Package: Rfast2 0.1.5.2

Manos Papadakis

Rfast2: A Collection of Efficient and Extremely Fast R Functions II

A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions. References: Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.

Authors:Manos Papadakis, Michail Tsagris, Stefanos Fafalios, Marios Dimitriadis and Manos Lasithiotakis.

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# Install Rfast2 in R:
install.packages('Rfast2', repos = c('https://fastverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rfastofficial/rfast2/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

190 exports 35 stars 4.10 score 7 dependencies 19 dependents 3.2k downloads

Last updated 3 months agofrom:645fdad275ca9ddf18aa91750aa66755d2cfd100

Exports:add.termbatch.logisticbenchmarkbernoulli.nbbernoullinb.predbeta.nbbetanb.predbic.regsbig.knnbigknn.cvbinom.regboot.hotel2boot.jamesboot.student2boot.ttest1cauchy.nbcauchy0.mlecauchynb.predcbern.mlecenspois.mlecensweib.regcensweibull.mlecirc.cor1circ.cors1clscluster.lmcol.waldpoisratcolaccscolbeta.mlecolborel.mlecolcauchy.mlecolcenspois.mlecolcensweibull.mlecolfbscorescolfmiscolfscorescolGroupcolhalfcauchy.mlecolhalfnorm.mlecoljack.meanscollogitnorm.mlecollognorm.mlecolmaescolmeansvarscolmsescolordinal.mlecolpinar1colpklcolpowerlaw.mlecolprecscolQuantilecolsenscolsp.mlecolspecscolspml.mlecolTrimMeancoluklcolunitweibull.mlecolwlsmetacor_testcovarcovdistcovequalcovlikelcovmtestcovrob.lmdcoraden.contoursdepth.mahaladifficdiscrimeel.cor.testel.cor.testembed.circaovempirical.entropyfbed.regfe.lmfitfedhc.skelfipois.regfisher.dafpgammapois.mlegammareggammaregsgee.reggnormal0.mlegumbel.reghalfcauchy.mlehcf.circaovhellinger.countreghet.circaovhet.lmfithp.regIntersectis.lower.triis.skew.symmetricis.upper.trijack.meanjbtestjbtestskmkumar.mlelaplace.nblaplacenb.predleveragelm.bsreglm.drop1lm.nonparbootlm.parbootlogiquant.regslogitnorm.nblogitnormnb.predlr.circaovludmciMergemle.ldammhc.skelmmpcmmpc2moranImultinom.regmultinomreg.cvmultispml.mlemultivm.mlemv.score.betaregsmv.score.expregsmv.score.gammaregsmv.score.glmsmv.score.invgaussregsmv.score.weibregsnb.cvnegbin.regnegbin.regsnormal.etestnormlog.nbnormlognb.predomp2overdispreg.testpc.selpcapcrperm.ttest2pinar1pooled.colVarspowerlaw.mleprophelling.regpropols.regpurka.mleQuantilerbeta1refmetareg.mle.ldaregmlelda.cvriagrm.hotelrowjack.meansrowQuantilerowTrimMeanRunifSampleSample.intsclrscore.zipregssimplex.mlesp.logiregssp.mlespml.nbspmlnb.predstud.tteststobit.regtrim.meantrunccauchy.mletruncexpmleunitweibull.mlevm.nbvmnb.predwald.poisratwalter.ciweib.regsweibull.nbweibullnb.predwelch.testswild.bootwlsmetazigamma.mlezigamma.regzil.mleziweibull.mleztp.reg

Dependencies:RcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRfastRnanoflann

