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