R extension in C, setting matrix row/column names

Question

I'm writing an R package that manipulates Matrices in C. Currently, the matrices returned to R have numbers for the row/column names. I would rather assign my own row/column names when modifying the object in C.

I've googled around for about an hour, but haven't found a good solution yet. The closest I've found is dimnames, but I want to name each column, not just the two dimensions. The matrices get larger than 4x4, below is just a small example of what I want to do.

The number of rows is 4^x where X is the length of the row name

Current
     [,1] [,2] [,3] [,4]
[1,] 0.20 0.00 0.00 0.80
[2,] 0.25 0.25 0.25 0.25
[3,] 0.25 0.25 0.25 0.25
[4,] 1.00 0.00 0.00 0.00
[5,] 0.20 0.00 0.00 0.80
[6,] 0.25 0.25 0.25 0.25
[7,] 0.25 0.25 0.25 0.25
[8,] 1.00 0.00 0.00 0.00
[9,] 0.20 0.00 0.00 0.80
[10,] 0.25 0.25 0.25 0.25
[11,] 0.25 0.25 0.25 0.25
[12,] 1.00 0.00 0.00 0.00
[13,] 0.20 0.00 0.00 0.80
[14,] 0.25 0.25 0.25 0.25
[15,] 0.25 0.25 0.25 0.25
[16,] 1.00 0.00 0.00 0.00

Desired
     [A] [C] [G] [T]
 [AA] 0.20 0.00 0.00 0.80
 [AC] 0.25 0.25 0.25 0.25
 [AG] 0.25 0.25 0.25 0.25
 [AT] 1.00 0.00 0.00 0.00
 [CA] 0.20 0.00 0.00 0.80
 [CC] 0.25 0.25 0.25 0.25
 [CG] 0.25 0.25 0.25 0.25
 [CT] 1.00 0.00 0.00 0.00
 [GA] 0.20 0.00 0.00 0.80
 [GC] 0.25 0.25 0.25 0.25
 [GG] 0.25 0.25 0.25 0.25
 [GT] 1.00 0.00 0.00 0.00
 [TA] 0.20 0.00 0.00 0.80
 [TC] 0.25 0.25 0.25 0.25
 [TG] 0.25 0.25 0.25 0.25
 [TT] 1.00 0.00 0.00 0.00

Answer 1

If you are open to C++ instead of C, then Rcpp can make this a little easier. We just create a list object with rows and column names as we would in R, and assign that to the dimnames attribute of the matrix object:

R> library(inline)                         # to compile, link, load the code here
R> src <- '
+   Rcpp::NumericMatrix x(2,2);
+   x.fill(42);                           // or more interesting values
+   // C++0x can assign a set of values to a vector, but we use older standard
+   Rcpp::CharacterVector rows(2); rows[0] = "aa"; rows[1] = "bb";
+   Rcpp::CharacterVector cols(2); cols[0] = "AA"; cols[1] = "BB";
+   // now create an object "dimnms" as a list with rows and cols
+   Rcpp::List dimnms = Rcpp::List::create(rows, cols);
+   // and assign it
+   x.attr("dimnames") = dimnms;
+   return(x);
+ '
R> fun <- cxxfunction(signature(), body=src, plugin="Rcpp")
R> fun()
   AA BB
aa 42 42
bb 42 42
R> 

The actual assignment of the column and row names is so manual ... because the current C++ standard does not allow direct assignment of vectors at initialization, but that will change.

Edit: I just realized that I can of course use static create() method on the row and colnames too, which makes this a little easier and shorter still

R> src <- '
+   Rcpp::NumericMatrix x(2,2);
+   x.fill(42);                           // or more interesting values
+   Rcpp::List dimnms =                   // two vec. with static names
+       Rcpp::List::create(Rcpp::CharacterVector::create("cc", "dd"),
+                          Rcpp::CharacterVector::create("ee", "ff"));
+   // and assign it
+   x.attr("dimnames") = dimnms;
+   return(x);
+ '
R> fun <- cxxfunction(signature(), body=src, plugin="Rcpp")
R> fun()
   ee ff
cc 42 42
dd 42 42
R> 

So we are down to three or four statements, no monkeying with PROTECT / UNPROTECT and no memory management.