Re: [Rd] SEXPs and slots

From: Patrick Leyshock <pleyshock_at_gmail.com>
Date: Mon, 15 Nov 2010 12:07:05 -0800

Thanks Martin and Hadley, this is very helpful.

I should also add that I'm constantly reading the source code, but sometimes a response like this one can eliminate many, many hours of puzzlement. Much appreciated.

Patrick

On Mon, Nov 15, 2010 at 10:01 AM, Martin Morgan <mtmorgan_at_fhcrc.org> wrote:

> On 11/15/2010 07:45 AM, Patrick Leyshock wrote:
> > Very helpful, thank you.
> >
> > A couple other questions, please:
> >
> > 1. I've got a function written in C, named "my_c_function". In my R
> > code I call this function, passing to it an INTSXP and a STRSXP,
> > respectively:
> >
> > result <- .Call("my_c_function", int_vector, str_vector)
> >
> > The prototype of "my_c_function" is:
> >
> > SEXP my_c_function(SEXP int_vec, SEXP str_vec);
> >
> > Within my_c_function I am able to extract the values within the integer
> > vector, e.g. I can grab the first value with these lines of code:
> >
> > int extracted_value;
> > extracted_value = *INTEGER(int_vec);
> >
> > What I cannot figure out how to do is extract the value from the
> > STRSXP. I'm assuming that I can create a pointer to a character array,
> > then malloc enough memory to hold the value. Is there an analogous
> > operation on "INTEGER" for STRSXPs?
>
> STRING_ELT(str_vec, 0)
>
> gets the 0th component of str_vec, which is a CHARSXP, i.e., an SEXP for
> a character string. The char* can be retrieved with CHAR, so the usual
> paradigm is
>
> const char *x = CHAR(STRING_ELT(str_vec, 0));
>
> note the const-ness of the char* -- it's not mutable, because R is
> managing char * memory.
>
> The converse action, of assigning to an element, is
>
> SET_STRING_ELT(str_vec, 0, mkChar("foo"));
>
> mkChar() is creating a copy (if necessary) of "foo", managing it, and
> returning a CHARSXP. Working through protection (which will likely be
> your next obstacle ;) in this last example is a good exercise.
>
> There is a parallel operation VECTOR_ELT / SET_VECTOR_ELT for lists.

>
> > 2. Any good references/resources for developing R? Nearly all the
> > documents I've found are for programming R as a user, not as a
> > developer. I have copies of the documentation, which are very helpful,
> > but it'd be helpful to have additional resources to fill in their gaps.
>
> Chambers, 2008, Software for Data Analysis: Programming with R chapters
> 11 & 12,
>
> Gentleman, 2008, R Programming for Bioinformatics chapter 6
>
> might be helpful, but by the time they arrive you might find that you're
> most of the way through the material covered...
>
> I guess my opinion is that Rcpp would not be useful for understanding
> R's C layer, whatever its merits for 'getting the job done'.
>
> Martin
>
> >
> > Thank you,
> >
> > Patrick
> >
> >
> > On Fri, Nov 12, 2010 at 4:36 PM, Martin Morgan <mtmorgan_at_fhcrc.org
> > <mailto:mtmorgan_at_fhcrc.org>> wrote:
> >
> > On 11/12/2010 02:31 PM, Patrick Leyshock wrote:
> > > Hello,
> > >
> > > I've created this class:
> > >
> > > setClass("example",
> > > representation (
> > > size = "numeric",
> > > id = "character"
> > > )
> > > )
> > >
> > > Suppose I create a new instance of this class:
> > >
> > >> x <- new("example", 4, "id_value")
> > >
> > > This creates an S4 object with two slots. Am I correct in
> > thinking that
> > > slots are "filled" by SEXPs?
> >
> > Hi Patrick --
> >
> > If I
> >
> > > eg = new("example", size=4, id="id_value")
> >
> > (note the named arguments) and take a peak at the str'ucture of eg,
> > I see
> >
> > > str(eg)
> > Formal class 'example' [package ".GlobalEnv"] with 2 slots
> > ..@ size: num 4
> > ..@ id : chr "id_value"
> >
> > so the @size slot is a numeric vector of length 1 containing the
> value
> > 4. One doesn't really have to know the detailed representation, but
> one
> > can find out from
> >
> > > .Internal(inspect(eg))
> > @df70e48 25 S4SXP g0c0 [OBJ,NAM(2),gp=0x10,ATT]
> > ATTRIB:
> > @df70ef0 02 LISTSXP g0c0 []
> > TAG: @769258 01 SYMSXP g1c0 [MARK] "size"
> > @c0f6db8 14 REALSXP g0c1 [NAM(2)] (len=1, tl=0) 4
> > TAG: @15b0228 01 SYMSXP g1c0 [MARK,NAM(2)] "id"
> > @c0f6178 16 STRSXP g0c1 [NAM(2)] (len=1, tl=0)
> > @12341c80 09 CHARSXP g0c2 [gp=0x20] "id_value"
> > TAG: @607ce8 01 SYMSXP g1c0 [MARK,NAM(2),gp=0x4000] "class"
> > @c0f6d58 16 STRSXP g0c1 [NAM(2),ATT] (len=1, tl=0)
> > @96ed08 09 CHARSXP g1c1 [MARK,gp=0x21] "example"
> > ATTRIB:
> > @df70fd0 02 LISTSXP g0c0 []
> > TAG: @624f70 01 SYMSXP g1c0 [MARK,NAM(2)] "package"
> > @c0f6d88 16 STRSXP g0c1 [NAM(2)] (len=1, tl=0)
> > @67f5e0 09 CHARSXP g1c2 [MARK,gp=0x21,ATT] ".GlobalEnv"
> >
> > that the 'eg' object is an S4SXP with an attribute that is a LISTSXP.
> > The LISTSXP has elements that are tagged with SYMSXP representing the
> > slot name, and values that are REALSXP (for 'size') or STRSXP (for
> > 'id'). The LISTSXP attribute itself has an attribute, which contains
> > information about the package where the class is defined. With these
> > hints one can see through the S4 interface to the underlying
> > implementation
> >
> > > attributes(eg)
> > $size
> > [1] 4
> >
> > $id
> > [1] "id_value"
> >
> > $class
> > [1] "example"
> > attr(,"package")
> > [1] ".GlobalEnv"
> >
> > But probably you have a specific goal in mind, and this is too much
> > information...
> >
> > Martin
> >
> > >
> > > Thanks, Patrick
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-devel_at_r-project.org <mailto:R-devel_at_r-project.org> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> > --
> > Computational Biology
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
> >
> >
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

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