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Romain François
@romain_francois
#useR2015, Aalborg
July 1, 2015
• Use R since 2002
• Consultant
• Rcpp since 2010
• Rcpp11, Rcpp14
• dplyr internals
• #rcatladies
• Occasional comedy
(…)
(…)
2002 2005 2009 2010 2013 2015
2002 2005 2009 2010 2013 2015
First time I used R, love at first sight
2002 2005 2009 2010 2013 2015
R Graph Gallery
2002 2005 2009 2010 2013 2015
rJava
2002 2005 2009 2010 2013 2015
Rcpp
2002 2005 2009 2010 2013 2015
dplyr
Performance
Usability
rJava
> d <- .jnew( "java/lang/Double", 42 )
>
> .jcall( d, "D", "doubleValue" )
[1] 42
rJava 0.7-*
> d <- new( J("java.lang.Double"), 42 )
> d$doubleValue()
[1] 42
rJava 0.8-*
> attach( javaImport( "java.lang" ) )
>
> d <- new( Double, 42 )
> d$doubleValue()
[1] 42
rJava 0.8-*
Rcpp
double add( double a, double b ){
return a + b ;
}
C/R API
#include <R.h>
#include <Rinternals.h>
double add( double a, double b ){
return a + b ;
}
SEXP add_fun( SEXP a_, SEXP b_){...
$ R CMD SHLIB add.c
clang -dynamiclib -Wl,-headerpad_max_install_names -
undefined dynamic_lookup -single_module -
multipl...
Rcpp
#include <Rcpp.h>
// [[Rcpp::export]]
double add( double a, double b ){
return a + b ;
}
> sourceCpp( "add.cpp" )
> add( 2...
accelerometry AdaptiveSparsity algstat ALKr Amelia apcluster ASPBay BaBooN BalancedSampling
BayesComm BayesFactor bayesm b...
accelerometry AdaptiveSparsity algstat ALKr Amelia apcluster ASPBay BaBooN BalancedSampling
BayesComm BayesFactor bayesm b...
A3 abbyyR abc ABCanalysis abcdeFBA ABCp2 abctools abd acc accelerometry accrual acid acm4r ACNE acp aCRM acs acss Actigrap...
A3 abbyyR abc ABCanalysis abcdeFBA ABCp2 abctools abd acc accelerometry accrual acid acm4r ACNE acp aCRM acs acss Actigrap...
V8 (Jeroen Ooms)
> ct <- new_context();
> ct$eval("var foo = 123")
> ct$eval("var bar = 456")
> ct$eval("foo+bar")
[1] 579
RcppParallel
(tbb)
x <- rnorm(1e6)
y <- rnorm(1e6)
list( sum(x), sum(y) )
#include <Rcpp.h>
using namespace Rcpp ;
// [[Rcpp::export]]
List foo_ser( NumericVector x, NumericVector y){
double sum_x...
#incluce <Rcpp.h>
#include <RcppParallel.h>
using namespace Rcpp ;
// [[Rcpp::export]]
List foo_par( NumericVector x, Nume...
> microbenchmark(foo_par(x, y), foo_ser(x, y))
Unit: microseconds
expr min lq mean median uq max neval
foo_par(x, y) 927.8...
y <- sqrt(x)
// [[Rcpp::export]]
NumericVector cpp_sqrt_ser( NumericVector x ){
int n = x.size();
NumericVector y = no_init(n) ;
std::t...
// [[Rcpp::export]]
NumericVector cpp_sqrt_par( NumericVector x ){
int n = x.size();
NumericVector y = no_init(n) ;
parall...
> microbenchmark(cpp_sqrt_ser(x), cpp_sqrt_par(x))
Unit: milliseconds
expr min lq mean median uq max neval
cpp_sqrt_ser(x)...
nucleusnucleus
dplyr
flights %>%
group_by(carrier) %>%
summarise(x = mean(dep_delay, na.rm = TRUE) )
Romain François
@romain_francois
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
user2015 keynote talk
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user2015 keynote talk

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user2015 keynote talk

  1. 1. Romain François @romain_francois #useR2015, Aalborg July 1, 2015
  2. 2. • Use R since 2002 • Consultant • Rcpp since 2010 • Rcpp11, Rcpp14 • dplyr internals • #rcatladies • Occasional comedy
  3. 3. (…)
  4. 4. (…)
  5. 5. 2002 2005 2009 2010 2013 2015
  6. 6. 2002 2005 2009 2010 2013 2015 First time I used R, love at first sight
  7. 7. 2002 2005 2009 2010 2013 2015 R Graph Gallery
  8. 8. 2002 2005 2009 2010 2013 2015 rJava
  9. 9. 2002 2005 2009 2010 2013 2015 Rcpp
  10. 10. 2002 2005 2009 2010 2013 2015 dplyr
  11. 11. Performance Usability
  12. 12. rJava
  13. 13. > d <- .jnew( "java/lang/Double", 42 ) > > .jcall( d, "D", "doubleValue" ) [1] 42 rJava 0.7-*
  14. 14. > d <- new( J("java.lang.Double"), 42 ) > d$doubleValue() [1] 42 rJava 0.8-*
  15. 15. > attach( javaImport( "java.lang" ) ) > > d <- new( Double, 42 ) > d$doubleValue() [1] 42 rJava 0.8-*
  16. 16. Rcpp
  17. 17. double add( double a, double b ){ return a + b ; }
  18. 18. C/R API
  19. 19. #include <R.h> #include <Rinternals.h> double add( double a, double b ){ return a + b ; } SEXP add_fun( SEXP a_, SEXP b_){ double a = REAL(a_)[0] ; double b = REAL(b_)[0] ; double res = add(a,b) ; SEXP result = PROTECT( allocVector( REALSXP, 1 ) ) ; REAL(result)[0] = res ; UNPROTECT(1) ; return result ; }
  20. 20. $ R CMD SHLIB add.c clang -dynamiclib -Wl,-headerpad_max_install_names - undefined dynamic_lookup -single_module - multiply_defined suppress -L/Library/Frameworks/ R.framework/Resources/lib -L/usr/local/lib -o add.so add.o -F/Library/Frameworks/R.framework/.. - framework R -Wl,-framework -Wl,CoreFoundation > dyn.load( "add.so") > add <- function(a, b){ .Call( "add_fun", a, b ) } > add( 21, 21 ) [1] 42
  21. 21. Rcpp
  22. 22. #include <Rcpp.h> // [[Rcpp::export]] double add( double a, double b ){ return a + b ; } > sourceCpp( "add.cpp" ) > add( 21, 21) [1] 42
  23. 23. accelerometry AdaptiveSparsity algstat ALKr Amelia apcluster ASPBay BaBooN BalancedSampling BayesComm BayesFactor bayesm bayou bcp bcpa bfa bfp bifactorial BIFIEsurvey BIPOD blockcluster blockmodels brms btf bvarsv CARBayes CARBayesST ccaPP cccp cda CDM cgAUC chopthin CIDnetworks cladoRcpp classify clere climdex.pcic clogitL1 clusteval ClustMMDD ClustVarLV CMF CompGLM ConConPiWiFun coneproj copCAR CorReg Coxnet cqrReg Crossover cxxfunplus dbmss ddalpha Delaporte dendextendRcpp DepthProc DetMCD devtools dfcomb dfmta dils disclapmix diversitree diveRsity DNAprofiles DNAtools dplyr dslice DStree ecp EditImputeCont eive emIRT EpiContactTrace ESGtoolkit evolqg EWGoF fastGHQuad FastHCS fastM FastPCS FastRCS FBFsearch fbroc fdaMixed FDGcopulas FDRreg FeatureHashing fICA FisHiCal flam flip FLSSS forecast forestFloor FRESA.CAD FSInteract fugeR FunChisq Funclustering fwsim gaselect GCPM gdm geiger GeneticTools GENLIB geoCount gkmSVM glcm glmgraph GMCM Gmisc gMWT GPareto GPvam graphicalVAR gRbase gRim growcurves growfunctions GSE GUILDS GUTS GxM h5 haven hawkes HLMdiag hsphase hts httpuv HUM hyperSpec hypervolume iBATCGH IBHM icamix iccbeta icd9 icensmis inarmix inline IsingSampler ISOpureR iterpc jaatha JAGUAR jiebaR kdecopula kergp KernSmoothIRT kmc Kmisc LaF lamW lbfgs lfl lifecontingencies lm.br lme4 lpme lsbclust lsgl Luminescence marked markovchain MAT matchingMarkets matchingR maxent mbbefd mcIRT metafolio mets mice miceadds minqa mirt mirtCAT miscF miscset missDeaths MixAll mixedMem mkde mlxR mmand Morpho mp Mposterior MPTinR MRIaggr msgl MTS multicool mvabund MVB mvnfast mwaved myTAI nabor NAM ndl NetSim ngspatial NHMM nonlinearTseries NPBayesImpute odeintr oem onlinePCA openair openxlsx orQA PAFit pander partialAR PBC pcalg PedCNV pedometrics penMSM PerMallows phom phylobase planar plotSEMM plyr poisDoubleSamp polywog PoweR PP PPtreeViz PReMiuM primes pROC propagate prospectr protViz pryr psd psgp pvar QRM quadrupen quanteda quantspec qVarSel randomUniformForest Rankcluster rankdist rARPACK Rborist Rclusterpp RcppAnnoy RcppAPT RcppArmadillo RcppBDT rcppbugs RcppClassic RcppClassicExamples RcppCNPy RcppDE RcppDL RcppEigen RcppExamples RcppFaddeeva RcppGSL RcppMLPACK RcppOctave RcppParallel RcppProgress RcppRedis RcppRoll RcppSMC RcppStreams RcppTOML RcppXts RcppZiggurat readr readstata13 readxl RealVAMS reconstructr recosystem redist relSim remote ReorderCluster repra resemble reshape2 revealedPrefs rexpokit rforensicbatwing rgam RInside ripa rivr rkvo Rlibeemd rlme RLRsim Rmalschains rmgarch Rmixmod RmixmodCombi rncl robustgam robustHD robustreg rococo rotations RoughSets roxygen2 rpg Rphylopars rplexos rPref RProtoBuf RQuantLib RSNNS RSNPset RSofia Rsomoclu rtkpp Rtsne Ruchardet rugarch Rvcg RVowpalWabbit sbmSDP SBSA scales scrm scrypt sdcMicro sdcTable SEERaBomb segmag seismicRoll SelvarMix sequences sgd sglOptim simFrame simPop sirt slfm SLOPE snipEM snplist SocialNetworks SOD spacodiR spaMM sparseHessianFD sparseLTSEigen SpatialEpi SpatialTools SpatPCA spBayesSurv staTools StereoMorph StMoSim stochvol stocks stosim strataG stream strum survAccuracyMeasures surveillance survSNP SVMMatch synlik systemicrisk tagcloud TAM TAQMNGR tbart tcR termstrc TESS textreg TFMPvalue timma tmg treeclim trustOptim tvd unmarked urltools V8 VarSelLCM VideoComparison VIM waffect WideLM wordcloud wsrf XBRL xergm xml2 zic 407
