[Rcpp-devel] Handling NAs in RcppMatrix

[Dirk Eddelbuettel]

Hi Leo,

On 6 February 2010 at 17:56, Leo Alekseyev wrote:
| Howdy folks,
| I started playing around with Rcpp recently, and so far haven't been
| able to figure out how to detect NAs in a matrix that I pass to the
| C++ code.
| My test code looks something like this:
| RcppExport SEXP rcpp_test(SEXP N1, SEXP V1, SEXP M1, SEXP parms) {
| .......
|     RcppMatrix<double> m1(M1);// double mtx based on M1
|     RcppVector<double> v1(V1);// double vector based on V1
|     RcppParams rparam(parms);       // parameter from R based on parms
|     RcppResultSet rs;
|     Rcpp::RObject n1sexp(N1);
| 
|     double n1 = n1sexp.asDouble();
|     Rprintf("The value of isna is %d\n",R_IsNA(n1));
| 
|     double element1 = v1(0);
|     if(R_IsNA(element1))
|       Rprintf("Found NA in vector!\n");
| 
|     double m00 = m1(0,0);
|     if(R_IsNA(m00))
|       Rprintf("Found NA in matrix!\n");
| ................

That looks like the right approach.

So to give this some meat on the bone and some comparability, I added a new
unit test:

test.RcppMatrix.double.na.nan <- function() {
    src <- 'RcppMatrix<double> m(x);
            RcppResultSet rs;
            rs.add("na_21",  R_IsNA(m(1,0)));
            rs.add("na_22",  R_IsNA(m(1,1)));
            rs.add("nan_31", R_IsNaN(m(2,0)));
            rs.add("nan_32", R_IsNaN(m(2,1)));
	    return rs.getReturnList();';
    funx <- cfunction(signature(x="numeric"), src, Rcpp=TRUE)
    M <- matrix(1:6,3,2,byrow=TRUE)
    M[2,1] <- NA
    M[3,1] <- NaN
    checkEquals(funx(x=M),
                list(na_21=1, na_22=0, nan_31=1, nan_32=0),
                msg = "RcppMatrix.double.na.nan")
}

This defines a function 'test.RcppMatrix.double.na.nan'. In it, we create a
function funx that evaluates the C++ code in src -- it tests positions (2,1),
(2,2), (3,1) and (3,2).  We then create this matrix

  R> M <- matrix(1:6,3,2,byrow=TRUE)
  R> M[2,1] <- NA
  R> M[3,1] <- NaN
  R> M
       [,1] [,2]
  [1,]    1    2
  [2,]   NA    4
  [3,]  NaN    6
  R> 

and the compare with the result specified in the checkEquals call.  And that
pans out:

  R>     checkEquals(funx(x=M),
  +                 list(na_21=1, na_22=0, nan_31=1, nan_32=0),
  +                 msg = "RcppMatrix.double.na.nan")
  [1] TRUE
  R> 

What version were you running?  I am at current SVN so somewhere past 0.7.4
and not quite release 0.7.5.
 
| The R_IsNA() appears to work fine on scalars and vectors, but fails to
| detect NA present in a matrix.  Is this a bug?.. feature?..  Is the
| handling of missing values documented anywhere other than the R
| Extensions manual?..

We do not transform anything.  R tests for NA and NaN with (IIRC) a
combination of IEEE754 (for NA) and a special value for NaN.  That works here
as we use the R tests for ot.
 
| On a (probably) unrelated note, I get the following error when
| compiling my C++ code:
| Error in RcppCxx0xFlags() : could not find function "capture.output"
| Calls: <Anonymous> -> cat -> RcppCxx0xFlags

Not here either:

  R> Rcpp:::RcppCxx0xFlags()
  [1] "-std=c++0x"
  R> 

| However, the code seems to compile fine.  The compilation script is simply
| #!/bin/bash
| export PKG_CPPFLAGS="-I. "$(r -e "Rcpp:::CxxFlags()" )
| export PKG_LIBS=$(r -e "Rcpp:::LdFlags()" )
| export CLINK_CPPFLAGS=$(r -e "Rcpp:::Cxx0xFlags()" )
| R CMD SHLIB "$@"

You may not need the third for CLINK_CPPFLAGS. We experimented with C++0x but
there are side effects on other OSs so we parked this for now.
 
| Complete output from compilation is pasted below -- is this an error I
| should be concerned about?..
|  ./buildAndRun.sh rcpp_test.cpp --clean
| Error in RcppCxx0xFlags() : could not find function "capture.output"
| Calls: <Anonymous> -> cat -> RcppCxx0xFlags
| Execution halted
| g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/lib
|  -fpic  -g -O2 -c rcpp_test.cpp -o rcpp_test.o
| Error in RcppCxx0xFlags() : could not find function "capture.output"
| Calls: <Anonymous> -> cat -> RcppCxx0xFlags
| Execution halted
| Error in RcppCxx0xFlags() : could not find function "capture.output"
| Calls: <Anonymous> -> cat -> RcppCxx0xFlags
| Execution halted
| g++ -shared -o rcpp_test.so rcpp_test.o
| -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp
| -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/lib/R/lib -lR
| Error in RcppCxx0xFlags() : could not find function "capture.output"
| Calls: <Anonymous> -> cat -> RcppCxx0xFlags
| Execution halted
| 
| 
| Thanks in advance for any help (and please let me know if this is not
| the correct mailing list for these sorts of questions!)

Very much the right list! Thanks for asking here.

If you post your full shell script / test code I can have a go at testing it.

Dirk
 
| --Leo Alekseyev
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