[R] Change R options only inside a package

Duncan Murdoch murdoch.duncan at gmail.com
Mon Jul 15 13:30:25 CEST 2013

On 13-07-15 5:27 AM, Helios de Rosario wrote:
> Hi,
> What should I do if I want to use "non-default" R-options for the
> functions inside a package, but not affect the options of the rest of
> the session? Specifically, I'm thinking of using "sum contrasts" instead
> of the default, in functions like "lm", etc. when they are called by
> other functions in a package.
> I can think on the following solutions:
> 1) Quick-and-dirty solution: use options() to modify the default
> contrasts before calling my functions. If I don't want to affect the
> rest of the session, I should reset the options before returning,
> preferably with exception handling to avoid that the options are not
> reset if my function fails.
> 2) Complex-but-tidier solution: Use function-specific arguments to tell
> the contrasts of the factors that I'm using. E.g., I should create a
> named list of contrasts and pass it as the argument "contrasts" every
> time I call "lm":
> mod <- lm(form, contrasts=list(factor1="contr.sum",
> factor2="contr.sum"))
> 3) Encapsulated solution: create package-specific (unexported) versions
> of "lm" and other functions, that already implement #2, e.g.:
> lm <- function(...)
> {
> # Code that examines dots, to get the factors of the model, and create
> the list of contrasts
> # Then call the stats lm (be sure that dots did not already include a
> "contrasts" element).
> stats::lm(..., contrasts = list.of.factors.with.sum.contrasts)
> }
> I don't like #1, because changing the options back and forth may be
> error-prone and lead to unexpected behaviour.
> #2 is better, but prone to programmer errors: I should be careful of
> not forgetting to set the "contrasts" argument every time I call "lm".
> I prefer #3, because it avoids the disadvantages of the previous
> solutions, but perhaps it is overkill, hence my question: Is there a
> "clean" way of setting the R-session options in such a way that they
> only affect the functions and data inside a package?

I'd recommend that in your own functions that need this, you put this at 
the beginning:

  saveOpts <- options(contrasts = c("contr.sum", "contr.sum"))

This means that the options will be changed just for the duration of the 
call.  If there are situations where users might not want this new 
default, make the new value a default of a function argument.

Duncan Murdoch

> Thanks and best regards
> Helios De Rosario
> Universidad Politécnica de Valencia • Edificio 9C
> Camino de Vera s/n • 46022 VALENCIA (ESPAÑA)
> Tel. +34 96 387 91 60 • Fax +34 96 387 91 69
> www.ibv.org
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