Rfast

Version 2.0.5

Improved (by speed, correctness or options)

Function What’s new!

Dist, total.dist, vecdist New distance algorithm named “haversine”.

gaussian.nb 3 times faster than the old version. Add new option for parallel which decreases execution 18 times.

checkUsage Fix a bug about “=function”. Optimized empty return values and error messages.

checkAliases, checkTF Optimized empty return values.

edist Fix a bug.

dirimultinom.mle Fix a bug.

Function	What’s new!
Dist, total.dist, vecdist	New distance algorithm named “haversine”.
gaussian.nb	3 times faster than the old version. Add new option for parallel which decreases execution 18 times.
checkUsage	Fix a bug about “=function”. Optimized empty return values and error messages.
checkAliases, checkTF	Optimized empty return values.
edist	Fix a bug.
dirimultinom.mle	Fix a bug.

Version 2.0.4

Improved (by speed, correctness or options)

Function What’s new!

nth Fix a bug using na_rm. In github is #52.

colsums,rowsums Add new option for removing NAs and optimize option indices.

Function	What’s new!
nth	Fix a bug using na_rm. In github is #52.
colsums,rowsums	Add new option for removing NAs and optimize option indices.

Version 2.0.0

Improved (by speed, correctness or options)

Function What’s new!

Var Time improvement for removing NAs.

checkUsage From now on check for S3methods and fix bug.

Tcrossprod Same as R’s tcrossprod.

Crossprod Same as R’s crossprod.

matrix_multiplication Add new arguments for perfoming cross or tcross product.

Function	What’s new!
Var	Time improvement for removing NAs.
checkUsage	From now on check for S3methods and fix bug.
Tcrossprod	Same as R’s tcrossprod.
Crossprod	Same as R’s crossprod.
matrix_multiplication	Add new arguments for perfoming cross or tcross product.

Version 1.9.9

Improved (by speed, correctness or options)

Function What’s new!

Var Time improvement for removing NAs.

colVars Time improvement and depricate argument “suma”.

rowVars Time improvement and depricate argument “suma”.

rowMedians Add option for removing NAs if any.

colMads Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.

rowMads Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.

mad2 Deprecated. Use “Mad” instead.

med Deprecated. Use “Median” instead.

colShuffle Fix a bug.

rowShuffle Fix a bug.

rmdp Fix a bug.

checkUsage From now on check for S3methods.

AddToNamespace From now on export S3methods.

checkAliases From now on check the S3methods.

checkNamespace Don’t use it for now.

Comments

From now on the Rfast can be used in C++ via “LinkingTo” mechanism. The main namespace is “Rfast”. Inside “Rfast” you will find two more namespaces, “vector” and “matrix”. Namespace “vector” for calling functions using an Rcpp’s or RcppArmadillo’s vector. Namespace “matrix” for calling functions using an Rcpp’s or RcppArmadillo’s matrices. The signatures of the functions and the arguments are the same that are exported in R.

For namespace “vector” the functions that are available are:

median(x)

var(x, std = false, na_rm = false)

mad(x, method = “median”, na_rm = false)

shuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.

For namespace “matrix” the functions that are available are:

transpose(x)

matrix_multiplication(x,y)

colSort(x, descend = false, stable = false, parallel = false)

rowSort(x, descend = false, stable = false, parallel = false)

is_symmetric(x)

colMedian(x, na_rm = false, parallel = false)

rowMedian(x, na_rm = false, parallel = false)

colVars(x, std = false, na_rm = false, parallel = false)

rowVars(x, std = false, na_rm = false, parallel = false)

colMads(x, method = “median”, na_rm = false, parallel = false)

rowMads(x, method = “median”, na_rm = false, parallel = false)

colShuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.

rowShuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.

How to use it:

Just add in “LinkingTo” in your NAMESPACE file the “Rfast” or in Rstudio add in the file “//[[Rcpp::depends(Rfast)]]”.

Include in your cpp files the header “Rfast.h” and enjoy!

Function	What’s new!
Var	Time improvement for removing NAs.
colVars	Time improvement and depricate argument “suma”.
rowVars	Time improvement and depricate argument “suma”.
rowMedians	Add option for removing NAs if any.
colMads	Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.
rowMads	Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.
mad2	Deprecated. Use “Mad” instead.
med	Deprecated. Use “Median” instead.
colShuffle	Fix a bug.
rowShuffle	Fix a bug.
rmdp	Fix a bug.
checkUsage	From now on check for S3methods.
AddToNamespace	From now on export S3methods.
checkAliases	From now on check the S3methods.
checkNamespace	Don’t use it for now.