  24. 24. accelerometry AdaptiveSparsity algstat ALKr Amelia apcluster ASPBay BaBooN BalancedSampling BayesComm BayesFactor bayesm bayou bcp bcpa bfa bfp bifactorial BIFIEsurvey BIPOD blockcluster blockmodels brms btf bvarsv CARBayes CARBayesST ccaPP cccp cda CDM cgAUC chopthin CIDnetworks cladoRcpp classify clere climdex.pcic clogitL1 clusteval ClustMMDD ClustVarLV CMF CompGLM ConConPiWiFun coneproj copCAR CorReg Coxnet cqrReg Crossover cxxfunplus dbmss ddalpha Delaporte dendextendRcpp DepthProc DetMCD devtools dfcomb dfmta dils disclapmix diversitree diveRsity DNAprofiles DNAtools dplyr dslice DStree ecp EditImputeCont eive emIRT EpiContactTrace ESGtoolkit evolqg EWGoF fastGHQuad FastHCS fastM FastPCS FastRCS FBFsearch fbroc fdaMixed FDGcopulas FDRreg FeatureHashing fICA FisHiCal flam flip FLSSS forecast forestFloor FRESA.CAD FSInteract fugeR FunChisq Funclustering fwsim gaselect GCPM gdm geiger GeneticTools GENLIB geoCount gkmSVM glcm glmgraph GMCM Gmisc gMWT GPareto GPvam graphicalVAR gRbase gRim growcurves growfunctions GSE GUILDS GUTS GxM h5 haven hawkes HLMdiag hsphase hts httpuv HUM hyperSpec hypervolume iBATCGH IBHM icamix iccbeta icd9 icensmis inarmix inline IsingSampler ISOpureR iterpc jaatha JAGUAR jiebaR kdecopula kergp KernSmoothIRT kmc Kmisc LaF lamW lbfgs lfl lifecontingencies lm.br lme4 lpme lsbclust lsgl Luminescence marked markovchain MAT matchingMarkets matchingR maxent mbbefd mcIRT metafolio mets mice miceadds minqa mirt mirtCAT miscF miscset missDeaths MixAll mixedMem mkde mlxR mmand Morpho mp Mposterior MPTinR MRIaggr msgl MTS multicool mvabund MVB mvnfast mwaved myTAI nabor NAM ndl NetSim ngspatial NHMM nonlinearTseries NPBayesImpute odeintr oem onlinePCA openair openxlsx orQA PAFit pander partialAR PBC pcalg PedCNV pedometrics penMSM PerMallows phom phylobase planar plotSEMM plyr poisDoubleSamp polywog PoweR PP PPtreeViz PReMiuM primes pROC propagate prospectr protViz pryr psd psgp pvar QRM quadrupen quanteda quantspec qVarSel randomUniformForest Rankcluster rankdist rARPACK Rborist Rclusterpp RcppAnnoy RcppAPT RcppArmadillo RcppBDT rcppbugs RcppClassic RcppClassicExamples RcppCNPy RcppDE RcppDL RcppEigen RcppExamples RcppFaddeeva RcppGSL RcppMLPACK RcppOctave RcppParallel RcppProgress RcppRedis RcppRoll RcppSMC RcppStreams RcppTOML RcppXts RcppZiggurat readr readstata13 readxl RealVAMS reconstructr recosystem redist relSim remote ReorderCluster repra resemble reshape2 revealedPrefs rexpokit rforensicbatwing rgam RInside ripa rivr rkvo Rlibeemd rlme RLRsim Rmalschains rmgarch Rmixmod RmixmodCombi rncl robustgam robustHD robustreg rococo rotations RoughSets roxygen2 rpg Rphylopars rplexos rPref RProtoBuf RQuantLib RSNNS RSNPset RSofia Rsomoclu rtkpp Rtsne Ruchardet rugarch Rvcg RVowpalWabbit sbmSDP SBSA scales scrm scrypt sdcMicro sdcTable SEERaBomb segmag seismicRoll SelvarMix sequences sgd sglOptim simFrame simPop sirt slfm SLOPE snipEM snplist SocialNetworks SOD spacodiR spaMM sparseHessianFD sparseLTSEigen SpatialEpi SpatialTools SpatPCA spBayesSurv staTools StereoMorph StMoSim stochvol stocks stosim strataG stream strum survAccuracyMeasures surveillance survSNP SVMMatch synlik systemicrisk tagcloud TAM TAQMNGR tbart tcR termstrc TESS textreg TFMPvalue timma tmg treeclim trustOptim tvd unmarked urltools V8 VarSelLCM VideoComparison VIM waffect WideLM wordcloud wsrf XBRL xergm xml2 zic 5.98%
  25. 25. A3 abbyyR abc ABCanalysis abcdeFBA ABCp2 abctools abd acc accelerometry accrual acid acm4r ACNE acp aCRM acs acss Actigraphy activity actuar ActuDistns adabag adaptDA AdaptFit AdaptFitOS AdaptiveSparsity adaptMCMC adaptsmoFMRI adaptTest additivityTests ade4 ade4TkGUI adegenet adegraphics adehabitat adehabitatHR adehabitatHS adehabitatLT adehabitatMA adephylo adhoc AdMit ADPclust ads aemo AER afex AFLPsim aftgee AGD agop agRee Agreement agricolae agridat AGSDest agsemisc ahaz AICcmodavg AID aidar ALDqr aLFQ algstat ALKr allan AlleleRetain alm alphahull alphaOutlier alphashape3d alr3 alr4 ALTopt Amelia amen aml AMOEBA AmpliconDuo anacor analogue analogueExtra AnalyzeFMRI anametrix AncestryMapper anchors AnDE anesrake anim.plots animalTrack animation anominate Anthropometry antitrust AntWeb aod aods3 AOfamilies aoos aop aoristic ApacheLogProcessor apcluster ape apex aplore3 apmsWAPP apple AppliedPredictiveModeling APSIM apsimr apt apTreeshape aqfig aqp aqr archdata archetypes archivist ArfimaMLM argparse ArgumentCheck arm aroma.affymetrix aroma.cn aroma.core ARPobservation arqas ARTIVA ARTool arules arulesNBMiner arulesSequences arulesViz aRxiv asbio ascii ASMap aspace ASPBay aspect asremlPlus assertive assertr assertthat assist AssocTests astro astrochron asVPC AtelieR ATmet atsd attribrisk AUCRF audiolyzR automap autopls AutoSEARCH aylmer B2Z babar babel BaBooN BACA backShift backtest BACprior bagRboostR BalancedSampling BaM bamdit BAMMtools bandit BANFF BANOVA barcode bartMachine baseline BaSTA BAT BatchExperiments BatchJobs BayesComm bayescount BayesDA bayesDccGarch bayesDem BayesFactor bayesGARCH bayesGDS BayesGESM BayesianAnimalTracker Bayesianbetareg BayesLCA bayesLife bayesm bayesMCClust BayesMed bayesmix bayesPop bayespref bayess BayesSAE BayesSingleSub BayesSummaryStatLM bayesSurv bayesTFR Bayesthresh BayesTree BayesVarSel BayesX BayesXsrc BayHaz bayou BaySIC BAYSTAR BB bbemkr BBEST BBmisc bbmle BBRecapture bc3net BCA BcDiag BCE BCEA BCEE BCEs0 Bchron Bclim bcp bcpa bcrm bcrypt bde BDgraph bdscale bdvis bdynsys beadarrayMSV beanplot bear BEDASSLE beepr benchmark benford.analysis BEQI2 ber Bergm BerlinData Bessel BEST bestglm betapart betaper betareg betas betategarch bfa bfast bfp bgeva bglm bgmm BHH2 BHMSMAfMRI biasbetareg biclust BiDimRegression bifactorial BIFIEsurvey biganalytics bigdata BIGDAWG bigGP biglars biglm bigml bigpca bigrf bigrquery bigRR bigtabulate BigTSP BinaryEPPM binda bindata binequality bingat binhf BinNonNor BinNor binom binomSamSize BinOrdNonNor bio3d BiodiversityR BioGeoBEARS biogram Biograph biom BioMark biomod2 biorxivr bios2mds biosignalEMG BioStatR biotools bipartite biplotbootGUI BiplotGUI BIPOD birdring bisectr BiSEp bisoreg BivarP biwavelet biwt bizdays BlandAltmanLeh Blaunet BLCOP blender blkergm blme blmeco blockcluster blockmodeling blockmodels blocksdesign blockTools blowtorch BMA bmd bmem bmk bmmix bmp BNDataGenerator bnlearn bnormnlr BNPTSclust BOG bold boolean3 BoolNet Boom BoomSpikeSlab boostr boostSeq boot bootES bootLR bootnet bootRes bootspecdens bootsPLS bootStepAIC bootSVD boottol boral Boruta boss BoSSA boxr bpca bpkde BradleyTerry2 BrailleR brainR breakpoint bReeze brewdata brglm brms broman broom Brq BRugs BSagri BSDA BSGS bshazard BSquare BSSasymp bst bsts btf BTSPAS BTYD bujar bvarsv BVS c060 c3net C50 ca CaDENCE CADFtest cAIC4 CALIBERrfimpute calibrate calmate CAM CAMAN camel cancerTiming candisc cape caper capm capushe car CARBayes CARBayesdata CARBayesST carcass cardidates care caret caretEnsemble CarletonStats caroline CARramps CARrampsOcl caschrono catdata CatDyn catenary cati catIrt caTools catspec causaleffect CausalFX CausalGAM causalsens Causata cba CBPS CCA ccaPP cccd ccChooser cccp cccrm ccda CCpop CCTpack cda cdcsis CDM CDNmoney cds CDVine CEGO celestial cellranger cellVolumeDist cem censReg CEoptim CePa cepp CerioliOutlierDetection cg cgam cgAUC ChainLadder changepoint CHAT CheckDigit checkmate checkpoint chemCal chemometrics ChemometricsWithR chemosensors ChemoSpec cherry chillR chipPCR chngpt CHNOSZ ChoiceModelR choplump chopthin chords choroplethr choroplethrAdmin1 choroplethrMaps chromer chromoR chron CHsharp CIDnetworks CINOEDV circlize CircOutlier CircStats circular CITAN cjoint Ckmeans.1d.dp Claddis cladoRcpp CLAG class classGraph classifly classify classInt classyfire clere clhs clickstream clifro ClimClass climdex.pcic climwin clisymbols CLME clogitL1 CLSOCP clue ClueR clues cluster clusterfly clustergas clusterGeneration clusterPower clusterSEs clusterSim clusteval ClustGeo clustMD ClustMMDD clustrd ClustVarLV clustvarsel clv clValid CMF CMPControl cmprskQR cmrutils cmsaf cmvnorm cncaGUI CNOGpro CNprep CNVassoc coalescentMCMC coarseDataTools COBRA cobs CoClust cocor cocorresp cocron coda codadiags codep coefficientalpha coefplot coenocliner CoImp coin CoinMinD CollocInfer coloc coloredICA colorfulVennPlot colorspace comato CombMSC