[Rcpp-devel] Rcpp: Distinguishing between input types to function call
Romain Francois
romain at r-enthusiasts.com
Wed Feb 20 10:21:46 CET 2013
Well,
as the funny name implies "Rf_inherits" comes from the R API.
Romain
Le 20/02/13 10:05, Søren Højsgaard a écrit :
> Thanks a lot!
>
> I thought that Rf_inherits was the Rcpp version of inherits (which gives what I expect).
>
>> XX1 <- letters[1:4] # character
>> XX2 <- 1:4 # integer
>> XX3 <- (1:4)+.5 # numeric
>> inherits(XX1, "character")
> [1] TRUE
>> inherits(XX1, "numeric")
> [1] FALSE
>> inherits(XX1, "integer")
> [1] FALSE
>> inherits(XX2, "character")
> [1] FALSE
>> inherits(XX2, "numeric")
> [1] FALSE
>> inherits(XX2, "integer")
> [1] TRUE
>> inherits(XX3, "character")
> [1] FALSE
>> inherits(XX3, "numeric")
> [1] TRUE
>> inherits(XX3, "integer")
> [1] FALSE
>
> Best regards
> Søren
>
> -----Original Message-----
> From: Romain Francois [mailto:romain at r-enthusiasts.com]
> Sent: 20. februar 2013 09:53
> To: Søren Højsgaard
> Cc: rcpp-devel at lists.r-forge.r-project.org
> Subject: Re: [Rcpp-devel] Rcpp: Distinguishing between input types to function call
>
> Hello,
>
> Here is a shorter version of your code. The key idea was to use TYPEOF instead of Rf_inherits which uses the class attribute (simple vectors don't have them).
>
> #include <Rcpp.h>
> using namespace Rcpp;
>
> template <int RTYPE>
> SEXP allpairsXtemplate_( SEXP XX_ ){
> Vector<RTYPE> X(XX_);
> Matrix<RTYPE> ans(2, X.size()*(X.size()-1)/2);
> int col=0;
> for (int ii=0; ii<X.size(); ii++){
> for (int jj=ii+1; jj<X.size(); jj++){
> ans(0,col) = X(ii);
> ans(1,col++) = X(jj);
> }
> }
> return ans ;
> };
>
> // [[Rcpp::export]]
> SEXP allpairsX_ ( SEXP XX_ ){
> int type = TYPEOF(XX_) ;
> switch( type ){
> case INTSXP : return allpairsXtemplate_<INTSXP> ( XX_ ) ;
> case REALSXP: return allpairsXtemplate_<REALSXP>( XX_ ) ;
> case STRSXP : return allpairsXtemplate_<STRSXP> ( XX_ ) ;
> }
> return R_NilValue ;
> }
>
>
> /*** R
>
> XX1 <- letters[1:4] # character
> XX2 <- 1:4 # integer
> XX3 <- (1:4)+.5 # numeric
>
> allpairsX_( XX1 )
> allpairsX_( XX2 )
> allpairsX_( XX3 )
>
> ***/
>
> Also, I'm templating allpairsXtemplate_ on the R type rather than the actual classes, because NumericVector = Vector<REALSXP>, etc ...
>
>
> About your code, with e.g. TT = NumericVector, you don't need as in :
>
> TT X = as<TT>(XX_);
>
> because NumericVector already has a SEXP constructor, that is why I do:
> Vector<RTYPE> X(XX_);
>
>
>
> Same for return(wrap(ans)); you don't need to call wrap here because
> ans can convert itself to SEXP.
