r/c++ talk at earl 2014
DESCRIPTION
R/C++ talk at EARL 2014. London.TRANSCRIPT
R / C++
Romain François @romain_francois
• Use R since 2002
• Consultant
• Rcpp since 2010
• Rcpp11 since 2013
• Performance
• Occasional comedy
useR2015 propaganda
Please
useR2015 propaganda
C/R API
Rcpp
ABSSeq accelerometry acer AdaptiveSparsity ALKr Amelia apcluster BalancedSampling BayesComm bayou bcp bcpa bfa bfp bifactorial BIFIEsurvey BIPOD blockcluster btf bvarsv CARBayes
CARBayesST ccaPP cda CDM cgAUC CIDnetworks cladoRcpp classify clere climdex.pcic clipper clogitL1 clusteval ClustVarLV CMF COMPASS CompGLM ConConPiWiFun coneproj copCAR CorReg
Crossover cxxfunplus dbmss ddgraph Delaporte dendextendRcpp DepthProc DESeq2 devtools dils disclapmix diversitree diveRsity DNAprofiles DNAtools dplyr dslice DStree ecp EDDA eive
EpiContactTrace ESGtoolkit EWGoF fastGHQuad FastHCS fastM FastPCS FastRCS FBFsearch fdaMixed FDRreg FisHiCal flip flowMatch flowType flowWorkspace FLSSS forecast fugeR Funclustering
fwsim geiger GeneNetworkBuilder GeneticTools geoCount glcm GMCM gMWT GOSemSim GOSim GOsummaries GPvam gRbase GRENITS gRim growcurves growfunctions GSE GUILDS GUTS GxM hawkes HDPenReg HLMdiag hsphase httpuv HUM hyperSpec hypervolume iBATCGH IBHM icamix icensmis
inarmix inline IsingSampler iterpc jaatha JAGUAR KernSmoothIRT kmc Kmisc LaF lbfgs lm.br lme4 lsgl marked maxent mcIRT messina metafolio metaSeq mets mice miceadds MIMOSA minqa mirt miscF
miscset mkde mmand Morpho mosaics Mposterior MPTinR msgl MSstats MTS mvabund MVB mvnfast mwaved mzR nabor ndl NetSim networkBMA ngspatial NPBayesImpute oem openair openxlsx orQA PBC pcalg pcaMethods PedCNV PerMallows phom phylobase planar plotSEMM plyr polywog PP PReMiuM
pROC pRoloc propagate prospectr protViz pryr psgp QRM quadrupen qVarSel randomUniformForest Rankcluster rARPACK Rchemcpp Rclusterpp RcppArmadillo RcppBDT rcppbugs RcppClassic
RcppClassicExamples RcppCNPy RcppDE RcppEigen RcppExamples RcppGSL RcppMLPACK RcppOctave RcppParallel RcppProgress RcppRedis RcppRoll RcppSMC RcppXts RcppZiggurat Rdisop recosystem remote ReorderCluster resemble reshape2 revealedPrefs rexpokit rforensicbatwing rgam RInside
ripa Risa rkvo rlme RLRsim Rmalschains RMassBank rmgarch Rmixmod RmixmodCombi robustgam robustHD rococo rotations roxygen2 rpg rplexos rPref RProtoBuf RQuantLib RSNNS RSNPset RSofia Rsomoclu rTANDEM Rtsne Ruchardet rugarch Rvcg RVowpalWabbit sapFinder SBSA scrypt sdcMicro sdcTable SelvarMix SeqArray sequences sglOptim simFrame sirt slfm snplist SocialNetworks SOD spacodiR spaMM sparseHessianFD sparseLTSEigen SpatialEpi SpatialTools spBayesSurv StereoMorph
stochvol stosim strum survAccuracyMeasures surveillance survSNP synlik TAM TAQMNGR tbart termstrc TFMPvalue treeclim trustOptim tvd unmarked VideoComparison VIM waffect WideLM
wordcloud wsrf XBRL zic
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int add( int a, int b){ return a + b ; }
#include <Rcpp.h> !
// [[Rcpp::export]] int add( int a, int b){ return a + b ; }
sourceCpp#include <Rcpp.h> !// [[Rcpp::export]] int add( int a, int b){ return a + b ; }
> sourceCpp( "add.cpp" ) > add( 2L, 3L) [1] 5
R/c++ classes
• NumericVector, IntegerVector, CharacterVector, …
• List
• Function
• Environment …
// [[Rcpp::export]] double sum( NumericVector x){ int n = x.size() ; !
double res = 0.0 ; for( int i=0; i<n; i++){ res += x[i] ; } !
return res ; }
List res = List::create( _["a"] = 1, _["b"] = "foo" );
res.attr( "class" ) = "myclass" ; !int a = res["a"] ;res["b"] = 42 ;
Function rnorm( "rnorm" ) ; !
NumericVector x = rnorm( 10, _["mean"] = 30, _["sd"] = 100 );
1998
C++1 14
C++
Range based for loopsfor( int i=0; i<x.size(); i++){ double d = x[i] ; // do something with d }
for( double d: x){ // do something with d }
C++
98C
++11
autostd::vector<double> v = ... ;
std::vector<double>::const_iterator it = v.begin() ;
auto it = v.begin() ;
C++98
C++11
Uniform initialization {…}
std::vector<std::string> x(2) ; x[0] = "foo"; x[1] = "bar" ;
std::vector<std::string> x = {"foo", "bar"} ;
C++98 typical functor bloatclass Predicate { public: Predicate( double y_ ) : y(y_){} ! inline bool operator()(double x){ return x < y ; } ! private: double y ; } ; ... !double y = 2.0 ; std::count_if( v.begin(), v.end(), Predicate(y)) ;
C++11 Lambda
double y = 2.0 ; std::count_if( v.begin(), v.end(), [=y](double x){ return x < y ; } ) ;
Rcpp11
Rcpp11
• C++ = C++11
• Smaller code base (than Rcpp)
• Header only
#include <Rcpp.h> !// [[Rcpp::export]] int foo(){ return 2 ; }
Rcpp
Rcpp11
0 1 2 3
Less code -> faster compiles
sapply + lambda
#include <Rcpp11> !// [[export]] NumericVector foo( NumericVector x ){ return sapply(x, [](double d){ return exp(d * 2) ; }); }
x <- 1:3 sapply( x, function(d){ exp(d*2) ; })
Rcpp11 release cycle
• Available from CRAN:
!
• Evolves quickly. Get it from github
!
• Current Version: 3.1.1 (same as R version)
> install.packages( "Rcpp11" )
> install_github( "Rcpp11/Rcpp11" )