commentr commonmark CommonTrend CommT COMMUNAL CommunityCorrelogram Comp2ROC CompareCausalNetworks compareGroups compeir compendiumdb CompGLM Compind complmrob compoisson compositions Compounding CompRandFld ConConPiWiFun cond coneproj confidence conformal confreq conjoint ConnMatTools ConSpline constrainedKriging conting contrast ConvergenceConcepts convevol cooccur cooptrees COP COPASutils copCAR cope copula copulaedas CopulaRegression CopulaREMADA CopyDetect corclass CORElearn corHMM CORM CorrBin CorReg Correlplot corrgram CorrMixed corrplot COSINE cosinor CosmoPhotoz cosso costat cotrend couchDB COUNT countrycode CountsEPPM covLCA covr CovSel covTest cowplot CoxBoost coxinterval coxme Coxnet cp4p cpca CPE CpGassoc cplm CPMCGLM Cprob cqrReg crackR cramer cranlogs crawl crayon crch CRF crimelinkage crn crossmatch Crossover crossReg crossval crp.CSFP crqa crrp crs crunch CrypticIBDcheck CryptRndTest csampling cSFM cshapes csrplus cstar cubfits Cubist cudaBayesreg cudia curl curvetest curvHDR cusp cutoffR cvAUC CVST CVThresh cvTools CVTuningCov cvxbiclustr cvxclustr cwhmisc cwm cxxfunplus cyphid cytoDiv D2C d3heatmap d3Network DAAG DAAGbio DAAGxtras dae daewr daff DAGGER Daim DAKS DAMisc DAMOCLES dams DandEFA darch Dark data.table data.tree DatABEL datacheck DataCombine datalist datamap datamart dataRetrieval datastepr datautils dataview DATforDCEMRI dave dawai db.r dbarts dbConnect DBI DBKGrad dbmss dbstats dcemriS4 DCGL dcGOR DCL dclone DCluster dcmle dcmr dcv ddalpha DDD ddeploy DDHFm decctools decisionSupport decode decompr Deducer DeducerExtras DeducerPlugInExample DeducerPlugInScaling DeducerSpatial DeducerSurvival DeducerText deducorrect degreenet Delaporte deltaPlotR Demerelate demi deming demography demoKde dendextend dendextendRcpp dendroextras DendSer dendsort denovolyzeR denstrip DEoptim depmix depmixS4 depth DepthProc Deriv descomponer DescribeDisplay DescTools deseasonalize desiR desirability DESnowball DESP detect DetMCD detrendeR Devore7 devtools df2json dfcomb dfexplore DFIT dfmta dga dglm dgmb dhglm diagonals DiagrammeR DiagTest3Grp DiceDesign DiceEval DiceKriging DiceOptim DiceView dielectric DiffCorr diffdepprop diffeR diffIRT diffusionMap DIFlasso difR Digiroo2 dils directlabels directPA DirichletReg disclapmix DiscML discreteRV DiscriMiner discSurv diseasemapping dismo disp2D disparityfilter disposables dissUtils Distance DistatisR distcomp distory distr distrDoc distrEllipse distrEx DistributionUtils distrMod distrom distrRmetrics distrSim distrTeach distrTEst divagis DivE diveMove diversitree diveRsity DivMelt divo dixon dlm dlmap dlmodeler DLMtool dlnm dma dmm dMod dmt DMwR dna DNAprofiles DNAtools dnet DNMF DOBAD doBy docopt DoE.base DoE.wrapper doMC Dominance doMPI doParallel doRedis doRNG DoseFinding doSNOW dosresmeta dostats dotenv DoubleCone downloader dpa dpcR dplR dplyr dpmixsim dpmr DPpackage DPw dr drat drc drfit dropR drsmooth DSBayes dse dslice dsm DSpat DSsim DStree DSviaDRM DT DTComPair dti DTR dtw dualScale dvfBm DVHmetrics dygraphs DYM dyn dynamicGraph dynatopmodel dynaTree dynlm DynNom dynsim dynsurv DynTxRegime e1071 earlywarnings earth EasyABC easyanova EasyHTMLReport EasyMARK eba ebdbNet EBMAforecast EBS Ecdat ecespa Ecfun ecipex eco ecoengine EcoGenetics EcoHydRology ecolMod EcoSimR ecospat ecp edgeRun EDISON EditImputeCont editrules EDR edrGraphicalTools eegAnalysis eegkit eeptools EFDR EffectLiteR effects EffectsRelBaseline EffectStars ega egcm eggCounts egonet EGRET eHOF EIAdata EILA eiPack eive eiwild elastic ElemStatLearn ellipse elliptic elmNN EloRating elrm ElstonStewart ELT ELYP EMA embryogrowth EMC EMCC EMCluster EMD emdbook emil emIRT emma EMMAgeo emme2 EMMIXskew EMMIXuskew EMMREML EMP emplik enaR endorse energy EngrExpt enigma ENiRG ENMeval ENmisc enpls EnQuireR EnsembleBase ensembleBMA EnsembleCV ensembleMOS EnsemblePCReg EnsemblePenReg ensurer entropart enviPick EnviroStat EnvNicheR EnvStats epade Epi EpiBayes EpiContactTrace EpiDynamics EpiModel epinet epiR episensr episplineDensity epoc epr EQL eqs2lavaan eqtl equateIRT equivalence erboost erer ergm ergm.count ergm.graphlets ergm.userterms eRm erpR esaBcv ESEA ESGtoolkit EstCRM etable ETAS etasFLP ETC ETLUtils etm eurostat EvalEst evaluate Evapotranspiration eventInterval eventstudies evmix evobiR evolqg evolvability evtree EWGoF ExceedanceTools excel.link exCon excursions ExomeDepth expands expectreg experiment expm expoRkit expoTree expp expsmooth exsic ExtDist extracat extraTrees extRemes ez ezsim FacPad FactMixtAnalysis FactoClass FactoMineR factorplot factorQR Factoshiny FADA Fahrmeir fail FAiR falsy fame Familias FAMILY fanc fanovaGraph fanplot FAOSTAT faoutlier far fArma fAsianOptions fAssets fast fastclime fastcox fastGHQuad FastHCS fastHICA fastICA FastImputation FastKNN fastM FastPCS fastR FastRCS fat2Lpoly FatTailsR FAwR fBasics fbati FBFsearch fBonds fbRanks fbroc fcd fCertificates FCMapper fCopulae FD fda fda.usc fdaMixed fdasrvf fdatest FDboost FDGcopulas fdrDiscreteNull FDRreg fds FeaLect feature FeatureHashing features FedData FeedbackTS fermicatsR fExoticOptions fExpressCertificates fExtremes ff ffbase FFD FField fGarch fgpt fheatmap FHtest fICA fields FieldSim fifer filehashSQLite filenamer fImport FinancialInstrument FinCal FindIt FindMinIC findpython FinTS FisherEM FisHiCal fishmethods fishmove fit.models FitAR FitARMA fitbitScraper fitdistrplus fitTetra flam flare flexclust flexCWM flexmix FlexParamCurve flexsurv FLIM flip FLLat flora flowfield flsa FLSSS flux fma FME fmri fMultivar FNN fNonlinear foodweb fOptions forams foreach ForeCA forecast forecTheta forensic forestFloor forestplot ForImp formatR formula.tools forward ForwardSearch fossil fpc fpca fpCompare fPortfolio fpp fracdiff fractal fractaldim fractalrock frailtyHL frailtypack frair Frames2 FRAPO FRB frbs FRCC FreeSortR freestats fRegression freqparcoord freqweights FRESA.CAD FrF2 FrF2.catlg128 frmqa frontier frontiles fscaret FSelector FSInteract fslr fso fSRM FTICRMS fTrading fts ftsa fueleconomy fugeR FunChisq FunCluster Funclustering FuncMap funFEM funHDDC 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ScrabbleScore ScreenClean scrime scrm scrypt sda SDaA sdcMicro sdcMicroGUI sdcTable sdcTarget SDD SDDE sde SDMTools sdmvspecies sdwd seacarb searchable seas season seasonal seawaveQ SEchart SECP secr secrdesign secrlinear seeg SEERaBomb seewave seg segmag seismicRoll SEL selectMeta selectr selectspm SeleMix selfea selfingTree SelvarMix sem semdiag semGOF semiArtificial SEMID SemiMarkov SemiPar SemiParBIVProbit SemiParSampleSel semisupKernelPCA semPlot semPLS semsfa semTools sensitivity SensoMineR sensory sensR SenSrivastava SensusR separationplot seqCBS SeqFeatR SeqGrapheR seqinr seqMeta seqminer sequences seriation seroincidence servr sesem SetMethods sets settings sExtinct sfsmisc sft SGCS sgd sglasso sglOptim sglr SGP sGPCA SGPdata sgPLS sgr sgt shapeR shapes ShapeSelectForest SharpeR sharpshootR sharx shiny shinyAce shinybootstrap2 shinyBS shinydashboard shinyFiles shinyjs shinyRGL shinythemes shinyTree shopifyr shotGroups showtext showtextdb shp2graph shrink siar SID sideChannelAttack sidier sigloc signal signal.hsmm Sim.DiffProc simba simboot simcausal SimComp SimCorMultRes simecol simex simFrame SIMMS simMSM simPH simpleboot simpleNeural SimpleTable simPop Simpsons SimRAD simrel simsalapar simsem simTool SINGLE siplab sirad siRSM sirt SIS sisus sisVIVE sitar sivipm SixSigma SiZer sjmisc sjPlot skatMeta skellam SkewHyperbolic Skillings.Mack skmeans sla slackr Sleuth2 Sleuth3 slfm SLOPE slp sm smacof smacpod smam smart SmarterPoland smatr smbinning smcfcs smcUtils smdc smds sme SMFI5 smint SMIR SmithWilsonYieldCurve SML SMNCensReg smnet smoof smoother SmoothHazard smoothie smoothmest smoothtail SMPracticals sms smss sna snht snipEM snp.plotter SNPassoc snpEnrichment snplist snpRF snpStatsWriter sns soc.ca SocialMediaMineR SocialNetworks SOD SODC Sofi softImpute soil.spec soilDB soilphysics soilprofile SoilR soiltexture soilwater solaR solarius solr SOMbrero somplot soobench SOPIE SOR SortableHTMLTables sortinghat sorvi sos sos4R sotkanet soundecology SoundexBR SOUP sp spa spaa SPACECAP spaceExt spacejam spacetime spacodiR spacom spam spaMM spanr spareserver spark sparkTable sparr sparseBC SparseGrid sparseHessianFD sparseLDA sparseLTSEigen sparseMVN