[Rcpp-devel] Handling NAs in RcppMatrix

[Dirk Eddelbuettel]

On 6 February 2010 at 22:08, Leo Alekseyev wrote:
| 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)

Yes, I see that too. Not sure yet why. 

Did you try any of the other types like Rcpp::NumericVector?  Is there
anything specific to RcppMatrix from what you cam see?
 
| As far as the compilation error messages -- looks like they were
| indeed byproducts of the CLINK_CPPFLAGS and didn't affect anything.

Ok.

Dirk
 
| 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!
| >

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