>
>
>
> Another way to write this using Rcpp's builtin dispatch mechanism is to
> use RCPP_RETURN_VECTOR. For example :
>
> #include <Rcpp.h>
> using namespace Rcpp;
>
> template <typename T>
> SEXP allpairsXtemplate_( const T& X){
> const int RTYPE = T::r_type::value ;
> Matrix<RTYPE> ans(2, X.size()*(X.size()-1)/2);
> int col=0;
> for (int ii=0; ii<X.size(); ii++){
> for (int jj=ii+1; jj<X.size(); jj++){
> ans(0,col) = X(ii);
> ans(1,col++) = X(jj);
> }
> }
> return ans ;
> };
>
> // [[Rcpp::export]]
> SEXP allpairsX_ ( SEXP XX_ ){
> RCPP_RETURN_VECTOR( allpairsXtemplate_, XX_ ) ;
> return R_NilValue ; // never used
> }
>
>
> So we call one of the generated overloads of allpairsXtemplate_ which
> takes a Vector as input. From this vector, we can deduce the RTYPE (at
> compile time):
>
> const int RTYPE = T::r_type::value ;
>
> use it to get the correct Matrix type : Matrix<RTYPE>.
>
>
>
> Yet another way, probably the one I would use:
>
> template <int RTYPE>
> Matrix<RTYPE> allpairsXtemplate_( const Vector<RTYPE>& X){
> Matrix<RTYPE> ans(2, X.size()*(X.size()-1)/2);
> int col=0;
> for (int ii=0; ii<X.size(); ii++){
> for (int jj=ii+1; jj<X.size(); jj++){
> ans(0,col) = X(ii);
> ans(1,col++) = X(jj);
> }
> }
> return ans ;
> };
>
> This works because RCPP_RETURN_VECTOR will cast to the appropriate
> Vector type.
>
> And knowing the RTYPE at first lets us use it on the output signture.
>
>
> RCPP_RETURN_VECTOR is defined in dispatch.h (macro haters beware):
>
> #define ___RCPP_HANDLE_CASE___( ___RTYPE___ , ___FUN___ , ___OBJECT___ ,
> ___RCPPTYPE___ ) \
> case ___RTYPE___ : \
> return ___FUN___( ::Rcpp::___RCPPTYPE___< ___RTYPE___ >(
> ___OBJECT___ ) ) ;
>
> #define ___RCPP_RETURN___( __FUN__, __SEXP__ , __RCPPTYPE__ ) \
> SEXP __TMP__ = __SEXP__ ; \
> switch( TYPEOF( __TMP__ ) ){ \
> ___RCPP_HANDLE_CASE___( INTSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( REALSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( RAWSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( LGLSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( CPLXSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( STRSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( VECSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> ___RCPP_HANDLE_CASE___( EXPRSXP , __FUN__ , __TMP__ , __RCPPTYPE__ ) \
> default: \
> throw std::range_error( "not a vector" ) ; \
> }
>
> #define RCPP_RETURN_VECTOR( _FUN_, _SEXP_ ) ___RCPP_RETURN___( _FUN_,
> _SEXP_ , Vector )
> #define RCPP_RETURN_MATRIX( _FUN_, _SEXP_ ) ___RCPP_RETURN___( _FUN_,
> _SEXP_ , Matrix )
>
>
>
> Romain
>
> Le 20/02/13 00:15, Søren Højsgaard a écrit :
>> Dear all
>>
>> I have tried to follow Romains suggestion (thanks) below to obtain all pairs of elements of a vector, for various input types; i.e.