Readme and manuals

Help Manual

Help pageTopics
Really fast R functionsRfast2-package
Add many single terms to a modeladd.term
Angular Gaussian random values simulationriag
Analysis of variance for circular dataembed.circaov hcf.circaov het.circaov lr.circaov
backward selection with the F test or the partial correlation coefficientlm.bsreg
Benchmark - Measure timebenchmark print.benchmark
BIC of many simple univariate regressions.bic.regs
Binomial regressionbinom.reg
Bootstrap James and Hotelling test for 2 independent sample mean vectorsboot.hotel2 boot.james
Bootstrap Student's t-test for 2 independent samplesboot.student2
Censored Weibull regression modelcensweib.reg
Check if a matrix is Lower or Upper triangularis.lower.tri is.upper.tri
Check whether a square matrix is skew-symmetricis.skew.symmetric
Circurlar correlations between two circular variablescirc.cor1 circ.cors1
Cluster robust wild bootstrap for linear modelswild.boot
Column and row-wise jackknife sample meanscoljack.means rowjack.means
Column-wise means and variances of a matrixcolmeansvars
Column-wise MLE of some univariate distributionscolbeta.mle colborel.mle colcauchy.mle colcenspois.mle colcensweibull.mle colhalfcauchy.mle colhalfnorm.mle collogitnorm.mle collognorm.mle colordinal.mle colpowerlaw.mle colsp.mle colunitweibull.mle
Column-wise MLE of the angular Gaussian distributioncolspml.mle
Column-wise pooled variances across groupspooled.colVars
Column-wise summary statistics with grouping variablescolGroup
Column-wise weighted least squares meta analysiscolwlsmeta
Conditional least-squares estimate for Poisson INAR(1) modelscolpinar1 pinar1
Constrained least squarescls
Contour plots of some bivariate distributionsden.contours
Correlation significance testing using Fisher's z-transformationcor_test
Covariance between a variable and a set of variablescovar
Cross-validation for the k-NN algorithm for really lage scale databigknn.cv
Cross-validation for the multinomial regressionmultinomreg.cv
Cross-validation for the naive Bayes classifiersnb.cv
Cross-validation for the regularised maximum likelihood linear discriminant analysisregmlelda.cv
Diagonal values of the Hat matrixleverage
Distance between two covariance matricescovdist
Distance correlation matrixdcora
Empirical and exponential empirical likelihood test for a correlation coefficienteel.cor.test el.cor.test
Empirical entropyempirical.entropy
Energy based normality testnormal.etest
Fisher's linear discriminant analysisfisher.da
Fixed effects regressionfe.lmfit
Fixed intercepts Poisson regressionfipois.reg
Forward Backward Early Dropping selection regressionfbed.reg
Fractional polynomial regression with one independent variable.fp
Gamma regression with a log-linkgammareg
GEE Gaussian regressiongee.reg
Gumbel regressiongumbel.reg
Hellinger distance based regression for count datahellinger.countreg
Hellinger distance based univariate regression for proportionsprophelling.reg
Heteroscedastic linear models for large scale datahet.lmfit
Hurdle-Poisson regressionhp.reg
Hypothesis test for equality of a covariance matrixcovequal
Hypothesis tests for equality of multiple covariance matricescovlikel covmtest
Intersect OperationIntersect
Item difficulty and discriminationdiffic discrim
Jackknife sample meanjack.mean
Kaplan-Meier estimate of a survival functionkm
Linear model with sandwich robust covariance estimatorcovrob.lm
Linear regression with clustered datacluster.lm
Logistic regression for large scale databatch.logistic
Mahalanobis depthdepth.mahala
Many 2 sample student's t-testsstud.ttests
Many approximate simple logistic regressions.sp.logiregs
Many binary classification metricscolaccs colfbscores colfmis colfscores colprecs colsens colspecs
Many Gamma regressionsgammaregs
Many Jarque-Bera normality testsjbtest jbtests
any metrics for a continuous response variablecolmaes colmses colpkl colukl
Many negative binomial regressionsnegbin.regs
