Rfast2

####New version Date release: 16/12/2019

###Statistical functions

Improved (by speed, correctness or options)

Function What’s new!

New

| Function | What’s new! | | gammareg | Gamma regression | | gammaregs | Many gamma regressions | | cor_test | Hypothesis testing for the correlation coefficient | | cor_test | Hypothesis testing for the correlation coefficient | | hcf.circaov | ANOVA for circular data | | het.circaov | ANOVA for circular data | | lr.circaov | ANOVA for circular data | | multivm.mle | Fitting many von Mises distributions | | multispml.mle | Fitting many von SPML distributions | | depth.mahala | Mahalanobis depth | | perm.ttest2 | Permutation based 2 sample t-test | | lm.parboot | Parametric bootstrap for linear models | | weibull.nb | Weibull Naive Bayes (NB) classifier | | weibullnb.pred | Prediction using Weibull NB classifier | | normlog.nb | Gaussian(log-link) NB classifier | | normlognb.pred | Prediction using Gaussian(log-link) NB classifier | | laplace.nb | Laplace NB classifier | | laplacenb.pred | Prediction using Laplace NB classifier | | vm.nb | von Mises NB classifier | | vmnb.pred | Prediction using von Mises NB classifier | | spml.nb | SPML NB classifier | | spml.pred | Prediction using SPML NB classifier |

###Utility functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

####Version Date release: 28/07/2019

###Statistical functions

Improved (by speed, correctness or options)

Function What’s new!

bic.regs Addition SPML and Weibull regression

pc.sel Time improvement

welch.tests Time improevement

New

Function What’s new!

cls Constrained least squares regression

cluster.lm Linear regression with clustered data

colborel.mle Column-wise MLE of the Borel distribution

collogitnorm.mle Column-wise MLE of the logistic normal distribution

collognorm.mle Column-wise MLE of the log-normal distribution

cospml.mle Column-wise MLE of the SPML distribution

empirical.entropy Empirical entropy estimation with continuous data

fbed.reg FBED variable selection algorithm

gumbel.reg Gumbel regression

moranI Moran’s I measure of spatial autocorrelation

multinom.reg Multinomial regression

negbin.reg Negative binomial regression

pca Principal component analysis

refmeta Random effects meta-analysis estimation

simplex.mle MLE of the simplex distribution

weib.regs Many simple weibull regressions

ztp.reg zero truncated Poisson regression

mmpc2 MMPC variable selection algorithm

###Utility functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

is.skew.symmetric Checking if the given matrix is skew-symmetric.

Function	What’s new!
bic.regs	Addition SPML and Weibull regression
pc.sel	Time improvement
welch.tests	Time improevement

Function	What’s new!
cls	Constrained least squares regression
cluster.lm	Linear regression with clustered data
colborel.mle	Column-wise MLE of the Borel distribution
collogitnorm.mle	Column-wise MLE of the logistic normal distribution
collognorm.mle	Column-wise MLE of the log-normal distribution
cospml.mle	Column-wise MLE of the SPML distribution
empirical.entropy	Empirical entropy estimation with continuous data
fbed.reg	FBED variable selection algorithm
gumbel.reg	Gumbel regression
moranI	Moran’s I measure of spatial autocorrelation
multinom.reg	Multinomial regression
negbin.reg	Negative binomial regression
pca	Principal component analysis
refmeta	Random effects meta-analysis estimation
simplex.mle	MLE of the simplex distribution
weib.regs	Many simple weibull regressions
ztp.reg	zero truncated Poisson regression
mmpc2	MMPC variable selection algorithm

Function	What’s new!
is.skew.symmetric	Checking if the given matrix is skew-symmetric.

####Version 0.03 Date release: 08/05/2019

###Statistical functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

###Utility functions

Improved (by speed, correctness or options)

Function What’s new!

benchmark fix a bug in printing names.

New

Function What’s new!

Function	What’s new!
benchmark	fix a bug in printing names.

####Version 0.0.2 Date release: 08/05/2019

###Statistical functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

gee.reg Gereneralised estimating equations Gaussian regression

halfcauchy.mle MLE of the half Cauchy distribution

kumar.mle MLE of the Kumaraswamy distribution

powerlaw.mle MLE of the power law distribution

reg.mle.lda Regularised maximum likleihood linear discriminant analysis

walter.ci Confidence interval for the relative risk using Walter’s method

welch.tests Many Welch t-tests

###Utility functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

Function	What’s new!
gee.reg	Gereneralised estimating equations Gaussian regression
halfcauchy.mle	MLE of the half Cauchy distribution
kumar.mle	MLE of the Kumaraswamy distribution
powerlaw.mle	MLE of the power law distribution
reg.mle.lda	Regularised maximum likleihood linear discriminant analysis
walter.ci	Confidence interval for the relative risk using Walter’s method
welch.tests	Many Welch t-tests

