Modifying an R package function for current R session; assignInNamespace not behaving like fixInNamespace?

Question

I would like to be able to modify a hidden function inside an R package in an "automated" way, like using fixInNamespace, but where I can write the code in advance, and not in an "edit" window which fixInNamespace does. I think assignInNamespace could do the job, but currently it's not working. Here's an example of the problem.

require(quantmod)

getSymbols("AAPL")

chartSeries(AAPL)  # Works fine up to here.

Now say I want to yaxis ticks to be drawn on the left side of the plot, instead of the right. This can be done by modifying the source code in the quantmod package. The relevant code for modifying the plot layout is in a hidden quantmod function called chartSeries.chob.

This could be done by doing this:

fixInNamespace("chartSeries.chob", ns = "quantmod")

and in the edit window, manually modify line 117 from axis(4) to axis(2), click OK, and again run chartSeries(AAPL) (now the y axis labels will plot on the left side of the plot). Everything is good, the plot is generated as expected, no problems.

But ... now suppose I want to modify chartSeries.chob in advance (in an automated way), presumably by sourcing a modified version of the chartSeries.chob function, without using the edit window. I might want modify dozens of lines in the function for example, and opening the edit window each time for a new R session is not practical.

How can I do this?

Right now I am doing this, which is not working:

assignInNamespace("chartSeries.chob", value = chartSeries.chob2, ns = "quantmod")

where I source from the console a full copy of chartSeries.chob with the modified code on line 117.

chartSeries.chob2 <- function (x) 
{
old.par <- par(c("pty", "mar", "xpd", "bg", "xaxs", "las", 
                   "col.axis", "fg"))
  on.exit(par(old.par))
....

[Edit On 117:] axis(2)
...
}

When I run from the console:

chartSeries(AAPL)

or

quantmod:::chartSeries(AAPL)

I get errors -- the calls to other functions in quantmod from within the chartSeries.chob function are not found, presumably because the edited chartSeries.chob function is not in the quantmod namespace?

I notice that when typing quantmod:::chartSeries.chob from the console after the assignInNamespace command, there is no environment: namespace:quantmod at the end of the function definition.

But if I do the fixInNamespace modification approach, when I type quantmod:::chartSeries.chob, then I do see environment: namespace:quantmod appended to the end of the function definition.

Greg Snow Greg Snow · Accepted Answer · 2014-04-24T21:43:25

Since fixInNamespace calls assignInNamespace you should be able to get it to work, the problem is probably that the environment is not the same and possibly some other attributes. If you change those to match then I would expect it to work better, possibly using code like:

tmpfun <- get("chartSeries.chob", envir = asNamespace("quantmod"))
environment(chartSeries.chob2) <- environment(tmpfun)
attributes(chartSeries.chob2) <- attributes(tmpfun)  # don't know if this is really needed
assignInNamespace("chartSeries.chob", chartseries.chob2, ns="quantmod")

Another option for some changes would be to use the trace function. This would make temporary changes and would be fine for inserting code, but I don't know if it would be reasonable for deleting commands or modifying in place (specifying an editor that changed the code rather than letting you change it might make this possible).

Modifying an R package function for current R session; assignInNamespace not behaving like fixInNamespace?

1 Answers