sparsenet SparseTSCGM spartan spatgraphs spatial spatial.gev.bma spatial.tools spatialEco SpatialEpi SpatialExtremes spatialnbda SpatialNP SpatialPack SpatialPosition spatialprobit spatialsegregation spatialTailDep SpatialTools SpatialVx SpatioTemporal SpatPCA spatstat spatsurv spBayes spBayesSurv spca spcadjust spcosa spd spdep spdynmod SpecHelpers SpeciesMix specificity spectral.methods speedglm speff2trial sperich sperrorest spfrontier spgrass6 spgwr sphereplot SpherWave sphet spider spiders spikeslab spikeSlabGAM splancs splitstackshape splm spls SPMS spnet spocc SPODT SportsAnalytics SPOT SPREDA sprint sprinter sprm SPSL spsmooth spsurvey spTDyn spTest spThin spTimer sptm spuRs sqldf sqliter sqlutils SQN srd ss3sim sscor SSDforR sse ssfa ssfit ssh.utils ssizeRNA ssmrob SSN sspse SSrat sss ssym st stab stabledist StableEstim stabs Stack stagePop stam StAMPP StanHeaders STAR statar statcheck StatDA statebins statfi stationaRy StatMatch StatMeasures StatMethRank statmod statnet statnetWeb Statomica staTools StatRank stcm stellaR Stem STEPCAM stepp StereoMorph stilt stm stmCorrViz STMedianPolish StMoMo StMoSim stocc stochprofML stochvol stocks Storm stosim stpp stppResid strap strataG StratSel stream StreamMetabolism streamMOA stremo stressr stringdist stringgaussnet stringr strucchange structSSI strum strvalidator stsm stylo SubLasso SubpathwayGMir subselect subsemble subtype SUE summarytools supclust superbiclust superdiag SuperLearner support.BWS support.CEs surface Surrogate surv2sampleComp survAccuracyMeasures survAUC SurvCorr surveillance survey surveydata survMisc survrec survsim survSNP svapls svcm svdvisual SVMMaj SVMMatch svSweave SvyNom svyPVpack swamp SWATmodel SweaveListingUtils sweidnumbr swirl SwissAir switchnpreg switchrGist SWMPr sybil sybilccFBA sybilcycleFreeFlux sybilDynFBA sybilEFBA sybilSBML symbolicDA symmoments synbreed SynchWave SYNCSA synlik synRNASeqNet Synth synthpop sysfonts systemfit systemicrisk syuzhet tab table1xls tableone tableplot tables tabplot tabplotd3 tagcloud TAM TANOVA TapeR TAQMNGR taRifx taRifx.geo tawny tawny.types taxize tbart tbdiag TBEST TBSSurvival TcGSA tclust tcR TDA TDAmapper TDboost TDD tdm TDMR tdr TeachingDemos TED tergm termstrc ternvis TESS tester TestSurvRec testthat testthatsomemore texmex texreg textir textreg TFMPvalue tfplot tframePlus tgp tgram TH.data Thermimage ThreeArmedTrials threeboost threejs ThresholdROC TiddlyWikiR tidyjson tidyr tiger tigerstats tikzDevice tileHMM timeit timeline timeordered TimeProjection timereg timeROC timesboot timeSeq timeSeries timeseriesdb timetree timma TIMP Tinflex tis titan TKF tkrgl tlemix tlm tlnise tm.plugin.webmining tmap TMDb tmg tmle tmle.npvi tmod tmvtnorm tnet TOC tolerance topicmodels TopKLists topologyGSA tourr tourrGui TPmsm TR8 TrackReconstruction traitr traits traj trajectories TraMineR TraMineRextras translateR translateSPSS2R trapezoid TreatmentSelection treatSens tree treebase treeclim treeClust treecm treemap TreePar TreeSim TreeSimGM treethresh trend TriMatch trimcluster trimTrees trioGxE trip tripEstimation TripleR TROM truncgof truncreg truncSP trustOptim TSA tsbridge tsbugs TSclust TScompare tscount 4476
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A3 abbyyR abc ABCanalysis abcdeFBA ABCp2 abctools abd acc accelerometry accrual acid acm4r ACNE acp aCRM acs acss Actigraphy activity actuar ActuDistns adabag adaptDA AdaptFit AdaptFitOS AdaptiveSparsity adaptMCMC adaptsmoFMRI adaptTest additivityTests ade4 ade4TkGUI adegenet adegraphics adehabitat adehabitatHR adehabitatHS adehabitatLT adehabitatMA adephylo adhoc AdMit ADPclust ads aemo AER afex AFLPsim aftgee AGD agop agRee Agreement agricolae agridat AGSDest agsemisc ahaz AICcmodavg AID aidar ALDqr aLFQ algstat ALKr allan AlleleRetain alm alphahull alphaOutlier alphashape3d alr3 alr4 ALTopt Amelia amen aml AMOEBA AmpliconDuo anacor analogue analogueExtra AnalyzeFMRI anametrix AncestryMapper anchors AnDE anesrake anim.plots animalTrack animation anominate Anthropometry antitrust AntWeb aod aods3 AOfamilies aoos aop aoristic ApacheLogProcessor apcluster ape apex aplore3 apmsWAPP apple AppliedPredictiveModeling APSIM apsimr apt apTreeshape aqfig aqp aqr archdata archetypes archivist ArfimaMLM argparse ArgumentCheck arm aroma.affymetrix aroma.cn aroma.core ARPobservation arqas ARTIVA ARTool arules arulesNBMiner arulesSequences arulesViz aRxiv asbio ascii ASMap aspace ASPBay aspect asremlPlus assertive assertr assertthat assist AssocTests astro astrochron asVPC AtelieR ATmet atsd attribrisk AUCRF audiolyzR automap autopls AutoSEARCH aylmer B2Z babar babel BaBooN BACA backShift backtest BACprior bagRboostR BalancedSampling BaM bamdit BAMMtools bandit BANFF BANOVA barcode bartMachine baseline BaSTA BAT BatchExperiments BatchJobs BayesComm bayescount BayesDA bayesDccGarch bayesDem BayesFactor bayesGARCH bayesGDS BayesGESM BayesianAnimalTracker Bayesianbetareg BayesLCA bayesLife bayesm bayesMCClust BayesMed bayesmix bayesPop bayespref bayess BayesSAE BayesSingleSub BayesSummaryStatLM bayesSurv bayesTFR Bayesthresh BayesTree BayesVarSel BayesX BayesXsrc BayHaz bayou BaySIC BAYSTAR BB bbemkr BBEST BBmisc bbmle BBRecapture bc3net BCA BcDiag BCE BCEA BCEE BCEs0 Bchron Bclim bcp bcpa bcrm bcrypt bde BDgraph bdscale bdvis bdynsys beadarrayMSV beanplot bear BEDASSLE beepr benchmark benford.analysis BEQI2 ber Bergm BerlinData Bessel BEST bestglm betapart betaper betareg betas betategarch bfa bfast bfp bgeva bglm bgmm BHH2 BHMSMAfMRI biasbetareg biclust BiDimRegression bifactorial BIFIEsurvey biganalytics bigdata BIGDAWG bigGP biglars biglm bigml bigpca bigrf bigrquery bigRR bigtabulate BigTSP BinaryEPPM binda bindata binequality bingat binhf BinNonNor BinNor binom binomSamSize BinOrdNonNor bio3d BiodiversityR BioGeoBEARS biogram Biograph biom BioMark biomod2 biorxivr bios2mds biosignalEMG BioStatR biotools bipartite biplotbootGUI BiplotGUI BIPOD birdring bisectr BiSEp bisoreg BivarP biwavelet biwt bizdays BlandAltmanLeh Blaunet BLCOP blender blkergm blme blmeco blockcluster blockmodeling blockmodels blocksdesign blockTools blowtorch BMA bmd bmem bmk bmmix bmp BNDataGenerator bnlearn bnormnlr BNPTSclust BOG bold boolean3 BoolNet Boom BoomSpikeSlab boostr boostSeq boot bootES bootLR bootnet bootRes bootspecdens bootsPLS bootStepAIC bootSVD boottol boral Boruta boss BoSSA boxr bpca bpkde BradleyTerry2 BrailleR brainR breakpoint bReeze brewdata brglm brms broman broom Brq BRugs BSagri BSDA BSGS bshazard BSquare BSSasymp bst bsts btf BTSPAS BTYD bujar bvarsv BVS c060 c3net C50 ca CaDENCE CADFtest cAIC4 CALIBERrfimpute calibrate calmate CAM CAMAN camel cancerTiming candisc cape caper capm capushe car CARBayes CARBayesdata CARBayesST carcass cardidates care caret caretEnsemble CarletonStats caroline CARramps CARrampsOcl caschrono catdata CatDyn catenary cati catIrt caTools catspec causaleffect CausalFX CausalGAM causalsens Causata cba CBPS CCA ccaPP cccd ccChooser cccp cccrm ccda CCpop CCTpack cda cdcsis CDM CDNmoney cds CDVine CEGO celestial cellranger cellVolumeDist cem censReg CEoptim CePa cepp CerioliOutlierDetection cg cgam cgAUC ChainLadder changepoint CHAT CheckDigit checkmate checkpoint chemCal chemometrics ChemometricsWithR chemosensors ChemoSpec cherry chillR chipPCR chngpt CHNOSZ ChoiceModelR choplump chopthin chords choroplethr choroplethrAdmin1 choroplethrMaps chromer chromoR chron CHsharp CIDnetworks CINOEDV circlize CircOutlier CircStats circular CITAN cjoint Ckmeans.1d.dp Claddis cladoRcpp CLAG class classGraph classifly classify classInt classyfire clere clhs clickstream clifro ClimClass climdex.pcic climwin clisymbols CLME clogitL1 CLSOCP clue ClueR clues cluster clusterfly clustergas clusterGeneration clusterPower clusterSEs clusterSim clusteval ClustGeo clustMD ClustMMDD clustrd ClustVarLV clustvarsel clv clValid CMF CMPControl cmprskQR cmrutils cmsaf cmvnorm cncaGUI CNOGpro CNprep CNVassoc coalescentMCMC coarseDataTools COBRA cobs CoClust cocor cocorresp cocron coda codadiags codep coefficientalpha coefplot coenocliner CoImp coin CoinMinD CollocInfer coloc coloredICA colorfulVennPlot colorspace comato CombMSC commentr commonmark CommonTrend CommT COMMUNAL CommunityCorrelogram Comp2ROC CompareCausalNetworks compareGroups compeir compendiumdb CompGLM Compind complmrob compoisson