# A Collection of Efficient and Extremely Fast R Functions ## Help Pages

 Rfast-package Really fast R functions

## -- A --

 acg.mle MLE of (hyper-)spherical distributions AddToNamespace Insert/remove function names in/from the NAMESPACE file allbetas Simple linear regressions coefficients allttests Matrix with all pairs of t-tests all_equals Equality of objects ancova1 Analysis of covariance ancovas Many ANCOVAs anova1 Multi-sample tests for vectors anovas Many multi-sample tests anova_propreg Significance testing for the coefficients of Quasi binomial or the quasi Poisson regression anova_qpois.reg Significance testing for the coefficients of Quasi binomial or the quasi Poisson regression anova_quasipois.reg ANOVA for two quasi Poisson regression models apply.condition Apply to each column a method under condition ar1 Estimation of an AR(1) model as.Rfast.function Convert R function to the Rfast's coresponding as_integer Check if values are integers and convert to integer auc Many are aunder the curve values

## -- B --

 bc Estimation of the Box-Cox transformation bcdcor Distance correlation beta.mle MLE of distributions defined in the (0, 1) interval betabinom.mle MLE of count data betageom.mle MLE of count data betaprime.mle MLE of continuous univariate distributions defined on the positive line bic.corfsreg BIC (using partial correlation) forward regression bic.fs.reg BIC forward regression with generalised linear models binary_search Binary search algorithm bincomb Permutation binom.mle MLE of count data block.anova Multi-sample tests for vectors block.anovas Many multi-sample tests boot.ttest2 Bootstrap t-test for 2 independent samples borel.mle MLE of count data bs.reg Backward selection regression btmprobs Fitted probabilities of the Terry-Bradley model

## -- C --

 cat.goftests Many one sample goodness of fit tests for categorical data cauchy.mle MLE of continuous univariate distributions defined on the real line checkAliases Check Namespace and Rd files checkExamples Check Namespace and Rd files checkNamespace Check Namespace and Rd files checkTF Check Namespace and Rd files checkUsage Check Namespace and Rd files check_data Search for variables with zero range in a matrix chi2Test G-square test of conditional indepdence chi2tests Many G-square tests of indepedence chi2Test_univariate Matrix with G-square tests of indepdence chisq.mle MLE of continuous univariate distributions defined on the positive line cholesky Cholesky decomposition of a square matrix Choose Binomial coefficient and its logarithm circlin.cor Circular-linear correlation col.coxpoisrat Cox confidence interval for the ratio of two Poisson variables col.yule Column-wise Yule's Y (coefficient of colligation) colAll Column and row-wise Any colanovas Many Welch's F-tests colAny Column and row-wise Any colar1 Estimation of an AR(1) model colaucs Many are aunder the curve values colCountValues Row - Wise matrix/vector count the frequency of a value colCumMaxs Colum-wise cumulative operations (sum, prod, min, max) colCumMins Colum-wise cumulative operations (sum, prod, min, max) colCumProds Colum-wise cumulative operations (sum, prod, min, max) colCumSums Colum-wise cumulative operations (sum, prod, min, max) colcvs Column and row wise coefficients of variation coldiffs Column-wise differences colexp2.mle Column-wise MLE of some univariate distributions colexpmle Column-wise MLE of some univariate distributions colFalse Column-wise true/false value of a matrix colgammamle Column-wise MLE of some univariate distributions colgeom.mle MLE for multivariate discrete data colhameans Column and row-wise means of a matrix colinvgauss.mle Column-wise MLE of some univariate distributions colkurtosis Column-wise kurtosis and skewness coefficients collaplace.mle Column-wise MLE of some univariate distributions collindley.mle Column-wise MLE of some univariate distributions colMads Column and row-wise mean absolute deviations colmaxboltz.mle Column-wise MLE of some univariate distributions colMaxs Column-wise minimum and maximum of a matrix colmeans Column and row-wise means of a matrix colMedians Column and row-wise medians colMins Column-wise minimum and maximum of a matrix colMinsMaxs Column-wise minimum and maximum of a matrix colnormal.mle Column-wise MLE of some univariate distributions colnormlog.mle Column-wise MLE of some univariate distributions colnth Column and row-wise nth smallest value of a matrix/vector colOrder Column and row-wise Order - Sort Indices colpareto.mle Column-wise MLE of some univariate distributions colPmax Column-row wise minima and maxima of two matrices colPmin Column-row wise minima and maxima of two matrices colpois.tests Many tests for the dispersion parameter in Poisson distribution colpoisdisp.tests Many tests for the dispersion parameter in Poisson distribution colpoisson.anovas Many ANOVAS for count data with Poisson or quasi Poisson models colpoisson.mle MLE for multivariate discrete data colprods Column and row-wise products colquasipoisson.anovas Many ANOVAS for count data with Poisson or quasi Poisson models colrange Column and row-wise range of values of a matrix. colRanks Column and row-wise ranks colrayleigh.mle Column-wise MLE of some univariate distributions colrint.regbx Many random intercepts LMMs for balanced data with a single identical covariate colrow.value Check if any column or row is fill with values colShuffle Column and row-wise Shuffle colskewness Column-wise kurtosis and skewness coefficients colSort Sorting of the columns-rows of a matrix colsums Column and row-wise sums of a matrix colTabulate Column and row-wise tabulate colTrue Column-wise true/false value of a matrix colTrueFalse Column-wise true/false value of a matrix columns Get specific columns/rows fo a matrix colvarcomps.mle Many moment and maximum likelihood estimations of variance components colvarcomps.mom Many moment and maximum likelihood estimations of variance components colVars Column and row-wise variances and standard deviations of a matrix colvm.mle Column-wise MLE of some univariate distributions colwatsons Column-wise uniformity tests for circular data colweibull.mle Column-wise MLE of some univariate distributions comb_n All k possible combinations from n elements cor.fbed FBED variable selection method using the correlation cor.fsreg Correlation based forward regression. cora Fast covariance and correlation matrix calculation corpairs Correlation between pairs of variables correls Correlation between a vector and a set of variables count_value Row - Wise matrix/vector count the frequency of a value cova Fast covariance and correlation matrix calculation cox.poisrat Cox confidence interval for the ratio of two Poisson variables cqtest Multi-sample tests for vectors cqtests Many multi-sample tests Crossprod Matrix multiplication, Cross and Tcross product. ct.mle MLE of continuous univariate distributions defined on the real line