Version 1.9.8

Improved (by speed, correctness or options)

Function What’s new!

spml.mle Fix of a bug.

dirknn Time improvement.

glm_logistic Made the code more robust.

vmf.mle Made the code more robust.

cor.fbed Fix of a bug.

Dist Fix of a bug.

Function	What’s new!
spml.mle	Fix of a bug.
dirknn	Time improvement.
glm_logistic	Made the code more robust.
vmf.mle	Made the code more robust.
cor.fbed	Fix of a bug.
Dist	Fix of a bug.

Version 1.9.4

Improved (by speed, correctness or options)

Function What’s new!

allbetas Time improvement

cor.fbed Time improvement

cor.fsreg Time improvement

omp Time improvement

ompr Time improvement

score.betaregs Time improvement

score.gammaregs Time improvement

score.glms Time improvement

score.invgaussregs Time improvement

score.negbinregs Time improvement

score.ztpregs Time improvement

group.any Deprecated and replaced by group

group.all Deprecated and replaced by group

group.min Deprecated and replaced by group

group.max Deprecated and replaced by group

group.min_max Deprecated and replaced by group

group.mean Deprecated and replaced by group

group.med Deprecated and replaced by group

group.mad Deprecated and replaced by group

group.var Deprecated and replaced by group

group.sum Deprecated and replaced by group

groupcolVars Deprecated and replaced by “Rfast2::colGroup(…,method=”var“)”

sort_mat Deprecated and replaced by “colSort” and “rowSort”

AddToNamespace remove unused option

nth fix bug

Function	What’s new!
allbetas	Time improvement
cor.fbed	Time improvement
cor.fsreg	Time improvement
omp	Time improvement
ompr	Time improvement
score.betaregs	Time improvement
score.gammaregs	Time improvement
score.glms	Time improvement
score.invgaussregs	Time improvement
score.negbinregs	Time improvement
score.ztpregs	Time improvement
group.any	Deprecated and replaced by group
group.all	Deprecated and replaced by group
group.min	Deprecated and replaced by group
group.max	Deprecated and replaced by group
group.min_max	Deprecated and replaced by group
group.mean	Deprecated and replaced by group
group.med	Deprecated and replaced by group
group.mad	Deprecated and replaced by group
group.var	Deprecated and replaced by group
group.sum	Deprecated and replaced by group
groupcolVars	Deprecated and replaced by “Rfast2::colGroup(…,method=”var“)”
sort_mat	Deprecated and replaced by “colSort” and “rowSort”
AddToNamespace	remove unused option
nth	fix bug

Version 1.9.3

Improved (by speed, correctness or options)

Function What’s new!

omp Time improvement.

sort_mat Replaced by “colSort” and “rowSort” and will be removed in the next udate.

checkUsage Remove uneccessary option.

read.examples Remove uneccessary option.

checkTF Remove uneccessary option.

checkAliases Remove uneccessary option.

comb_n Add option for return list or matrix.

rownth Fix of a bug.

New

Function What’s new!

omp Multinomial regression now added.

omp Option to standardise the predictor variables.

cor.fbed Option to standardise the predictor variables.

cor.fsreg Option to standardise the predictor variables.

el.test2 Empirical likelihood test for two sample means.

Function	What’s new!
omp	Time improvement.
sort_mat	Replaced by “colSort” and “rowSort” and will be removed in the next udate.
checkUsage	Remove uneccessary option.
read.examples	Remove uneccessary option.
checkTF	Remove uneccessary option.
checkAliases	Remove uneccessary option.
comb_n	Add option for return list or matrix.
rownth	Fix of a bug.

Function	What’s new!
omp	Multinomial regression now added.
omp	Option to standardise the predictor variables.
cor.fbed	Option to standardise the predictor variables.
cor.fsreg	Option to standardise the predictor variables.
el.test2	Empirical likelihood test for two sample means.

Version 1.9.2

Improved (by speed, correctness or options)

Function What’s new!

omp Time improvement.

ompr Time improvement.

cor.fbed Time improvement.

multinom.mle Time improvement.

weib.reg Fix a bug and time improvement.

spatmed.reg Time improvement.

invgauss.reg Time improvement.

invgauss.regs Time improvement.

gammareg Time improvement.

gammaregs Time improvement.

gammacon Time improvement.

colvm.mle Time improvement.

gammaregs Time improvement.

el.test1 Time improvement.