compositions Compounding CompRandFld ConConPiWiFun cond coneproj confidence conformal confreq conjoint ConnMatTools ConSpline constrainedKriging conting contrast ConvergenceConcepts convevol cooccur cooptrees COP COPASutils copCAR cope copula copulaedas CopulaRegression CopulaREMADA CopyDetect corclass CORElearn corHMM CORM CorrBin CorReg Correlplot corrgram CorrMixed corrplot COSINE cosinor CosmoPhotoz cosso costat cotrend couchDB COUNT countrycode CountsEPPM covLCA covr CovSel covTest cowplot CoxBoost coxinterval coxme Coxnet cp4p cpca CPE CpGassoc cplm CPMCGLM Cprob cqrReg crackR cramer cranlogs crawl crayon crch CRF crimelinkage crn crossmatch Crossover crossReg crossval crp.CSFP crqa crrp crs crunch CrypticIBDcheck CryptRndTest csampling cSFM cshapes csrplus cstar cubfits Cubist cudaBayesreg cudia curl curvetest curvHDR cusp cutoffR cvAUC CVST CVThresh cvTools CVTuningCov cvxbiclustr cvxclustr cwhmisc cwm cxxfunplus cyphid cytoDiv D2C d3heatmap d3Network DAAG DAAGbio DAAGxtras dae daewr daff DAGGER Daim DAKS DAMisc DAMOCLES dams DandEFA darch Dark data.table data.tree DatABEL datacheck DataCombine datalist datamap datamart dataRetrieval datastepr datautils dataview DATforDCEMRI dave dawai db.r dbarts dbConnect DBI DBKGrad dbmss dbstats dcemriS4 DCGL dcGOR DCL dclone DCluster dcmle dcmr dcv ddalpha DDD ddeploy DDHFm decctools decisionSupport decode decompr Deducer DeducerExtras DeducerPlugInExample DeducerPlugInScaling DeducerSpatial DeducerSurvival DeducerText deducorrect degreenet Delaporte deltaPlotR Demerelate demi deming demography demoKde dendextend dendextendRcpp dendroextras DendSer dendsort denovolyzeR denstrip DEoptim depmix depmixS4 depth DepthProc Deriv descomponer DescribeDisplay DescTools deseasonalize desiR desirability DESnowball DESP detect DetMCD detrendeR Devore7 devtools df2json dfcomb dfexplore DFIT dfmta dga dglm dgmb dhglm diagonals DiagrammeR DiagTest3Grp DiceDesign DiceEval DiceKriging DiceOptim DiceView dielectric DiffCorr diffdepprop diffeR diffIRT diffusionMap DIFlasso difR Digiroo2 dils directlabels directPA DirichletReg disclapmix DiscML discreteRV DiscriMiner discSurv diseasemapping dismo disp2D disparityfilter disposables dissUtils Distance DistatisR distcomp distory distr distrDoc distrEllipse distrEx DistributionUtils distrMod distrom distrRmetrics distrSim distrTeach distrTEst divagis DivE diveMove diversitree diveRsity DivMelt divo dixon dlm dlmap dlmodeler DLMtool dlnm dma dmm dMod dmt DMwR dna DNAprofiles DNAtools dnet DNMF DOBAD doBy docopt DoE.base DoE.wrapper doMC Dominance doMPI doParallel doRedis doRNG DoseFinding doSNOW dosresmeta dostats dotenv DoubleCone downloader dpa dpcR dplR dplyr dpmixsim dpmr DPpackage DPw dr drat drc drfit dropR drsmooth DSBayes dse dslice dsm DSpat DSsim DStree DSviaDRM DT DTComPair dti DTR dtw dualScale dvfBm DVHmetrics dygraphs DYM dyn dynamicGraph dynatopmodel dynaTree dynlm DynNom dynsim dynsurv DynTxRegime e1071 earlywarnings earth EasyABC easyanova EasyHTMLReport EasyMARK eba ebdbNet EBMAforecast EBS Ecdat ecespa Ecfun ecipex eco ecoengine EcoGenetics EcoHydRology ecolMod EcoSimR ecospat ecp edgeRun EDISON EditImputeCont editrules EDR edrGraphicalTools eegAnalysis eegkit eeptools EFDR EffectLiteR effects EffectsRelBaseline EffectStars ega egcm eggCounts egonet EGRET eHOF EIAdata EILA eiPack eive eiwild elastic ElemStatLearn ellipse elliptic elmNN EloRating elrm ElstonStewart ELT ELYP EMA embryogrowth EMC EMCC EMCluster EMD emdbook emil emIRT emma EMMAgeo emme2 EMMIXskew EMMIXuskew EMMREML EMP emplik enaR endorse energy EngrExpt enigma ENiRG ENMeval ENmisc enpls EnQuireR EnsembleBase ensembleBMA EnsembleCV ensembleMOS EnsemblePCReg EnsemblePenReg ensurer entropart enviPick EnviroStat EnvNicheR EnvStats epade Epi EpiBayes EpiContactTrace EpiDynamics EpiModel epinet epiR episensr episplineDensity epoc epr EQL eqs2lavaan eqtl equateIRT equivalence erboost erer ergm ergm.count ergm.graphlets ergm.userterms eRm erpR esaBcv ESEA ESGtoolkit EstCRM etable ETAS etasFLP ETC ETLUtils etm eurostat EvalEst evaluate Evapotranspiration eventInterval eventstudies evmix evobiR evolqg evolvability evtree EWGoF ExceedanceTools excel.link exCon excursions ExomeDepth expands expectreg experiment expm expoRkit expoTree expp expsmooth exsic ExtDist extracat extraTrees extRemes ez ezsim FacPad FactMixtAnalysis FactoClass FactoMineR factorplot factorQR Factoshiny FADA Fahrmeir fail FAiR falsy fame Familias FAMILY fanc fanovaGraph fanplot FAOSTAT faoutlier far fArma fAsianOptions fAssets fast fastclime fastcox fastGHQuad FastHCS fastHICA fastICA FastImputation FastKNN fastM FastPCS fastR FastRCS fat2Lpoly FatTailsR FAwR fBasics fbati FBFsearch fBonds fbRanks fbroc fcd fCertificates FCMapper fCopulae FD fda fda.usc fdaMixed fdasrvf fdatest FDboost FDGcopulas fdrDiscreteNull FDRreg fds FeaLect feature FeatureHashing features FedData FeedbackTS fermicatsR fExoticOptions fExpressCertificates fExtremes ff ffbase FFD FField fGarch fgpt fheatmap FHtest fICA fields FieldSim fifer filehashSQLite filenamer fImport FinancialInstrument FinCal FindIt FindMinIC findpython FinTS FisherEM FisHiCal fishmethods fishmove fit.models FitAR FitARMA fitbitScraper fitdistrplus fitTetra flam flare flexclust flexCWM flexmix FlexParamCurve flexsurv FLIM flip FLLat flora flowfield flsa FLSSS flux fma FME fmri fMultivar FNN fNonlinear foodweb fOptions forams foreach ForeCA forecast forecTheta forensic forestFloor forestplot ForImp formatR formula.tools forward ForwardSearch fossil fpc fpca fpCompare fPortfolio fpp fracdiff fractal fractaldim fractalrock frailtyHL frailtypack frair Frames2 FRAPO FRB frbs FRCC FreeSortR freestats fRegression freqparcoord freqweights FRESA.CAD FrF2 FrF2.catlg128 frmqa frontier frontiles fscaret FSelector FSInteract fslr fso fSRM FTICRMS fTrading fts ftsa fueleconomy fugeR FunChisq FunCluster Funclustering FuncMap funFEM funHDDC fUnitRoots funreg funtimes FusedPCA futile.any futile.logger futile.matrix future fuzzyMM FuzzyNumbers FuzzyStatProb FWDselect fwsim fxregime G1DBN G2Sd GA GAabbreviate GABi GAD galts gam GAMBoost gamboostLSS gamboostMSM gamclass games GameTheory gamlr gamlss gamlss.add gamlss.cens gamlss.demo gamlss.dist gamlss.mx gamlss.nl gamlss.spatial gamlss.tr gamlss.util gamm4 gammSlice gamsel gap gapmap gapminder GAR gaselect gb GB2 gbm gbm2sas gbs gcbd GCD gcdnet gclus gcmr gcookbook GCPM GDAdata gdalUtils GDAtools GDELTtools gdimap gdistance gdm gee geeM geesmv geiger gems gemtc GenABEL genasis gender genderizeR GENEAread GeneCycle GeneFeST Geneland GeneNet GeneralizedHyperbolic GeneReg geneSignatureFinder genetics GeneticTools GenKern genlasso GENLIB genMOSS genoPlotR GenOrd genpathmox genridge geoBayes geocodeHERE geoCount GeoDE GeoGenetix geojsonio GeoLight GEOmap geomapdata geometry geomorph geophys geoR geoRglm georob geospacom geosphere geospt geosptdb geostatsp geotopbricks GeoXp geozoo GESTr getopt GetoptLong GetR gets gettingtothebottom GEVcdn GEVStableGarch gfcanalysis GGally ggdendro GGEBiplotGUI ggenealogy ggExtra GGIR ggm ggmap ggmcmc GGMselect ggparallel ggplot2 ggRandomForests ggROC ggsubplot ggswissmaps ggtern ggthemes ggvis GHQp ghyp GibbsACOV gimme giRaph GISTools gistr gitter Giza gkmSVM glarma glassomix glcm gld GLDEX GLDreg glinternet glmc glmgraph glmm glmmBUGS glmmLasso glmnet glmnetcr glmulti glmvsd glmx globalboosttest GlobalFit GlobalOptions glogis GLSME gmailr GMCM gMCP GMD GMDH Gmisc gmm GMMBoost gmnl gmodels gmp gMWT GNE gnm gof GoFKernel GOGANPA gogarch googleVis GOplot goric gpairs GPareto GPC GPCSIV GPFDA GPfit gplm gplots gpmap gProfileR gptk GPvam GRaF gRain gramEvol GrammR granova granovaGG gRapfa graphicalVAR GraphPCA graphscan GrassmannOptim gRbase gRc greport greyzoneSurv Grid2Polygons gridBase gridDebug gridExtra gridGraphics gridGraphviz gridSVG GriegSmith gRim grImport groc gromovlab grouped growcurves growfunctions growthrate grpreg grt gsarima gsbDesign gsDesign GSE gset gsg gsheet GSIF gskat gstat gsubfn gtable gte gtop Guerry GUIDE GUILDS GUIProfiler GUniFrac GUTS gvc gvcm.cat GWAF gwerAM gWidgets2RGtk2 gWidgets2tcltk GWLelast GWmodel gwrr GxM h2o h5 haarfisz HAC HadoopStreaming hamlet HandTill2001 HAP.ROR Haplin haplo.ccs haplo.stats HaploSim haplotypes HardyWeinberg HarmonicRegression harvestr hash haven hawkes hazus hbm hbsae