####Version 0.0.1 Date release: 19/03/2019

###Statistical functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

add.term Add many single terms to a model.

bic.regs BIC of many univariate regressions.

censpois.mle MLE of the left censored Poisson distribution.

cesweibull.mle MLE of the censored Weibull distribution.

circ.cor1 Circurlar correlations between two circular variables.

circ.cors1 Circurlar correlations between a circular and many circular variables.

colmeansvars Column-wise means and variances of a matrix.

covar Covariance betweeen a vector and a matrix.

diffic Difficulty of items (psychometric theory).

discrim Discrimination of items (psychometric theory).

gammapois.mle MLE of the gamma-Poisson distribution.

km Kaplan-Meier estimate of a survival function.

logiquant.regs Many simple quantile regressions using logistic regressions.

mle.lda Maximum likelihood linear discriminant analysis.

pc.sel Variable selection using the PC-simple algorithm.

pooled.colVars Column-wise pooled variances across groups.

purka.mle MLE of the Purkayastha distribution.

sp.logiregs Many approximate simple logistic regressionss.

trunccauchy.mle MLE of the truncated Cauchy distribution.

truncexpmle MLE of the truncated exponential distribution.

wald.poisrat Wald confidence interval for the ratio of two Poisson variables.

col.waldpoisrat Column-wise Wald confidence interval for the ratio of two Poisson variables.

welch.tests Many Welch tests.

zigamma.mle MLE of the zero inflated Gamma distribution.

ziweibull.mle MLE of the zero inflated Weibull distribution.

zil.mle MLE of the zero inflated logistic normal distribution.

Function	What’s new!
add.term	Add many single terms to a model.
bic.regs	BIC of many univariate regressions.
censpois.mle	MLE of the left censored Poisson distribution.
cesweibull.mle	MLE of the censored Weibull distribution.
circ.cor1	Circurlar correlations between two circular variables.
circ.cors1	Circurlar correlations between a circular and many circular variables.
colmeansvars	Column-wise means and variances of a matrix.
covar	Covariance betweeen a vector and a matrix.
diffic	Difficulty of items (psychometric theory).
discrim	Discrimination of items (psychometric theory).
gammapois.mle	MLE of the gamma-Poisson distribution.
km	Kaplan-Meier estimate of a survival function.
logiquant.regs	Many simple quantile regressions using logistic regressions.
mle.lda	Maximum likelihood linear discriminant analysis.
pc.sel	Variable selection using the PC-simple algorithm.
pooled.colVars	Column-wise pooled variances across groups.
purka.mle	MLE of the Purkayastha distribution.
sp.logiregs	Many approximate simple logistic regressionss.
trunccauchy.mle	MLE of the truncated Cauchy distribution.
truncexpmle	MLE of the truncated exponential distribution.
wald.poisrat	Wald confidence interval for the ratio of two Poisson variables.
col.waldpoisrat	Column-wise Wald confidence interval for the ratio of two Poisson variables.
welch.tests	Many Welch tests.
zigamma.mle	MLE of the zero inflated Gamma distribution.
ziweibull.mle	MLE of the zero inflated Weibull distribution.
zil.mle	MLE of the zero inflated logistic normal distribution.

###Utility functions

Improved (by speed, correctness or options)

Function What’s new!

New

Function What’s new!

Intersect Intersect as R’s.

is.lower.tri Check if a matrix is lower triangular.

is.upper.tri Check if a matrix is upper triangular.

lud Split a matrix to a lower,upper matrix and diagonal vector.

Merge Merge 2 sorted vectors to a sorted vector.

benchmark Measure code’s execution time.

colGroup Apply Rfast’s gorup function to each column with some restrictions.

Quantile Quantile(s) of a vector.

colQuantile Column-wise quantile(s) of a matrix.

rowQuantile Row-wise quantile(s) of a matrix.

trim.mean Trimmed mean of a vector.

colTrimMean Column-wise trimmed mean of a matrix.

rowTrimMean Row-wise trimmed mean of a matrix.

Function	What’s new!
Intersect	Intersect as R’s.
is.lower.tri	Check if a matrix is lower triangular.
is.upper.tri	Check if a matrix is upper triangular.
lud	Split a matrix to a lower,upper matrix and diagonal vector.
Merge	Merge 2 sorted vectors to a sorted vector.
benchmark	Measure code’s execution time.
colGroup	Apply Rfast’s gorup function to each column with some restrictions.
Quantile	Quantile(s) of a vector.
colQuantile	Column-wise quantile(s) of a matrix.
rowQuantile	Row-wise quantile(s) of a matrix.
trim.mean	Trimmed mean of a vector.
colTrimMean	Column-wise trimmed mean of a matrix.
rowTrimMean	Row-wise trimmed mean of a matrix.