>>
>> XX1 <- letters[1:4] # character
>> XX2 <- 1:4 # integer
>> XX3 <- (1:4)+.5 # numeric
>> combn(XX1, 2)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] "a" "a" "a" "b" "b" "c"
>> [2,] "b" "c" "d" "c" "d" "d"
>> combn(XX2, 2)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] 1 1 1 2 2 3
>> [2,] 2 3 4 3 4 4
>> combn(XX3, 2)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] 1.5 1.5 1.5 2.5 2.5 3.5
>> [2,] 2.5 3.5 4.5 3.5 4.5 4.5
>>
>> My take on this is as follows:
>> ------------------------------
>> #include <Rcpp.h>
>>
>> #ifndef BEGIN_RCPP
>> #define BEGIN_RCPP
>> #endif
>>
>> #ifndef END_RCPP
>> #define END_RCPP
>> #endif
>>
>> using namespace Rcpp;
>>
>> // [[Rcpp::export]]
>> template <typename TT, typename UU>
>> SEXP allpairsXtemplate_( SEXP XX_ ){
>> TT X = as<TT>(XX_);
>> UU ans(2, X.size()*(X.size()-1)/2);
>> int col=0;
>> for (int ii=0; ii<X.size(); ii++){
>> for (int jj=ii+1; jj<X.size(); jj++){
>> ans(0,col) = X(ii);
>> ans(1,col++) = X(jj);
>> }
>> }
>> return(wrap(ans));
>> };
>>
>> // [[Rcpp::export]]
>> RcppExport SEXP allpairsX_char ( SEXP XX_ ){
>> return allpairsXtemplate_<CharacterVector, CharacterMatrix>(XX_);
>> }
>>
>> // [[Rcpp::export]]
>> RcppExport SEXP allpairsX_int ( SEXP XX_ ){
>> return allpairsXtemplate_<IntegerVector, IntegerMatrix>(XX_);
>> }
>>
>> // [[Rcpp::export]]
>> RcppExport SEXP allpairsX_num ( SEXP XX_ ){
>> return allpairsXtemplate_<NumericVector, NumericMatrix>(XX_);
>> }
>>
>> // [[Rcpp::export]]
>> RcppExport SEXP allpairsX_ ( SEXP XX_ ){
>> if( Rf_inherits( XX_, "character" ) ){
>> Rcout << "character\n";
>> return allpairsXtemplate_<CharacterVector, CharacterMatrix>(XX_);
>> }
>> if (Rf_inherits( XX_, "integer" ) ){
>> Rcout << "integer\n";
>> return allpairsXtemplate_<IntegerVector, IntegerMatrix>(XX_);
>> }
>> if (Rf_inherits( XX_, "numeric" ) ){
>> Rcout << "numeric\n";
>> return allpairsXtemplate_<NumericVector, NumericMatrix>(XX_);
>> }
>> return R_NilValue;
>> }
>>
>> ------------------------------
>>
>> I correctly get:
>>
>> dyn.load("template.dll")
>> .Call("allpairsX_char", XX1)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] "a" "a" "a" "b" "b" "c"
>> [2,] "b" "c" "d" "c" "d" "d"
>> .Call("allpairsX_int", XX2)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] 1 1 1 2 2 3
>> [2,] 2 3 4 3 4 4
>> .Call("allpairsX_num", XX3)
>> [,1] [,2] [,3] [,4] [,5] [,6]
>> [1,] 1.5 1.5 1.5 2.5 2.5 3.5
>> [2,] 2.5 3.5 4.5 3.5 4.5 4.5
>> dyn.unload("template.dll")
>>
>> However the function allpairsX_ fails:
>>
>> dyn.load("template.dll")
>> .Call("allpairsX_", XX1)
>> NULL
>> .Call("allpairsX_", XX2)
>> NULL
>> .Call("allpairsX_", XX3)
>> NULL
>> dyn.unload("template.dll")
>>
>> Now for the questions:
>>
>> 1) From various tests it seems that Rf_inherits does not work - or perhaps I have misunderstood its usage. Any experiences with that? Any other suggestions on how to dispatch on the input type?
>>
>> 2) I have never used templates before. Is the approach above what "one would normally do"?