## -- D --

 data.frame.to_matrix Convert a dataframe to matrix dcor Distance correlation dcor.ttest Hypothesis test for the distance correlation dcov Distance variance and covariance design_matrix Design Matrix Diag.fill Diagonal Matrix Diag.matrix Diagonal Matrix Digamma Natural logarithm of the gamma function and its derivatives. diri.nr2 Fitting a Dirichlet distribution via Newton-Rapshon dirimultinom.mle MLE for multivariate discrete data dirknn k-NN algorithm using the arc cosinus distance dirknn.cv Cross-Validation for the k-NN algorithm using the arc cosinus distance Dist Distance matrix dista Distance between vectors and a matrix dmvnorm Density of the multivariate normal and t distributions dmvt Density of the multivariate normal and t distributions dvar Distance variance and covariance

## -- E --

 eachcol.apply Operations between two matrices or matrix and vector eachrow Operations between two matrices or matrix and vector edist Energy distance between matrices eel.test1 Empirical and exponential empirical likelihood tests for one sample eel.test2 Empirical and exponential empirical likelihood tests for two samples eigen.sym Limited number of eigenvalues and eigenvectors of a symmetric matrix el.test1 Empirical and exponential empirical likelihood tests for one sample el.test2 Empirical and exponential empirical likelihood tests for two samples Elem Iterator Elem.iterator Iterator Elem<- Iterator Elem<-.iterator Iterator env.copy Deep copy exact.ttest2 Exact t-test for 2 independent samples exp2.mle MLE of continuous univariate distributions defined on the positive line expmle MLE of continuous univariate distributions defined on the positive line expregs Many exponential regressions

## -- F --

 fish.kent Hypothesis test for von Mises-Fisher distribution over Kent distribution floyd Floyd-Warshall algorithm for shortest paths in a directed graph foldnorm.mle MLE of continuous univariate distributions defined on the positive line freq.max Minimum and maximum frequencies of a vector freq.min Minimum and maximum frequencies of a vector fs.reg Variable selection in generalised linear regression models with forward selection ftest Multi-sample tests for vectors ftests Many multi-sample tests