HBSTM hda HDclassif hddplot hddtools hdi hdlm HDMD HDPenReg hdrcde heatmap3 HelpersMG helsinki heplots hergm heritability hermite het.test hett hexbin hgam hglasso hglm hglm.data HH HHG hht HiDimDA HiDimMaxStable hierarchicalDS hierband hierfstat HIest highD2pop HighDimOut highfrequency highr highTtest hillmakeR HiPLARM hiPOD hisemi hisse HistData HistDAWass HistogramTools historydata HiveR HLMdiag HLSM hmeasure Hmisc hmmm HMP HMPTrees hnp hoardeR homals HomoPolymer hot.deck hotspots HPbayes hpcwld hpoPlot HSAUR HSAUR2 HSAUR3 hsdar hSDM hsphase HSROC htmlTable htmltools HTMLUtils htmlwidgets hts HTSCluster httk httpuv httr huge HUM humanFormat HWEBayes hwriterPlus hwwntest HWxtest hybridEnsemble hybridHclust HybridMC hydroGOF HydroMe hydroPSO hydrostats hydroTSM HyperbolicDist hyperdirichlet hypergeo hyperSpec hypervolume HyPhy hysteresis hzar IAT IATscores iBATCGH ibd IBDsim ibeemd IBHM ibmdbR IBrokers iBUGS ic.infer iC10 icamix icaOcularCorrection iccbeta icd9 ICE ICEbox ICEinfer icenReg icensmis ICGE iCluster ICS ICSNP ICsurv idm IDPmisc iDynoR iFad ifctools iFes IFP ifultools iGasso IgorR igraph igraphdata igraphtosonia ihs iki.dataclim ilc IM imguR ImpactIV import imprProbEst imputeLCMD imputeR in2extRemes inarmix incReg indicoio indicspecies inference inferference influence.ME influence.SEM infoDecompuTE informR infuser infutil INLABMA inline insideRODE insol installr intamap intamapInteractive InteractiveIGraph interAdapt Interatrix intergraph internetarchive interplot Interpol.T interpretR interval IntLik inTrees intReg introgress intsvy InvariantCausalPrediction InventorymodelPackage investr invGauss io ipdmeta ipdw iplots IPMpack ipred ips IPSUR IQCC iRefR iRegression irlba irtoys irtProb irtrees IRTShiny isa2 isdals IsingFit IsingSampler ISLR ismev IsoCI isocir IsoGene isopam ISOpureR isotonic.pen IsotopeR ISOweek isva ISwR iteRates iterpc itertools itertools2 itree its itsadug IUPS ivivc ivlewbel ivmodel ivpack iWeigReg jaatha JADE jagsUI JAGUAR james.analysis JBTools JGL JGR jiebaR jiebaRD JM JMbayes Jmisc joineR JointRegBC jomo JOP JoSAE js jSonarR jsonlite jtrans KappaV kaps KATforDCEMRI kdecopula kdetrees kelvin Kendall kequate kerdiest kergp kernelFactory Kernelheaping KernSmooth KernSmoothIRT KFAS kfigr KFKSDS kimisc kineticF kinship2 kissmig kitagawa kknn klaR klausuR klin kmc kmi Kmisc kml kml3d kmodR knitcitations knitLatex knitr knitrBootstrap knnGarden knockoff kobe KODAMA KOGMWU kohonen KoNLP koRpus Kpart kpodclustr KrigInv KRLS krm ks kselection kst ktsolve kulife kwb.hantush kyotil kzs l2boost labdsv laeken LaF laGP Lahman LakeMetabolizer lakemorpho laketemps lambda.tools Lambda4 LambertW lamW landsat languageR lar laser lassoscore latentnet Laterality lattice latticeDensity latticeExtra LatticeKrig lava lava.tobit lavaan lavaan.survey lawn lawstat lazyData lazyeval lazyWeave lba lbfgs lbiassurv LCAextend lcd lcda lctools lda LDAvis ldbounds LDcorSV LDheatmap ldlasso LDOD LDPD ldr LDRTools leaflet leafletR LEAPFrOG leapp leaps learningr learnstats lefse lessR lestat letsR lfe lfl lfstat lga lgarch lgcp libamtrack LICORS LICurvature lifecontingencies LifeTables LIHNPSD likelihood likelihoodAsy likeLTD likert LIM limSolve linbin LindenmayeR LinearizedSVR lineup linkcomm LinRegInteractive LINselect lint lintr liso list llama lle lllcrc LLSR lm.br lme4 lmeNB lmenssp LMERConvenienceFunctions lmerTest lmeSplines LMest lmeVarComp lmfor lmmfit lmmlasso lmmot lmms lmSupport lmtest LncMod loa localdepth localgauss localsolver LocFDRPois locfit locits lodGWAS loe log4r LogConcDEAD logconcens logcondens logcondens.mode logcondiscr LogicForest LOGICOIL logistf LogisticDx logmult LogrankA lokern longitudinalData longmemo longpower longurl loo loop LoopAnalyst loopr lordif LOST LPCM lpme LPmerge LPTime lqmm lrmest LS2W LS2Wstat LSAfun lsbclust LSC lsgl lsmeans LSMonteCarlo lspls lss ltbayes ltm ltmle ltsbase ltsk lubridate luca lucid Luminescence lvm4net LVMMCOR lymphclon M3 maboost MAc MAclinical MAd mada mads Maeswrap magicaxis magrittr mailR MAINT.Data MALDIquant MALDIquantForeign MAMA managelocalrepo manifestoR MAPA mapDK mapfit MapGAM MAPLES mapmisc mapStats maptools maptpx maptree mAr MAR1 mar1s marelac marg markdown marked maRketSim markovchain MarkowitzR marmap MARSS maSAE MASS MasterBayes MAT Matching MatchingFrontier matchingMarkets matchingR MatchIt matie matR Matrix MatrixModels matrixpls matrixStats MAVIS MAVTgsa maxent maxLik maxlike MaxPro maxstat MazamaSpatialUtils MBA mbbefd MBESS mbest MBmca mbmdr mboost mc2d MCDA mcgibbsit mcheatmaps mcIRT MCL mcll mclogit mclust MCMC.OTU MCMC.qpcr MCMCglmm MCMCpack mcmcplots mco Mcomp MCPAN MCPerm MCPMod mcprofile mcsm McSpatial mda MDM MDPtoolbox MDR mdscore mdsdt MDSGUI measuRing meboot mederrRank medflex mediation medicalrisk MEET mefa mefa4 megaptera meifly mem memgene memisc MEMSS MenuCollection MergeGUI MESS meta MetABEL MetabolAnalyze metabolomics metacom metafolio metafor metagear metagen MetaLandSim metamisc metaMix MetaPCA metaplus MetaQC metaSEM metasens Metatron meteo meteoForecast meteogRam Meth27QC MethComp Methplot metricsgraphics metRology mets MetSizeR MetStaT MFHD mFilter MfUSampler mfx mgcv mglmn mgpd mgraph MGSDA mGSZ MHadaptive mht mhurdle mi mice miceadds micEcon micEconAids micEconCES micEconSNQP microbenchmark MicroDatosEs micromap micromapST micropan MicSim midasr MigClim migration.indices migui MIICD MIIVsem MImix miniCRAN minimist minPtest minqa minque MInt MIPHENO mirt mirtCAT miRtest misc3d miscF miscFuncs miscset miscTools missDeaths missForest MissingDataGUI missMDA mistat mistral MitISEM mitml mitools mixAK MixAll mixcat mixedMem MixedTS mixexp MixGHD mixlm mixlow MixMAP mixOmics mixPHM mixsep MixSim mixtools mizer mkde mkin MKmisc mlbench MLCIRTwithin mlDNA mldr MLDS mlearning mleur mlgt MLmetrics mlmRev mlogit mlogitBMA mlr mlVAR mlxR MM MM2S MM2Sdata mma mmand mme mmeta mmm mmm2 MMMS mmod MMS mmtfa mnlogit MNM MNP Mobilize MOCCA Modalclust modeest ModelGood ModelMap modiscloud modMax modQR modTempEff MOJOV mokken mombf Momocs mondate MonetDB.R mongolite monitoR monomvn moonBook morgenstemning Morpho morse MortalitySmooth mosaic mosaicData moult mountainplot move movMF mp mpa MPAgenomics mpath MPDiR MPINet mplot MplusAutomation mpm mpMap mpmcorrelogram mpmi mpoly Mposterior MPSEM MPTinR mQTL mratios MRCV mrds MRH MRIaggr mritc MRMR mRMRe MRwarping msap msarc msBP MSBVAR msda MSeasy MSeasyTkGUI MSG msgl msir MSIseq msm msme msos MSQC msr msSurv MST MSwM mtk MTS mtsdi MUCflights MuFiCokriging muir multcomp multcompView MultEq multgee multiAssetOptions multibiplotGUI multic multicon multicool multiDimBio multigroup MultiLCIRT multilevel multilevelPSA multimark MultiMeta multinomRob MultiOrd MultiPhen multipleNCC multiplex MultiRR multisensi MultiSV multitable multitaper multiwayvcov muma MuMIn munfold munsell musicNMR mutoss mutossGUI MVA mvabund MVB mvc mvctm mvcwt mvglmmRank mvinfluence mvmesh mvmeta mvMORPH MVN mvna mvnfast mvoutlier mvProbit MVR mvSLOUCH mwa mwaved MXM mycor myTAI mztwinreg nabor nadiv NAM nanop NanoStringNorm NAPPA nat nat.nblast nat.templatebrains nat.utils naturalsort nbpMatching nCal ncappc ncdf.tools NCmisc ndl ndtv NeatMap needy NEff neldermead neotoma NestedCohort nestedRanksTest netassoc netClass NetCluster netgen netgsa NetIndices netmeta nets NetSim nettools netweavers network networkD3 networkDynamic networkDynamicData networkreporting networksis networkTomography neuralnet NeuralNetTools neuroim nFactors ngramr ngramrr ngspatial NHEMOtree nhlscrapr NHMM NHMSAR NHPoisson nicheROVER Nippon nlme nlmeODE nlmeU nlmrt nloptr NLPutils nlreg nlsem NlsyLinks nlts nLTT nlWaldTest NMF NMOF nnet NNTbiomarker nodeHarvest nodiv nomclust NominalLogisticBiplot nonlinearTseries nonnest2 nonparaeff NonpModelCheck nonrandom nontarget nopp nor1mix NormalGamma NormalLaplace NORRRM NORTARA np nparcomp nparLD NPBayesImpute npbr NPC NPCD NPCirc npcp npde npIntFactRep nplr npmlreg NPMPM npsm npsp NSA nscancor nsga2R nsgp NSM3 nsprcomp NSUM nullabor numbers nutshell nutshell.audioscrobbler nutshell.bbdb nycflights13 oapackage OasisR oaxaca oblique.tree obliqueRF oc oce OceanView ODB odeintr odfWeave odfWeave.survey oem oglmx OjaNP okmesonet OLScurve OmicKriging oncomodel Oncotree onemap onlinePCA OpasnetUtils OPDOE openair opencpu OpenMx OpenRepGrid