>>
>> 3) Using sourceCpp I get the following:
>>
>> sourceCpp("template.cpp")
>> g++ -m64 -I"C:/programs/R/current/include" -DNDEBUG -I"C:/programs/R/current/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c template.cpp -o template.o template.cpp: In function 'SEXPREC* sourceCpp_55702_allpairsXtemplate_(SEXP)': template.cpp:67:5: error: a template declaration cannot appear at block scope template.cpp:68:5: error: expected ';' before 'return' template.cpp:66:10: warning: unused variable 'XX_' [-Wunused-variable] template.cpp: In function 'SEXPREC* sourceCpp_55702_allpairsX_char(SEXP)': template.cpp:76:5: error: expected unqualified-id before string constant template.cpp:77:23: error: '__result' was not declared in this scope template.cpp:75:10: warning: unused variable 'XX_' [-Wunused-variable] template.cpp: In function 'SEXPREC* sourceCpp_55702_allpairsX_int(SEXP)': template.cpp:85:5: error: expected unqualified-id before string constant template.cpp:86:23: error: '__result' was not declared in
t
> his scope
> template.cpp:84:10: warning: unused variable 'XX_' [-Wunused-variable] template.cpp: In function 'SEXPREC* sourceCpp_55702_allpairsX_num(SEXP)': template.cpp:94:5: error: expected unqualified-id before string constant template.cpp:95:23: error: '__result' was not declared in this scope template.cpp:93:10: warning: unused variable 'XX_' [-Wunused-variable] template.cpp: In function 'SEXPREC* sourceCpp_55702_allpairsX_(SEXP)': template.cpp:103:5: error: expected unqualified-id before string constant template.cpp:104:23: error: '__result' was not declared in this scope template.cpp:102:10: warning: unused variable 'XX_' [-Wunused-variable] make: *** [template.o] Error 1
>> Error in sourceCpp("template.cpp") :
>> Error 1 occurred building shared library.
>>
>> It seems that the error occurs because of the template. Am I doing something wrong or is it just not possible to use sourceCpp when templates are involved.
>>
>> 4) Not a question, but an observation: On windows the above error message comes as one long line which means that I must manually scroll to the end of the line ("to the far right"). Slightly annoying. For comparison, cxxfunction() produces error in more readable form: One line per error. It would be nice if sourceCpp did the same thing.
>>
>> Thanks in advance - and thanks for making Rcpp available.
>>
>> Best regards
>> Søren
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: rcpp-devel-bounces at lists.r-forge.r-project.org [mailto:rcpp-devel-bounces at lists.r-forge.r-project.org] On Behalf Of Romain Francois
>> Sent: 3. december 2012 23:18
>> To: rcpp-devel at lists.r-forge.r-project.org
>> Subject: Re: [Rcpp-devel] Rcpp: Distinguishing between input types to function call
>>
>>
>> Hello,
>>
>> I have not tested this, but I think you are looking for templates. So you'd put generic code in this template function:
>>
>> template <typename T>
>> SEXP topoSort( SEXP XX_ ){
>> const T X = Rcpp::as<T>(XX_) ;
>>
>> ...
>> }
>>
>>
>> and two other functions to instantiate the template:
>>
>> RcppExport SEXP C_topoSort_st ( SEXP XX_ ){
>> return topoSort< Eigen::Map<Eigen::MatrixXi> >( XX_ ) ; }
>>
>> RcppExport SEXP C_topoSort_sp ( SEXP XX_ ){
>> return topoSort< Eigen::MappedSparseMatrix<double> >( XX_ ) ; }
>>
>> or Perhaps you would have one instead of the two, something like this:
>>
>> RcppExport SEXP topoSort_facade ( SEXP XX_ ){
>>
>> if( Rf_inherits( XX_, "dgCMatrix" ) ){
>> return topoSort< Eigen::MappedSparseMatrix<double> >( XX_ ) ;
>> } else {
>> return topoSort< Eigen::Map<Eigen::MatrixXi> >( XX_ ) ;
>> }
>> }
>>
>>
>>
>>
>> Le 03/12/12 22:58, Søren Højsgaard a écrit :
>>> Dear list,
>>>
>>> I represent a directed acyclic graph (DAG) as an adjacency matrix. This can be either a "standard matrix" in R or as a sparse matrix (dgCMatrix from the matrix package). I have implemented a topological sort function for DAGs for these two representations (using the RcppEigen package):
>>>
>>> // standard matrix
>>> RcppExport SEXP C_topoSort_st ( SEXP XX_ ){
>>> typedef Eigen::Map<Eigen::MatrixXi> MapMati;
>>> const MapMati X(Rcpp::as<MapMati>(XX_));
>>> //typedef Eigen::MappedSparseMatrix<double> MSpMat;
>>> //const MSpMat X(as<MSpMat>(XX_));
>>> .... some code
>>> }
>>>
>>> // sparse matrix
>>> RcppExport SEXP C_topoSort_sp ( SEXP XX_ ){
>>> // typedef Eigen::Map<Eigen::MatrixXi> MapMati;
>>> // const MapMati X(Rcpp::as<MapMati>(XX_));
>>> typedef Eigen::MappedSparseMatrix<double> MSpMat;
>>> const MSpMat X(as<MSpMat>(XX_));
>>> .... some code
>>> }
>>>
>>> Notice: The functions only differ with respect to the first four lines.
