A Collection of Efficient and Extremely Fast R Functions

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Documentation for package ‘Rfast’ version 2.1.0

• DESCRIPTION file.
• Package NEWS.

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A B C D E F G H I J K L M N O P Q R S T U V W X Y Z misc

Rfast-package

A Collection of Efficient and Extremely 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 area under 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
coeff	Coefficient matrices.
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 area under 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
colmeans.data.frame	Column and row-wise means of a matrix
colmeans.matrix	Column and row-wise means of a matrix
colMedians	Column and row-wise medians of a matrix or median of a vector.
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	Minima and maxima of two vectors/matrices and Column-row wise minima and maxima of two matrices
colPmin	Minima and maxima of two vectors/matrices and 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
colVars.data.frame	Column and row-wise variances and standard deviations of a matrix
colVars.matrix	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 - Sum of all pairwise distances in a distance matrix
dista	Distance between vectors and a matrix - Sum of all pairwise distances in a distance 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.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	Column and row-wise mean absolute deviations
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	Column and row-wise medians of a matrix or median of a vector.
Median	Column and row-wise medians of a matrix or 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 and Column-row wise minima and maxima of two matrices
Pmin	Minima and maxima of two vectors/matrices and Column-row wise minima and maxima of two matrices
Pmin_Pmax	Minima and maxima of two vectors/matrices and Column-row wise minima and maxima of two 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	Column and row-wise ranks
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 of a matrix or median of a vector.
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	Distance matrix - Sum of all pairwise distances in a distance matrix
total.dista	Distance between vectors and a matrix - 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 - Sum of all pairwise distances in a 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