Many score based regressions with muliple response variables and a single predictor variablemv.score.betaregs mv.score.expregs mv.score.gammaregs mv.score.glms mv.score.invgaussregs mv.score.weibregs
Many score based zero inflated Poisson regressionsscore.zipregs
Many simple quantile regressions using logistic regressions.logiquant.regs
Many simple Weibull regressions.weib.regs
Many Welch tests.welch.tests
Max-Min Parents and Children variable selection algorithm for continuous responsesmmpc
Max-Min Parents and Children variable selection algorithm for non continuous responsesmmpc2
Maximum likelihood linear discriminant analysismle.lda
Merge 2 sorted vectors in 1 sorted vectorMerge
MLE of continuous univariate distributions defined on the positive linehalfcauchy.mle powerlaw.mle
MLE of distributions defined for proportionscbern.mle kumar.mle simplex.mle sp.mle unitweibull.mle zil.mle
MLE of some circular distributions with multiple samplesmultispml.mle multivm.mle
MLE of some truncated distributionstrunccauchy.mle truncexpmle
MLE of the Cauchy and generalised normal distributions with zero locationcauchy0.mle gnormal0.mle
MLE of the censored Weibull distributioncensweibull.mle
MLE of the gamma-Poisson distributiongammapois.mle
MLE of the left censored Poisson distributioncenspois.mle
MLE of the Purkayastha distributionpurka.mle
MLE of the zero inflated Gamma and Weibull distributionszigamma.mle ziweibull.mle
Monte Carlo Integration with a normal distributionmci
Moran's I measure of spatial autocorrelationmoranI
Multinomial regressionmultinom.reg
Naive Bayes classifier for binary Bernoulli databernoulli.nb
Naive Bayes classifiersbeta.nb cauchy.nb laplace.nb logitnorm.nb normlog.nb weibull.nb
Naive Bayes classifiers for directional dataspml.nb vm.nb
Negative binomial regressionnegbin.reg
Non linear least squares regression for percentages or proportionspropols.reg
One sample bootstrap t-test for a vectorboot.ttest1
Orthogonal matching variable selectionomp2
Parametric and non-parametric bootstrap for linear regression modellm.nonparboot lm.parboot
Permutation t-test for 2 independent samplesperm.ttest2
Prediction with naive Bayes classifier for binary (Bernoulli) databernoullinb.pred
Prediction with some naive Bayes classifiersbetanb.pred cauchynb.pred laplacenb.pred logitnormnb.pred normlognb.pred weibullnb.pred
Prediction with some naive Bayes classifiers for circular dataspmlnb.pred vmnb.pred
Principal component analysispca
Principal components regressionpcr
Random effects and weighted least squares meta analysisrefmeta wlsmeta
Random integer values simulationSample Sample.int
Random values generation from a Be(a, 1) distributionrbeta1
Random values simulation from the uniform distributionRunif
Regularised maximum likelihood linear discriminant analysisreg.mle.lda
Repeated measures ANOVA (univariate data) using Hotelling's T^2 testrm.hotel
Sample quantiles and col/row wise quantilescolQuantile colQuantile.data.frame colQuantile.matrix Quantile rowQuantile
Scaled logistic regressionsclr
Score test for overdispersion in Poisson regressionoverdispreg.test
Single terms deletion hypothesis testing in a linear regression modellm.drop1
The skeleton of a Bayesian network produced by the FEDHC algorithmfedhc.skel
The skeleton of a Bayesian network learned with the MMHC algorithmmmhc.skel
Split the matrix in lower, upper triangular and diagonallud
The k-NN algorithm for really lage scale databig.knn
Tobit regressiontobit.reg
Trimmed meancolTrimMean colTrimMean.data.frame colTrimMean.matrix rowTrimMean trim.mean
Variable selection using the PC-simple algorithmpc.sel
Wald confidence interval for the ratio of two Poisson variablescol.waldpoisrat wald.poisrat
Walter's confidence interval for the ratio of two binomial variables (and the relative risk)walter.ci
Zero inflated Gamma regressionzigamma.reg
Zero truncated Poisson regressionztp.reg