openssl OpenStreetMap opentraj openxlsx operator.tools operators optAUC optBiomarker optCluster optimbase optimsimplex optimx optiRum optiscale optmatch optparse optpart optrees ora ordBTL orddom ORDER2PARENT orderbook orderedLasso OrdFacReg ordinal ordinalCont OrdinalLogisticBiplot OrdNor ordPens ore OrgMassSpecR orgR orientlib oro.dicom oro.nifti oro.pet orQA orsk osmar ouch outbreaker OutbreakTools OutlierDC OutlierDM OutrankingTools OUwie P2C2M pa packdep packrat pacman Pade PAFit PAGI PAGWAS PairedData pairsD3 PairViz pairwise pairwiseCI palaeoSig paleobioDB paleofire paleoMAS paleotree palr pamctdp pamm pampe pamr pan PANDA pander panelaggregation panelAR PANICr papeR ParallelForest parallelMap parallelML parallelSVM ParamHelpers paramlink paran parboost parcor parfm parfossil parma parsedate partDSA partialAR partialOR partitionMap partitions party partykit parviol PAS pass pastecs pastis PASWR PASWR2 patchDVI patchPlot patchSynctex pathClass pathdiagram pathmox pathological PatternClass pauwels2014 pavo PAWL pbatR PBC PBD pbdPROF PBImisc pbkrtest pbo PBSadmb PBSddesolve PBSmapping PBSmodelling pca3d pcaBootPlot pcalg PCGSE pcnetmeta PCovR PCPS pcrcoal PCS pdc pdfCluster pdfetch pdmod PDQutils pec pedantics PedCNV pedgene pedigree pedigreemm pedometrics pegas PEIP penalizedLDA penalizedSVM pencopula pendensity penDvine penMSM pensim peperr PepPrep peptider pequod perARMA PerFit PerformanceAnalytics performanceEstimation perm PerMallows permGPU permute perry perspectev perturb pez PGICA pgirmess pglm pGLS PGRdup phalen phangorn PhaseType phcfM pheatmap phenability phenex phenmod pheno pheno2geno phenology phia phmm phom phonR PhViD phyclust phylin phylobase phyloclim phylocurve phyloland phylolm PhyloMeasures phylosim phylotools phyloTop physiology phytools phytotools pi0 picante picasso PIGShift pingr pipe.design pipeR pitchRx PivotalR PKfit pkgKitten pkgmaker PKgraph PKPDmodels PKreport pks planar plaqr playwith plfm plgp plm plmDE plmm plot2groups plot3D plot3Drgl plotGoogleMaps plotKML plotMCMC plotmo plotROC plotSEMM pls PLSbiplot1 plsdepot plsdof plsgenomics plspm plsRbeta plsRcox plsRglm plumbr plusser plyr PMA pmc pmclust pmg pmml pmmlTransformations pnmtrem pnn pocrm pogit PogromcyDanych pointRes PoisBinNonNor PoisBinOrd PoisBinOrdNonNor PoisBinOrdNor poisDoubleSamp PoisNonNor PoisNor poLCA polidata pollstR polyapost polycor polyCub polysat polySegratioMM polytomous polywog pomp popdemo PopED popgen PopGenome PopGenReport popgraph popKorn poplite poppr popRange popReconstruct popsom PopVar portes portfolio PortfolioAnalytics portfolioSim PortRisk PottsUtils PoweR poweRlaw PP ppiPre ppls ppmlasso PPtree PPtreeViz pqantimalarials prabclus PracTools prc precintcon PredictABEL predictmeans prefmod PReMiuM presens PResiduals prettyunits prevalence PrevMap prevR pRF prim primer primerTree primes PRISMA prLogistic prob probFDA ProbForecastGOP pROC ProDenICA prodlim PROFANCY ProfileLikelihood profileModel profileR profr ProgGUIinR progress ProjectTemplate propagate prospectr proteomicdesign proteomics protiq protoclass protr protViz provenance proxy PRROC pryr PSAboot PSCBS pscl pscore psd psData pse psgp psidR PSM pssm PST PsumtSim psych psychometric psychomix psychotools psychotree psyphy psytabs pt PTE ptinpoly pubmed.mineR PubMedWordcloud pumilioR PurBayes pushoverr PVAClone pvar pvclass pvclust PVR pvrank pvsR pxR pxweb pycno qat QCAGUI QCAtools qcc qclust qcr qdap qdapRegex qdapTools qgraph qgtools qicharts qiimer qlcMatrix qmap qmethod QoLR qpcR qqman qqtest qrfactor qrLMM QRM qrmtools qrNLMM qtl qtlbook qtlhot qtlnet QTLRel QuACN quadrupen QualInt qualityTools qualV Quandl quantchem quanteda quantification QuantifQuantile quantmod QuantPsyc quantreg quantregForest quantregGrowth quantspec QuantumClone QuasiSeq questionr quickpsy quint quipu qVarSel qvcalc qwraps2 R.devices R.filesets R.matlab R.rsp R0 R2admb R2BayesX r2d2 r2dRue R2GUESS R2HTML R2jags R2MLwiN R2OpenBUGS R2STATS R2SWF R2WinBUGS R330 R4CouchDB r4ss R6 race RAD RADami radiant radir RadOnc rags2ridges rainbow raincpc rainfreq rAltmetric RAM Rambo Ramd ramify RAMpath ramps randNames random random.polychor.pa RandomFields randomForest randomForestSRC randomGLM randomizationInference randomizr randomLCA randomNames randomUniformForest RandVar rangeMapper RankAggreg Rankcluster rankdist rankhazard RANN RANN.L1 RapidPolygonLookup RAPIDR RAppArmor rappdirs rapport rapportools rareGE rareNMtests rARPACK rasclass raster rasterVis rattle rAvis rbefdata rbhl RbioRXN rbison Rbitcoin rbmn Rborist rbounds RBPcurve rbugs rbundler RCA RCALI rCarto rcbalance Rcell rchallenge Rchoice rcicr RClimMAWGEN rClinicalCodes rclinicaltrials Rclusterpp Rcmdr RcmdrMisc RcmdrPlugin.BCA RcmdrPlugin.coin RcmdrPlugin.depthTools RcmdrPlugin.DoE RcmdrPlugin.doex RcmdrPlugin.EACSPIR RcmdrPlugin.EBM RcmdrPlugin.EcoVirtual RcmdrPlugin.epack RcmdrPlugin.EZR RcmdrPlugin.FactoMineR RcmdrPlugin.HH RcmdrPlugin.IPSUR RcmdrPlugin.KMggplot2 RcmdrPlugin.lfstat RcmdrPlugin.MA RcmdrPlugin.mosaic RcmdrPlugin.MPAStats RcmdrPlugin.NMBU RcmdrPlugin.orloca RcmdrPlugin.plotByGroup RcmdrPlugin.pointG RcmdrPlugin.qual RcmdrPlugin.RMTCJags RcmdrPlugin.ROC RcmdrPlugin.sampling RcmdrPlugin.SCDA RcmdrPlugin.seeg RcmdrPlugin.SLC RcmdrPlugin.SM RcmdrPlugin.sos RcmdrPlugin.StatisticalURV RcmdrPlugin.steepness RcmdrPlugin.survival RcmdrPlugin.TeachingDemos RcmdrPlugin.temis RcmdrPlugin.UCA RCMIP5 Rcolombos rcorpora RCPmod RcppAnnoy RcppAPT RcppArmadillo RcppBDT rcppbugs RcppClassic RcppClassicExamples RcppCNPy RcppDE RcppDL RcppEigen RcppExamples RcppFaddeeva RcppGSL RcppMLPACK RcppOctave RcppParallel RcppProgress RcppRedis RcppRoll RcppSMC RcppStreams RcppTOML RcppXts RcppZiggurat rcrossref rCUR Rd2roxygen RDataCanvas rdatamarket rdd rDEA Rdistance RDML rDNA rdrop2 rdryad RDS RDSTK rDVR readbitmap reader readGenalex readODS readr readstata13 readxl RealVAMS reams REBayes rebird rebmix rebus RECA recluster recommenderlab recommenderlabBX recommenderlabJester reconstructr RecordLinkage recosystem REdaS redcapAPI REDCapR redist REEMtree referenceIntervals RefFreeEWAS refGenome RefManageR refset refund refund.wave reGenotyper regexr reglogit regress RegressionFactory regRSM rehh relaimpo relations relaxnet reldist relevent ReliabilityTheory relimp relSim RelValAnalysis remix rEMM remote Renext RenextGUI rentrez Reol ReorderCluster RepeatedHighDim repijson replicatedpp2w replicationInterval repmis repolr ReporteRs reportRx reports REPPlab repra reproducer rerddap resemble reshape reshape2 reshapeGUI ResourceSelection REST restimizeapi restlos retistruct retrosheet reutils reval revealedPrefs RevEcoR rex rexpokit Rfacebook RFGLS RFgroove rfigshare RFinanceYJ rfishbase rfisheries Rfit RFLPtools RFmarkerDetector rfoaas RFOC RForcecom rfordummies rforensicbatwing rfPermute rfUtilities RGA rgam rgauges rgbif RGCCA rgdal RGENERATE RGENERATEPREC rgeos rgexf rggobi rgl rglobi RGoogleAnalytics RgoogleMaps rgp rgpui rgr RGraphics rgrass7 RH2 rhandsontable rHealthDataGov RHRV riceware rich ridigbio RIGHT RImageJROI rinat RInside rio rioja ripa riskRegression risksetROC rite RItools riv Rivivc rivr rjade RJafroc rjags RJDBC RJSDMX rjstat rknn rkvo rLakeAnalyzer Rlibeemd rLiDAR Rlinkedin rlist rlme RLRsim RLumShiny RM2 Rmalschains RMark rmarkdown rmatio RMAWGEN RMediation rmetasim rmgarch rminer Rmisc Rmixmod RmixmodCombi rmngb RMOA rmongodb Rmonkey Rmosek Rmpfr RMRAINGEN rms RMySQL rnaseqWrapper RnavGraph RnavGraphImageData rnbn RNCEP rncl RNetLogo RNeXML rngtools RNiftyReg rNMF rnoaa rNOMADS rnrfa RobAStBase robCompositions robcor robfilter RobLox RobLoxBioC RobPer RobRex RObsDat robust RobustAFT robustbase robustDA RobustEM robustfa robustgam robustHD robustlmm robustloggamma robustreg robustvarComp robustX rocc rockchalk RockFab rococo ROCR ROCS RODBCext rodd RODM ROptEst ROptEstOld ROptRegTS ror ROracle rorutadis ROSE rotations Rothermel roughrf RoughSets roxygen2 RPANDA rpanel rpartitions rpartScore RPCLR Rpdb RPEnsemble rpf rpg rphast Rphylip Rphylopars rPlant rplexos rplos RPMM RPostgreSQL RPPanalyzer rPref rprime rprintf RProtoBuf rpubchem RPublica RPyGeo RQDA rqPen Rquake RQuantLib rr rrcov rrcovHD rrcovNA RRF rriskDistributions rrlda RRreg RRTCS RSA rsae RSAGA Rsampletrees RSAP rsatscan RSDA rsdmx RSeed RSelenium rsem rSFA rsgcc RSiena rsig