[Rcpp-devel] Handling NAs in RcppMatrix

[Leo Alekseyev]

Thanks for the response.  Your new unit test runs, but I still see the
problem (running 0.7.4 installed from CRAN).  Consider this version of
the test -- the only difference is that it uses a 2x2 matrix and
checks for NAs:

test.RcppMatrix.double.na <- function() {
  src <- 'RcppMatrix<double> m(x);
           RcppResultSet rs;
           rs.add("na_11",  R_IsNA(m(0,0)));
           rs.add("na_12",  R_IsNA(m(0,1)));
           rs.add("na_21",  R_IsNA(m(1,0)));
           rs.add("na_22",  R_IsNA(m(1,1)));
           return rs.getReturnList();';
  funx <- cfunction(signature(x="numeric"), src, Rcpp=TRUE)
  M <- matrix(1:4,2,2,byrow=TRUE)
  M[2,1] <- NA
  checkEquals(funx(x=M),
              list(na_11=0, na_12=0, na_21=1, na_22=0),
              msg = "RcppMatrix.double.na")
}

This fails for me:

Error in checkEquals(funx(x = M), list(na_11 = 0, na_12 = 0, na_21 = 1,  :
  Component 3: Mean absolute difference: 1RcppMatrix.double.na
test.RcppMatrix.double.na.nan: (1 checks) ... OK (0.92 seconds)

As far as the compilation error messages -- looks like they were
indeed byproducts of the CLINK_CPPFLAGS and didn't affect anything.

Thanks,
--Leo


On Sat, Feb 6, 2010 at 8:01 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> 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
> | _______________________________________________
> | Rcpp-devel mailing list
> | Rcpp-devel at lists.r-forge.r-project.org
> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
> --
>  Registration is open for the 2nd International conference R / Finance 2010
>  See http://www.RinFinance.com for details, and see you in Chicago in April!
>