean.default
rollmean.default <- function(x, ...) 100 * rollmean.default0(x, ...)

# test

rollmean(1:5, 3) # 100* used
rollmean(zoo(1:5), 3)  # 100* used


On 7/20/06, Steven McKinney <smckinney at bccrc.ca>
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.
>
> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>