A Collection of Efficient and Extremely Fast R Functions


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Documentation for package ‘Rfast’ version 2.0.6

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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 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