>>>
>>> Question: Is there any way in which I can "reduce" these two functions to only one which then checks the "type" of XX_ at the entry and then creates the appropriate "type" of X?
>>
>> Templates.
>>
>>> Question: Is it correct (haven't tried, just guessing from what I've read) that I can not directly store 'some code' in an inline function (because the correct type of X would need to be known?
>>
>> I think I understand what you mean, and that you are fine.
>>
>>> Apologies for trivial C++ questions - I am working on learning it...
>>
>> Those are good kind of questions to ask yourself. I hope this will give you enough motivation to find out more about C++ templates.
>>
>> Romain
>>
>>> The functions are listed below.
>>>
>>> Best regards
>>> Søren
>>>
>>> ----------------------------------
>>>
>>> # include <RcppEigen.h>
>>> # include <Rcpp.h>
>>>
>>> #ifndef BEGIN_RCPP
>>> #define BEGIN_RCPP
>>> #endif
>>>
>>> #ifndef END_RCPP
>>> #define END_RCPP
>>> #endif
>>>
>>> using namespace Rcpp;
>>>
>>> // standard matrix
>>> RcppExport SEXP C_topoSort_st ( SEXP XX_ ){
>>> typedef Eigen::Map<Eigen::MatrixXi> MapMati;
>>> const MapMati X(Rcpp::as<MapMati>(XX_));
>>> //typedef Eigen::MappedSparseMatrix<double> MSpMat;
>>> //const MSpMat X(as<MSpMat>(XX_));
>>> int ii, jj, kk=0, count=0, ll=0, flagsum=0;
>>> int ncX(X.rows());
>>> Eigen::VectorXi indegree(ncX);
>>> Eigen::VectorXi flag(ncX);
>>> Eigen::VectorXi ans(ncX);
>>>
>>> for (ii = 0; ii < ncX; ii++) {
>>> indegree[ii] = 0; flag[ii] = 0; ans[ii] = 0;
>>> }
>>> for (jj = 0; jj < ncX; jj++)
>>> for (ii = 0; ii < ncX; ii++)
>>> indegree[jj] = indegree[jj] + X.coeff(ii,jj);
>>>
>>> /* Rcout<<"indegree: ";for (ii=0;ii<ncX;ii++) Rcout << indegree[ii]<<" " ; Rcout << std::endl;*/
>>> /* Rcout<<"flag : ";for (ii=0;ii<ncX;ii++) Rcout << flag[ii]<<" " ; Rcout << std::endl;*/
>>> while (count < ncX){
>>> /* Rcout << "count=" << count << std::endl;*/
>>> for (kk = 0; kk < ncX; kk++){
>>> /* Rcout <<" kk="<<kk<<" indeg="<<indegree[kk]<<" flag="<<flag[kk] << std::endl;*/
>>> if ((indegree[kk] == 0) && (flag[kk] == 0)){
>>> /*Rcout << " no incomming:" << kk << std::endl;*/
>>> ans[ll++] = kk+1;
>>> flag[kk] = 1;
>>> flagsum++;
>>> for (jj = 0; jj < ncX; jj++){
>>> /* Rcout <<"kk,jj="<<kk<<","<<jj<<" entry=" << X.coeff(kk,jj) << std::endl;*/
