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I've built a large function which calls numerous gbm functions in a big loop. All I'm trying to do is increase the thickness of the tickmarks in rug() which is called by gbm.plot.

I was hoping to use (e.g.)

body(gbm.plot)[[24]][[4]][[3]][[3]][[3]][[3]][[2]]$ylab <- "change value"

From this page's examples, which I've used successfully elsewhere, but the section in question in gbm.plot is in an IF statement, so as.list doesn't nicely recurse the lines (because arguably it's all one huge long line). You can get to them by just manually [[trying]][[successive]][[combinations]] until you get to the right place, but since I'm trying to insert a piece of code , lwd=6 into a bracketed statement, rather than assigning a value to a named subobject, I'm not sure how to get trace to do this.

?trace says:

When the at argument is supplied, it can be a vector of integers referring to the substeps of the body of the function (this only works if the body of the function is enclosed in { ...}. In this case tracer is not called on entry, but instead just before evaluating each of the steps listed in at. (Hint: you don't want to try to count the steps in the printed version of a function; instead, look at as.list(body(f)) to get the numbers associated with the steps in function f.)

The at argument can also be a list of integer vectors. In this case, each vector refers to a step nested within another step of the function. For example, at = list(c(3,4)) will call the tracer just before the fourth step of the third step of the function

So I tried pasting the whole line with the lwd bit added in, hoping that it would overwrite it with the small addition:

trace (gbm.plot, quote(rug(quantile(data[, gbm.call$gbm.x[variable.no]], probs = seq(0, 1, 0.1), na.rm = TRUE),lwd=6)), at=c(22,4,7,3,3,3,2))

...as well as putting objects in & out of {brackets}, all to no avail. Does anyone know either the correct way of using trace for this, or can suggest a better way? Thanks

p.s. it needs to be done automatically with coding so users can load the function which will load the vanilla gbm functions from CRAN and then make tweaks as required.

EDIT: found a workaround. But generalisable question: how can one insert elements into an IF statemented part of a function? e.g. From

rug(quantile(data[, gbm.call$gbm.x[variable.no]], probs=seq(0, 1, 0.1), na.rm=TRUE))

to

rug(quantile(data[, gbm.call$gbm.x[variable.no]], probs=seq(0, 1, 0.1), na.rm=TRUE),lwd=6)
dez93_2000
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  • I'm a bit confused by exactly what you're trying to accomplish. First, where exactly does the `gbm.plot` function come from? Can you make it clear what the before and after should be? – MrFlick Sep 02 '14 at 18:24
  • What package is this? And are you sure you can't pass `lwd` by means of the ellipsis arguments? – Carl Witthoft Sep 02 '14 at 18:37
  • Sorry gents, I figured out I didn't need to do so as one can alter those elements with specific calls from gmb.plot (which is from dismo or gbm package, I think you need both to run them) – dez93_2000 Sep 02 '14 at 19:35
  • Then either delete this question or post your own answer as a solution to close it out. – MrFlick Sep 03 '14 at 00:46
  • well my generalisable question, which I came here to ask, still remains, clarified in the edit: how can one automatically edit functions when the section to edit is within an IF? – dez93_2000 Sep 03 '14 at 01:17
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    The answer is: don't. If you want to modify a function, either write your own version or write a wrapper function which modifies the inputs to force the function to do what you want. – Carl Witthoft Sep 03 '14 at 11:49
  • Thanks Carl. So is it legit practice to copy the entirety of someone's function so as to rerun it, slightly changed, within your own function? – dez93_2000 Sep 03 '14 at 17:39

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