## -- G --

 g2Test G-square test of conditional indepdence g2tests Many G-square tests of indepedence g2tests_perm Many G-square tests of indepedence g2Test_perm G-square test of conditional indepdence g2Test_univariate Matrix with G-square tests of indepdence g2Test_univariate_perm Matrix with G-square tests of indepdence gammacon Gamma regression with a log-link gammamle MLE of continuous univariate distributions defined on the positive line gammanb Naive Bayes classifiers gammanb.pred Prediction with some naive Bayes classifiers gammareg Gamma regression with a log-link gammaregs Many simple regressions for positive valued data gaussian.nb Naive Bayes classifiers gaussiannb.pred Prediction with some naive Bayes classifiers gchi2Test Chi-square and G-square tests of (unconditional) indepdence geom.anova Analysis of variance with a count variable geom.anovas Many analysis of variance tests with a discrete variable geom.mle MLE of count data geom.nb Naive Bayes classifiers geom.regs Many simple geometric regressions. geomnb.pred Prediction with some naive Bayes classifiers ginis Many Gini coefficients glm_logistic Logistic and Poisson regression models glm_poisson Logistic and Poisson regression models group Some summary statistics of a vector for each level of a grouping variable. group.mean Some summary statistics of a vector for each level of a grouping variable. group.sum Some summary statistics of a vector for each level of a grouping variable. groupcorrels Correlation between a vector and a set of variables gumbel.mle MLE of continuous univariate distributions defined on the real line

## -- H --

 halfnorm.mle MLE of continuous univariate distributions defined on the positive line Hash Hash object hash.find Find the given value in a hash table Hash.key.multi Hash object hash.list Hash - Pair function hash2list Hash object to a list object hd.eigen Eigenvalues in high dimensional principal component analysis hsecant01.mle MLE of distributions defined in the (0, 1) interval

## -- I --

 iag.mle MLE of (hyper-)spherical distributions ibeta.mle MLE of distributions defined in the (0, 1) interval invdir.mle MLE of the inverted Dirichlet distribution invgauss.mle MLE of continuous univariate distributions defined on the positive line invgauss.reg Inverese Gaussian regression with a log-link invgauss.regs Many simple regressions for positive valued data is.symmetric Check whether a square matrix is symmetric is_element Find element is_integer Check if values are integers and convert to integer iterator Iterator

## -- J --

 james James multivariate version of the t-test

## -- K --

 knn k nearest neighbours algorithm (k-NN) knn.cv Cross-Validation for the k-NN algorithm kruskaltest Multi-sample tests for vectors kruskaltests Many multi-sample tests kuiper Uniformity tests for circular data kurt Skewness and kurtosis coefficients kurt.test2 Hypothesis testing between two skewness or kurtosis coefficients

## -- L --

 laplace.mle MLE of continuous univariate distributions defined on the real line Lbeta Natural logarithm of the beta function Lchoose Binomial coefficient and its logarithm length.Hash Hash object Lgamma Natural logarithm of the gamma function and its derivatives. lindley.mle MLE of continuous univariate distributions defined on the positive line list.ftests Many F-tests with really huge matrices lmfit Linear models for large scale data Log Natural Logarithm each element of a matrix logcauchy.mle MLE of continuous univariate distributions defined on the positive line logistic.cat1 Logistic or Poisson regression with a single categorical predictor logistic.mle MLE of continuous univariate distributions defined on the real line logistic_only Many univariate simple binary logistic regressions logitnorm.mle MLE of distributions defined in the (0, 1) interval loglogistic.mle MLE of continuous univariate distributions defined on the positive line lognorm.mle MLE of continuous univariate distributions defined on the positive line logseries.mle MLE of count data lomax.mle MLE of continuous univariate distributions defined on the positive line lower_tri Lower and Upper triangular of a matrix lower_tri.assign Lower and Upper triangular of a matrix

## -- M --

 Mad Mean - Median absolute deviation of a vector mad2 Mean - Median absolute deviation of a vector mahala Mahalanobis distance mat.mat Number of equal columns between two matrices mat.mult Matrix multiplication, Cross and Tcross product. Match Match match.coefs Column-wise matching coefficients matrnorm Generates random values from a normal and puts them in a matrix maxboltz.mle MLE of continuous univariate distributions defined on the positive line mcnemar Multi-sample tests for vectors mcnemars Many 2 sample tests tests med Median of a vector Median Median of a vector mediandir Fast calculation of the spherical and hyperspherical median min_max Minimum and maximum of a vector multinom.mle MLE for multivariate discrete data multinom.nb Naive Bayes classifiers multinom.reg Multinomial regression multinom.regs Many simple multinomial regressions. multinomnb.pred Prediction with some naive Bayes classifiers multivmf.mle MLE of (hyper-)spherical distributions mv.eeltest1 Exponential empirical likelihood for a one sample mean vector hypothesis testing mv.eeltest2 Exponential empirical likelihood hypothesis testing for two mean vectors mvbetas Many multivariate simple linear regressions coefficients mvkurtosis Multivariate kurtosis mvlnorm.mle MLE of the multivariate (log-) normal distribution mvnorm.mle MLE of the multivariate (log-) normal distribution mvt.mle MLE of the multivariate t distribution