>>> if (X.coeff(kk,jj) == 1){
>>> indegree[jj]--;
>>> /* Rcout <<" updating indegree at entry="<<jj<<std::endl;*/
>>> }
>>> }
>>> }
>>> /* Rcout<<"indegree: ";for (ii=0;ii<ncX;ii++) Rcout << indegree[ii]<<" " ; Rcout << std::endl; */
>>> }
>>> if (flagsum==ncX)
>>> break;
>>> count++;
>>> /* Rcout<<"flag : ";for (ii=0;ii<ncX;ii++) Rcout << flag[ii]<<" " ; Rcout << std::endl; */
>>> }
>>> if (flagsum<ncX)
>>> ans[0] = -1;
>>> return(wrap(ans));
>>> }
>>>
>>> // sparse matrix
>>> RcppExport SEXP C_topoSort_sp ( SEXP XX_ ){
>>> // typedef Eigen::Map<Eigen::MatrixXi> MapMati;
>>> // const MapMati X(Rcpp::as<MapMati>(XX_));
>>> typedef Eigen::MappedSparseMatrix<double> MSpMat;
>>> const MSpMat X(as<MSpMat>(XX_));
>>> int ii, jj, kk=0, count=0, ll=0, flagsum=0;
>>> int ncX(X.rows());
>>> Eigen::VectorXi indegree(ncX);
>>> Eigen::VectorXi flag(ncX);
>>> Eigen::VectorXi ans(ncX);
>>>
>>> for (ii = 0; ii < ncX; ii++) {
>>> indegree[ii] = 0; flag[ii] = 0; ans[ii] = 0;
>>> }
>>> for (jj = 0; jj < ncX; jj++)
>>> for (ii = 0; ii < ncX; ii++)
>>> indegree[jj] = indegree[jj] + X.coeff(ii,jj);
>>>
>>> /* Rcout<<"indegree: ";for (ii=0;ii<ncX;ii++) Rcout << indegree[ii]<<" " ; Rcout << std::endl;*/
>>> /* Rcout<<"flag : ";for (ii=0;ii<ncX;ii++) Rcout << flag[ii]<<" " ; Rcout << std::endl;*/
>>> while (count < ncX){
>>> /* Rcout << "count=" << count << std::endl;*/
>>> for (kk = 0; kk < ncX; kk++){
>>> /* Rcout <<" kk="<<kk<<" indeg="<<indegree[kk]<<" flag="<<flag[kk] << std::endl;*/
>>> if ((indegree[kk] == 0) && (flag[kk] == 0)){
>>> /*Rcout << " no incomming:" << kk << std::endl;*/
>>> ans[ll++] = kk+1;
>>> flag[kk] = 1;
>>> flagsum++;
>>> for (jj = 0; jj < ncX; jj++){
>>> /* Rcout <<"kk,jj="<<kk<<","<<jj<<" entry=" << X.coeff(kk,jj) << std::endl;*/
>>> if (X.coeff(kk,jj) == 1){
>>> indegree[jj]--;
>>> /* Rcout <<" updating indegree at entry="<<jj<<std::endl;*/
>>> }
>>> }
>>> }
>>> /* Rcout<<"indegree: ";for (ii=0;ii<ncX;ii++) Rcout << indegree[ii]<<" " ; Rcout << std::endl; */
>>> }
>>> if (flagsum==ncX)
>>> break;
>>> count++;
>>> /* Rcout<<"flag : ";for (ii=0;ii<ncX;ii++) Rcout << flag[ii]<<" " ; Rcout << std::endl; */
>>> }
>>> if (flagsum<ncX)
>>> ans[0] = -1;
>>> return(wrap(ans));
>>> }
>
>
--
Romain Francois
Professional R Enthusiast
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