Subset views in R

August 28, 2010
By

(This article was first published on Struggling Through Problems » R, and kindly contributed to R-bloggers)

I don’t know how to do this in R. So let me just say why I can’t.

I wanted something akin to Boost‘s sub-matrix views, where you can have indexes map back to the original matrix, so you don’t create a new object.

Sounds straightforward, just overload ‘[[' to subtract the offset and check the length. Alas, no dice. R zealously copies objects to the point this is not (as far as I know, which isn't much) possible.

To demonstrate, the following function executes and times expressions operating on a vector called "M".

time.op = function(N, Exp) {
        Exp = parse(text=Exp)
        M = numeric(N)

        N.Trials = 10
        Times = numeric(N.Trials)

        for (II in 1:N.Trials) {
                Times[[II]] = system.time(eval(Exp))[['elapsed']]
        }

        mean(Times)
}

Like

> time.op(1e5, 'sqrt(M)')
[1] 0.0024

Then see, does the size of M affect the time of the operation?

time.test = function(Exp) {
        Ns = 10^(1:6)
        Times = sapply(Ns, time.op, Exp=Exp)

        data.frame(Ns, Times)
}
> time.test('sqrt(M)')
     Ns  Times
1 1e+01 0.0000
2 1e+02 0.0000
3 1e+03 0.0001
4 1e+04 0.0004
5 1e+05 0.0027
6 1e+06 0.0274

(obviously)

And here's why we know it's copying:

> time.test('list(M)')
     Ns  Times
1 1e+01 0.0001
2 1e+02 0.0001
3 1e+03 0.0002
4 1e+04 0.0000
5 1e+05 0.0004
6 1e+06 0.0086

Or with attributes

> time.test('attr(M, "name") = "mike"')
     Ns  Times
1 1e+01 0.0000
2 1e+02 0.0000
3 1e+03 0.0000
4 1e+04 0.0000
5 1e+05 0.0006
6 1e+06 0.0081

Good luck making a subset without copying!

And here's the relevant parts of the R code.

Making a list (main/builtin.c)

    for (i = 0; i < n; i++) {
                if (TAG(args) != R_NilValue) {
                    SET_STRING_ELT(names, i, PRINTNAME(TAG(args)));
                    havenames = 1;
                }
                else {
                    SET_STRING_ELT(names, i, R_BlankString);
                }
                if (NAMED(CAR(args)))
                    SET_VECTOR_ELT(list, i, duplicate(CAR(args)));
                else
                    SET_VECTOR_ELT(list, i, CAR(args));
                args = CDR(args);
            }
            if (havenames) {
                setAttrib(list, R_NamesSymbol, names);
    }

Note the repeated calls to "duplicate".

And yes, duplicate does copy, and it is deep (main/duplicate.c):

case VECSXP:
        n = LENGTH(s);
        PROTECT(s);
        PROTECT(t = allocVector(TYPEOF(s), n));
        for(i = 0 ; i < n ; i++)
            SET_VECTOR_ELT(t, i, duplicate1(VECTOR_ELT(s, i)));
        DUPLICATE_ATTRIB(t, s);
        SET_TRUELENGTH(t, TRUELENGTH(s));
        UNPROTECT(2);
        break;

To leave a comment for the author, please follow the link and comment on his blog: Struggling Through Problems » R.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Tags:

Comments are closed.