[Rcpp-devel] Handling NAs in RcppMatrix
Leo Alekseyev
dnquark at gmail.com
Sun Feb 7 14:11:48 CET 2010
D'oh, I should have guessed it was an integer/double issue -- I
actually tried to check by testing something like c(1.0:2.2,NA), but
this of course still produced an integer.
So as a general question -- would you recommend using the new API
(Rcpp::CharacterVector, Rcpp::NumericVector) over RcppMatrix et al?..
Are there any particularly useful docs / code samples illustrating the
use of it?..
On Sun, Feb 7, 2010 at 4:33 AM, Romain Francois
<romain.francois at dbmail.com> wrote:
> I've logged this as a bug in Rcpp's bug tracker :
> https://r-forge.r-project.org/tracker/?atid=637&group_id=155&func=browse
>
> Romain
>
> On 02/07/2010 10:15 AM, Romain Francois wrote:
>>
>> Hello,
>>
>> I think the problem is that c(1:2, NA) produces an __integer__ vector,
>> and RcppVector<double> does not take care of coercion properly.
>>
>> > typeof( c(1:2,NA) )
>> [1] "integer"
>> > typeof( c(1,2,NA) )
>> [1] "double"
>>
>> The "garbage value" you get I suppose is -2^31, which is how R
>> represents NA for integer vectors. Because RcppVector<> of RcppMatrix<>
>> does not deal with coercion, you just get essentially a cast to -2^31 as
>> a double.
>>
>> The good news is that the new API does take care of coercion, so when
>> you create a Rcpp::NumericVector and feed it with an integer vector, the
>> integer NA is coerced to a double NA.
>>
>> Also note that despite the name NumericVector, the class also offers
>> matrix-like indexing. So if you pass a matrix to NumericVector, you can
>> use matri indexing down in C++. See for example the
>> 'test.NumericVector.matrix.indexing' unit test in :
>>
>> > system.file( "unitTests", "runit.NumericVector.R", package = "Rcpp" )
>> [1] "/usr/local/lib/R/library/Rcpp/unitTests/runit.NumericVector.R"
>>
>> Also, as from Rcpp 0.7.1 you don't need the
>> try/catch/copyMessageToR/Rf_error idom anymore because if you don't
>> catch an exception in C++, it is recycled as an R exception, so you can
>> catch it in R instead.
>>
>> Romain
>>
>> On 02/07/2010 07:42 AM, Leo Alekseyev wrote:
>>>
>>> The behavior I'm seeing is a bit bizarre. The NaN conversion seems to
>>> fail for RcppMatrix and RcppVector, but not for NumericVector. The
>>> most interesting bit is this: if I run the test code on e.g.
>>> c(NA,1,2), RcppVector works (NA is printed as nan), whereas if I use
>>> c(NA,1:2), instead of nan it prints a garbage value.
>>>
>>> Here's the code I was using (just a bunch of Rprintfs, really):
>>>
>>> RcppExport SEXP rcpp_test3(SEXP N1, SEXP V1, SEXP M1, SEXP parms) {
>>>
>>> SEXP rl=R_NilValue;
>>> char* exceptionMesg=NULL;
>>>
>>> try {
>>>
>>> RcppMatrix<double> m1(M1);// double mtx
>>> RcppVector<double> v1(V1);// double vector
>>> RcppParams rparam(parms);
>>> RcppResultSet rs;
>>> Rcpp::RObject n1sexp(N1);
>>> double n1 = n1sexp.asDouble();
>>> Rcpp::NumericVector nv1(V1);
>>>
>>> Rprintf("Printing number:\n%f\n",n1);
>>> Rprintf("Printing matrix:\n");
>>> for(int i=0; i< m1.rows(); i++){
>>> for(int j=0; j< m1.cols(); j++)
>>> Rprintf("(%d,%d):%f ",i,j,m1(i,j));
>>> Rprintf("\n");
>>> }
>>> Rprintf("Printing vector:\n");
>>> for(int i=0; i< v1.size(); i++)
>>> Rprintf("%f, ",v1(i));
>>> Rprintf("\n");
>>> Rprintf("Printing Numeric vector:\n");
>>> for(int i=0; i< nv1.size(); i++)
>>> Rprintf("%f, ",nv1(i));
>>> Rprintf("\n");
>>>
>>> rl = rs.getReturnList();
>>>
>>> } catch(std::exception& ex) {
>>> exceptionMesg = copyMessageToR(ex.what());
>>> } catch(...) {
>>> exceptionMesg = copyMessageToR("unknown reason");
>>> }
>>>
>>> if (exceptionMesg != NULL)
>>> Rf_error(exceptionMesg);
>>>
>>> return rl;
>>> }
>>>
>>>
>>>
>>> On Sat, Feb 6, 2010 at 11:19 PM, Dirk Eddelbuettel<edd at debian.org>
>>> wrote:
>>>>
>>>> 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
>
>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> |- http://tr.im/MPYc : RProtoBuf: protocol buffers for R
> |- http://tr.im/KfKn : Rcpp 0.7.2
> `- http://tr.im/JOlc : External pointers with Rcpp
>
>
>
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