What Ways Are There to Edit a Function in R

What ways are there to edit a function in R?

Or take a look at the debugging function trace(). It is probably not exactly what you are looking for but it lets you play around with the changes and it has the nice feature that you can always go back to your original function with untrace().
trace() is part of the base package and comes with a nice and thorough help page.

Start by calling as.list (body(foo)) to see all the lines of your code.

as.list(body(foo))
[[1]]
`{`

[[2]]
line1 <- x

[[3]]
line2 <- 0

[[4]]
line3 <- line1 + line2

[[5]]
return(line3)

Then you simply define what to add to your function and where to place it by defining the arguments in trace().

trace (foo, quote(line2 <- 2), at=4)
foo (2)
[1] 4

I said in the beginning that trace() might not be exactly what you are looking for since you didn't really change your third line of code and instead simply reassigned the value to the object line2 in the following, inserted line of code. It gets clearer if you print out the code of your now traced function

body (foo)
{
    line1 <- x
    line2 <- 0
    {
        .doTrace(line2 <- 2, "step 4")
        line3 <- line1 + line2
    }
    return(line3)
}

Modify package function

I finally found a solution that should work in all situations!

environment(customGenomePlot) <- asNamespace('snapCGH')
assignInNamespace("genomePlot", customGenomePlot, ns = "snapCGH")

The call to environment() assures that the function will be able to call other hidden functions from the package.

The call to assignInNamespace() assures that other functions from the package will call your updated version of the function.

It is possible that in certain situation, you need only one of these, but in general you need both. I struggled to find this general solution, found many other which are not working in some cases, like this (need opposite order), or this (misses the second part), or this (throws the error "cannot add bindings to a locked environment").

Customize existing function in R

find the location in the function that you want to change

as.list(body(psych::polychoric))

Change the function

trace(psych::polychoric, quote(nvalues > 10), at=11)

Check to see that you changed what you want to change

trace(psych::polychoric, edit=TRUE)

Set the function back to original

untrace(psych::polychoric)

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Seems like fix may be easier for you to implement for this task

fix(polychoric)

opens a pane that you can change the code in - change and hit save.

This will make the function local to your global environment you can check this by looking at the original function trace(polychoric, edit = T) will show nvalues > 10, and trace(psych::polychoric, edit = T) will show nvalues > 8. The next time you reload psych you will be using the original function. Bit of a manual hack - but hopefully works for this one off situation.

How to edit a function with a specific environment defined in R

As you are just creating a new function in the GlobalEnvironment it doesn't know where to find functions that are not exported from the pacakge of the original function. You just need to tell it explicitly where to find them using the ::: operator. So e.g.

cv.glm2 <-
function (data, glmfit, cost = function(y, yhat) mean((y - yhat)^2), 
    K = n) 
{
    #  // Some other code here //  #

    #  Tell it which package the unexported  function resides in
    s <- boot:::sample0(rep(1L:K, f), n)
}

Editing a function from a package in R?

In the beginning of the package there is a line

data(sysdata, envir=environment())

See here: https://github.com/cran/referenceIntervals/tree/master/data/sysdata.rda

I suspect that "nonparRanks" is defined there as I don't see it defined anywhere else. So perhaps you could download that file, write your own function, then run that same line before running your function and it may work.

EDIT:
Download the file then run:

load("C:/sysdata.rda")

With your path to the file and then your function will work.

How to modify pre-existing function in local environment in R

If New is the new function copied from camtrapR then use

environment(New) <- asNamespace("camtrapR")

to ensure that the function calls in its body are looked up in the correct places.

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