RsimMosaic RSiteCatalyst RSKC rsm rsml RSNNS rsnps RSNPset RSocrata RSofia Rsomoclu rspa rSPACE rspear RSPS RSQLite RSQLServer Rssa rstackdeque RStorm rsunlight RSurveillance RSurvey rtable rTableICC RTDE rtdists rtematres RTextTools rtf rtfbs rtkpp RTOMO rtop rts Rtsne rtype Ruchardet rucm rugarch rUnemploymentData runittotestthat runjags RunuranGUI RVAideMemoire Rvcg rversions rvertnet rvest RVFam rvgtest RVideoPoker RVowpalWabbit RVsharing RVtests rWBclimate RWBP RWebLogo RWeka RWiener rworldmap rworldxtra RxCEcolInf RXKCD RxnSim ryouready rYoutheria rysgran Rz s2dverification s4vd saccades sadists sads sae sae2 SAENET saeSim SamplerCompare sampleSelection samplesize4surveys sampling samplingbook sampSurf samr SAMUR SAMURAI sand sandwich sapa SASmixed SAVE saws sbmSDP SBRect SBSA sca Scale scales scalreg scam scape scaRabee SCBmeanfd SCEPtER SCEPtERbinary SCGLR scholar SCI scidb SciencesPo SciViews score scoring ScrabbleScore ScreenClean scrime scrm scrypt sda SDaA sdcMicro sdcMicroGUI sdcTable sdcTarget SDD SDDE sde SDMTools sdmvspecies sdwd seacarb searchable seas season seasonal seawaveQ SEchart SECP secr secrdesign secrlinear seeg SEERaBomb seewave seg segmag seismicRoll SEL selectMeta selectr selectspm SeleMix selfea selfingTree SelvarMix sem semdiag semGOF semiArtificial SEMID SemiMarkov SemiPar SemiParBIVProbit SemiParSampleSel semisupKernelPCA semPlot semPLS semsfa semTools sensitivity SensoMineR sensory sensR SenSrivastava SensusR separationplot seqCBS SeqFeatR SeqGrapheR seqinr seqMeta seqminer sequences seriation seroincidence servr sesem SetMethods sets settings sExtinct sfsmisc sft SGCS sgd sglasso sglOptim sglr SGP sGPCA SGPdata sgPLS sgr sgt shapeR shapes ShapeSelectForest SharpeR sharpshootR sharx shiny shinyAce shinybootstrap2 shinyBS shinydashboard shinyFiles shinyjs shinyRGL shinythemes shinyTree shopifyr shotGroups showtext showtextdb shp2graph shrink siar SID sideChannelAttack sidier sigloc signal signal.hsmm Sim.DiffProc simba simboot simcausal SimComp SimCorMultRes simecol simex simFrame SIMMS simMSM simPH simpleboot simpleNeural SimpleTable simPop Simpsons SimRAD simrel simsalapar simsem simTool SINGLE siplab sirad siRSM sirt SIS sisus sisVIVE sitar sivipm SixSigma SiZer sjmisc sjPlot skatMeta skellam SkewHyperbolic Skillings.Mack skmeans sla slackr Sleuth2 Sleuth3 slfm SLOPE slp sm smacof smacpod smam smart SmarterPoland smatr smbinning smcfcs smcUtils smdc smds sme SMFI5 smint SMIR SmithWilsonYieldCurve SML SMNCensReg smnet smoof smoother SmoothHazard smoothie smoothmest smoothtail SMPracticals sms smss sna snht snipEM snp.plotter SNPassoc snpEnrichment snplist snpRF snpStatsWriter sns soc.ca SocialMediaMineR SocialNetworks SOD SODC Sofi softImpute soil.spec soilDB soilphysics soilprofile SoilR soiltexture soilwater solaR solarius solr SOMbrero somplot soobench SOPIE SOR SortableHTMLTables sortinghat sorvi sos sos4R sotkanet soundecology SoundexBR SOUP sp spa spaa SPACECAP spaceExt spacejam spacetime spacodiR spacom spam spaMM spanr spareserver spark sparkTable sparr sparseBC SparseGrid sparseHessianFD sparseLDA sparseLTSEigen sparseMVN sparsenet SparseTSCGM spartan spatgraphs spatial spatial.gev.bma spatial.tools spatialEco SpatialEpi SpatialExtremes spatialnbda SpatialNP SpatialPack SpatialPosition spatialprobit spatialsegregation spatialTailDep SpatialTools SpatialVx SpatioTemporal SpatPCA spatstat spatsurv spBayes spBayesSurv spca spcadjust spcosa spd spdep spdynmod SpecHelpers SpeciesMix specificity spectral.methods speedglm speff2trial sperich sperrorest spfrontier spgrass6 spgwr sphereplot SpherWave sphet spider spiders spikeslab spikeSlabGAM splancs splitstackshape splm spls SPMS spnet spocc SPODT SportsAnalytics SPOT SPREDA sprint sprinter sprm SPSL spsmooth spsurvey spTDyn spTest spThin spTimer sptm spuRs sqldf sqliter sqlutils SQN srd ss3sim sscor SSDforR sse ssfa ssfit ssh.utils ssizeRNA ssmrob SSN sspse SSrat sss ssym st stab stabledist StableEstim stabs Stack stagePop stam StAMPP StanHeaders STAR statar statcheck StatDA statebins statfi stationaRy StatMatch StatMeasures StatMethRank statmod statnet statnetWeb Statomica staTools StatRank stcm stellaR Stem STEPCAM stepp StereoMorph stilt stm stmCorrViz STMedianPolish StMoMo StMoSim stocc stochprofML stochvol stocks Storm stosim stpp stppResid strap strataG StratSel stream StreamMetabolism streamMOA stremo stressr stringdist stringgaussnet stringr strucchange structSSI strum strvalidator stsm stylo SubLasso SubpathwayGMir subselect subsemble subtype SUE summarytools supclust superbiclust superdiag SuperLearner support.BWS support.CEs surface Surrogate surv2sampleComp survAccuracyMeasures survAUC SurvCorr surveillance survey surveydata survMisc survrec survsim survSNP svapls svcm svdvisual SVMMaj SVMMatch svSweave SvyNom svyPVpack swamp SWATmodel SweaveListingUtils sweidnumbr swirl SwissAir switchnpreg switchrGist SWMPr sybil sybilccFBA sybilcycleFreeFlux sybilDynFBA sybilEFBA sybilSBML symbolicDA symmoments synbreed SynchWave SYNCSA synlik synRNASeqNet Synth synthpop sysfonts systemfit systemicrisk syuzhet tab table1xls tableone tableplot tables tabplot tabplotd3 tagcloud TAM TANOVA TapeR TAQMNGR taRifx taRifx.geo tawny tawny.types taxize tbart tbdiag TBEST TBSSurvival TcGSA tclust tcR TDA TDAmapper TDboost TDD tdm TDMR tdr TeachingDemos TED tergm termstrc ternvis TESS tester TestSurvRec testthat testthatsomemore texmex texreg textir textreg TFMPvalue tfplot tframePlus tgp tgram TH.data Thermimage ThreeArmedTrials threeboost threejs ThresholdROC TiddlyWikiR tidyjson tidyr tiger tigerstats tikzDevice tileHMM timeit timeline timeordered TimeProjection timereg timeROC timesboot timeSeq timeSeries timeseriesdb timetree timma TIMP Tinflex tis titan TKF tkrgl tlemix tlm tlnise tm.plugin.webmining tmap TMDb tmg tmle tmle.npvi tmod tmvtnorm tnet TOC tolerance topicmodels TopKLists topologyGSA tourr tourrGui TPmsm TR8 TrackReconstruction traitr traits traj trajectories TraMineR TraMineRextras translateR translateSPSS2R trapezoid TreatmentSelection treatSens tree treebase treeclim treeClust treecm treemap TreePar TreeSim TreeSimGM treethresh trend TriMatch trimcluster trimTrees trioGxE trip tripEstimation TripleR TROM truncgof truncreg truncSP trustOptim TSA tsbridge tsbugs TSclust TScompare tscount 65.72
  27. 27. V8 (Jeroen Ooms) > ct <- new_context(); > ct$eval("var foo = 123") > ct$eval("var bar = 456") > ct$eval("foo+bar") [1] 579
  28. 28. RcppParallel (tbb)
  29. 29. x <- rnorm(1e6) y <- rnorm(1e6) list( sum(x), sum(y) )
  30. 30. #include <Rcpp.h> using namespace Rcpp ; // [[Rcpp::export]] List foo_ser( NumericVector x, NumericVector y){ double sum_x = sum(x) ; double sum_y = sum(y) ; return List::create( sum_x, sum_y ) ; }
  31. 31. #incluce <Rcpp.h> #include <RcppParallel.h> using namespace Rcpp ; // [[Rcpp::export]] List foo_par( NumericVector x, NumericVector y){ double sum_x, sum_y ; tbb::parallel_invoke( [&]{ sum_x = sum(x); }, [&]{ sum_y = sum(y); } ); return List::create( sum_x, sum_y ) ; }
  32. 32. > microbenchmark(foo_par(x, y), foo_ser(x, y)) Unit: microseconds expr min lq mean median uq max neval foo_par(x, y) 927.881 953.1895 978.1571 962.404 979.2335 1359.195 100 foo_ser(x, y) 1729.898 1743.2565 1834.9246 1781.639 1843.0930 3065.796 100
  33. 33. y <- sqrt(x)
  34. 34. // [[Rcpp::export]] NumericVector cpp_sqrt_ser( NumericVector x ){ int n = x.size(); NumericVector y = no_init(n) ; std::transform( x.begin(), x.end(), y.begin(), ::sqrt ) ; return y ; }
  35. 35. // [[Rcpp::export]] NumericVector cpp_sqrt_par( NumericVector x ){ int n = x.size(); NumericVector y = no_init(n) ; parallel_for( blocked_range<int>(0, n), [&]( const blocked_range<int>& r ){ std::transform( x.begin() + r.begin(), x.begin() + r.end(), y.begin() + r.begin(), ::sqrt ) ; }) ; return y ; }
  36. 36. > microbenchmark(cpp_sqrt_ser(x), cpp_sqrt_par(x)) Unit: milliseconds expr min lq mean median uq max neval cpp_sqrt_ser(x) 53.73738 55.13791 59.42455 57.56475 61.08836 106.12388 100 cpp_sqrt_par(x) 15.85457 16.85143 18.06249 17.54641 18.61418 47.86795 100
  37. 37. nucleusnucleus
  38. 38. dplyr
  39. 39. flights %>% group_by(carrier) %>% summarise(x = mean(dep_delay, na.rm = TRUE) )
  40. 40. Romain François @romain_francois

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