## -- N --

 negative Apply method to Positive and Negative number negbin.mle MLE of count data Norm Norm of a matrix normal.mle MLE of continuous univariate distributions defined on the real line normlog.mle MLE of continuous univariate distributions defined on the positive line normlog.reg Gaussian regression with a log-link normlog.regs Many simple regressions for positive valued data nth Column and row-wise nth smallest value of a matrix/vector

## -- O --

 odds Many odds ratio tests odds.ratio Odds ratio and relative risk omp Orthogonal matching pursuit variable selection ompr Orthogonal matching pursuit variable selection Order Column and row-wise Order - Sort Indices ordinal.mle MLE of the ordinal model without covariates Outer Outer function

## -- P --

 pareto.mle MLE of continuous univariate distributions defined on the positive line pc.skel The skeleton of a Bayesian network produced by the PC algorithm percent.ttest Hypothesis test for two means of percentages percent.ttests Many hypothesis tests for two means of percentages permcor Permutation based p-value for the Pearson correlation coefficient permutation Permutation permutation.next Permutation permutation.prev Permutation Pmax Minima and maxima of two vectors/matrices Pmin Minima and maxima of two vectors/matrices Pmin_Pmax Minima and maxima of two vectors/matrices pois.test Tests for the dispersion parameter in Poisson distribution poisdisp.test Tests for the dispersion parameter in Poisson distribution poisson.anova Analysis of variance with a count variable poisson.anovas Many analysis of variance tests with a discrete variable poisson.cat1 Logistic or Poisson regression with a single categorical predictor poisson.mle MLE of count data poisson.nb Naive Bayes classifiers poissonnb.pred Prediction with some naive Bayes classifiers poisson_only Many univariate simple binary logistic regressions poly.cor Polyserial correlation pooled.cov Pooled covariance matrix positive Apply method to Positive and Negative number positive.negative Apply method to Positive and Negative number print.Hash Hash object print.iterator Iterator print.ufactor Fast and general represantation of a factor variable prop.reg Quasi binomial regression for proportions prop.regs Quasi binomial regression for proportions proptest Many one sample tests proptests Many 2 sample proportions tests

## -- Q --

 qpois.reg Quasi Poisson regression qpois.regs Quasi Poisson regression quasi.poisson_only Many univariate simple poisson regressions quasipoisson.anova Analysis of variance with a count variable quasipoisson.anovas Many analysis of variance tests with a discrete variable

## -- R --

 racg Angular central Gaussian random values simulation Rank Ranks of the values of a vector rayleigh.mle MLE of continuous univariate distributions defined on the positive line rbing Simulating from a Bingham distribution rbingham Simulation of random values from a Bingham distribution with any symmetric matrix read.directory Reading the files of a directory read.examples Reading the files of a directory regression Many univariate simple linear regressions rel.risk Odds ratio and relative risk RemoveFromNamespace Insert/remove function names in/from the NAMESPACE file rep_col Replicate columns/rows rep_row Replicate columns/rows rint.mle Moment and maximum likelihood estimation of variance components rint.reg Random intercepts linear mixed models rint.regbx Random intercepts linear mixed models rint.regs Many simple linear mixed model regressions rm.anova Repeated measures anova rm.anovas Many regression based tests for single sample repeated measures rm.lines Many regression based tests for single sample repeated measures rmdp High dimensional MCD based detection of outliers rmvlaplace Multivariate Laplace random values simulation rmvnorm Multivariate normal and t random values simulation rmvt Multivariate normal and t random values simulation Rnorm Simulation of random values from a normal distribution Round Round each element of a matrix/vector rowAll Column and row-wise Any rowAny Column and row-wise Any rowCountValues Row - Wise matrix/vector count the frequency of a value rowcvs Column and row wise coefficients of variation rowFalse Row-wise true value of a matrix rowhameans Column and row-wise means of a matrix rowMads Column and row-wise mean absolute deviations rowMaxs Row-wise minimum and maximum of a matrix. rowmeans Column and row-wise means of a matrix rowMedians Column and row-wise medians rowMins Row-wise minimum and maximum of a matrix. rowMinsMaxs Row-wise minimum and maximum of a matrix. rownth Column and row-wise nth smallest value of a matrix/vector rowOrder Column and row-wise Order - Sort Indices rowprods Column and row-wise products rowrange Column and row-wise range of values of a matrix. rowRanks Column and row-wise ranks rows Get specific columns/rows fo a matrix rowShuffle Column and row-wise Shuffle rowSort Sorting of the columns-rows of a matrix rowsums Column and row-wise sums of a matrix rowTabulate Column and row-wise tabulate rowTrue Row-wise true value of a matrix rowTrueFalse Row-wise true value of a matrix rowVars Column and row-wise variances and standard deviations of a matrix rvmf Random values simulation from a von Mises-Fisher distribution rvonmises Random values simulation from a von Mises distribution

## -- S --

 score.betaregs Many score based regressions score.expregs Many score based regressions score.gammaregs Many score based regressions score.geomregs Many score based regressions score.glms Many score based regressions score.invgaussregs Many score based regressions score.multinomregs Many score based regressions score.negbinregs Many score based regressions score.weibregs Many score based regressions score.ztpregs Many score based regressions sftest Many Shapiro-Francia normality tests sftests Many Shapiro-Francia normality tests skew Skewness and kurtosis coefficients skew.test2 Hypothesis testing between two skewness or kurtosis coefficients Sort Sort - Integer Sort - Sort a vector coresponding to another Sort.int Sort - Integer Sort - Sort a vector coresponding to another sort_cor_vectors Sort - Integer Sort - Sort a vector coresponding to another sort_mat Sorting of the columns-rows of a matrix sort_unique Sort and unique sort_unique.length Sort and unique sourceR Source many R files sourceRd Source many R files spat.med Spatial median for Euclidean data spatmed.reg Spatial median regression spdinv Inverse of a symmetric positive definite matrix spml.mle MLE of some circular distributions spml.reg Circular or angular regression spml.regs Many simple circular or angular regressions squareform Vector allocation in a symmetric matrix sscov Spatial sign covariance matrix Stack Represantation of Stack standardise Standardisation submatrix Sub-matrix

## -- T --

 Table Table Creation - Frequency of each value Table.sign Table Creation - Frequency of each value Tcrossprod Matrix multiplication, Cross and Tcross product. tmle MLE of continuous univariate distributions defined on the real line tobit.mle MLE of the tobit model topological_sort Topological sort of a DAG total.dist Sum of all pairwise distances in a distance matrix total.dista Sum of all pairwise distances in a distance matrix transpose Transpose of a matrix Trigamma Natural logarithm of the gamma function and its derivatives. ttest Many one sample tests ttest1 One sample t-test for a vector ttest2 Multi-sample tests for vectors ttests Many 2 sample tests tests ttests.pairs Matrix with all pairs of t-tests twoway.anova Multi-sample tests for vectors twoway.anovas Many two-way ANOVAs

## -- U --

 ufactor Fast and general represantation of a factor variable univglms Many univariate generalised linear regressions univglms2 Many univariate generalised linear regressions upper_tri Lower and Upper triangular of a matrix upper_tri.assign Lower and Upper triangular of a matrix

## -- V --

 Var Variance (and standard deviation) of a vector var2test Multi-sample tests for vectors var2tests Many 2 sample tests tests varcomps.mle Moment and maximum likelihood estimation of variance components varcomps.mom Moment and maximum likelihood estimation of variance components vartest Many one sample tests vartests Many multi-sample tests vecdist Distance matrix vm.mle MLE of some circular distributions vmf.mle MLE of (hyper-)spherical distributions

## -- W --

 watson Uniformity tests for circular data weib.reg Weibull regression model weibull.mle MLE of continuous univariate distributions defined on the positive line which.is Index of the columns of a data.frame which are a specific type wigner.mle MLE of continuous univariate distributions defined on the real line wrapcauchy.mle MLE of some circular distributions

## -- X --

 XopY.sum Operations between two matrices or matrix and vector

## -- Y --

 yule Yule's Y (coefficient of colligation)

## -- Z --

 zip.mle MLE of count data ztp.mle MLE of count data

## -- misc --

 !=.iterator Iterator ==.iterator Iterator [.Hash Hash object [.ufactor Fast and general represantation of a factor variable [<-.Hash Hash object