Norm Fix a bug.

which_isFactor Removed and replaced by “which.is”.

checkUsage Fix a bug.

colsums Time improvement for integer matrices.

rowsums Time improvement for integer matrices.

med Faster **version.

sort.unique.length slightly faster **version.

sort.unique slightly faster **version.

Stack Fix a bug and add function clear for efficient reuse of the Stack.

read.example Fix a bug.

New

Function What’s new!

omp Multinomial regression now added.

Comments

From now on the Rfast needs R version >= 3.5

Function	What’s new!
omp	Time improvement.
ompr	Time improvement.
cor.fbed	Time improvement.
multinom.mle	Time improvement.
weib.reg	Fix a bug and time improvement.
spatmed.reg	Time improvement.
invgauss.reg	Time improvement.
invgauss.regs	Time improvement.
gammareg	Time improvement.
gammaregs	Time improvement.
gammacon	Time improvement.
colvm.mle	Time improvement.
gammaregs	Time improvement.
el.test1	Time improvement.
Norm	Fix a bug.
which_isFactor	Removed and replaced by “which.is”.
checkUsage	Fix a bug.
colsums	Time improvement for integer matrices.
rowsums	Time improvement for integer matrices.
med	Faster **version.
sort.unique.length	slightly faster **version.
sort.unique	slightly faster **version.
Stack	Fix a bug and add function clear for efficient reuse of the Stack.
read.example	Fix a bug.

Function	What’s new!
omp	Multinomial regression now added.

Version 1.9.1

Improved (by speed, correctness or options)

Function What’s new!

ompr Time improvement.

omp Time improvement .

cholesky Time improvement.

colnth, rownth Add extra options, “na.rm” and “descending” order and “index.return”.

colrow.zero deprecate it and replaced by “colrow.value”.

New

Function What’s new!

which.is The same with which_isFactor but general. Use this instead of which_isFactor.

colrow.value Search if a column and row is filled with a specific value.

Function	What’s new!
ompr	Time improvement.
omp	Time improvement .
cholesky	Time improvement.
colnth, rownth	Add extra options, “na.rm” and “descending” order and “index.return”.
colrow.zero	deprecate it and replaced by “colrow.value”.

Function	What’s new!
which.is	The same with which_isFactor but general. Use this instead of which_isFactor.
colrow.value	Search if a column and row is filled with a specific value.

Version 1.9.0

Improved (by speed, correctness or options)

Function What’s new!

topological_sort Time improvement.

permcor Fix a bug.

omp Time improvement.

normlog.regs Fix a bug.

cova Added an extra argument.

ompr Time improvement.

as_integer Fix a bug.

Round Fix a bug. digit argument can be up to 15.

matrix.sum Deprecate it.

countNA Deprecate it.

sort_unique.length Deprecate it for numeric numbers.

Rank Deprecate method=“first”.

Match Improved.

nth Improved method for integers.

colshuffle Fix a bug.

transpose Now can handle generic matrix using parallel

colshuffle Fix a bug.

New

Function What’s new!

betabinom.mle MLE of the beta binomial distribution.

betageom.mle MLE of the beta geometric distribution.

multivt.mle MLE of the multivariate t distribution.

colpoisson.anovas Column-wise ANOVA with Poisson distribution.

colquasipoisson.anovas Column-wise ANOVA with quasi Poisson.

exact.ttest2 Exact permutations 2-sample t-test.

chi2Test Chi-squared test of independence.

gchi2Test G-square and Chi-square tests of indepdence.

chi2tests Many chi-squared tests of independence.

chi2Test_univariate Matrix with chi-square tests of indepedence.

mvlnorm.mle MLE of the multivariate lognormal distribution.

poly.cor Polychoric correlation.

pooled.cov Pooled covariance matrix.

spatmed.reg Spatial median (multivariate) regression.

sscov Spatial sign covariance matrix.

trim.colmeans Trimmed column-wise means.

trim.rowmeans Trimmed row-wise means.

eigs.sym Extract some principal components from a symmetric matrix.

invgauss.regs Many simple inverse Gaussian regressions with a log link.

invgauss.reg Inverse Gaussian regression with a log link.

gammaregs Many simple Gamma regressions with a log link.

gammareg Gamma regression with a log link.

gammacon Gamma regression with a constant term only.

Outer like R’s outer.

RemoveFromNamespace remove exported functions.

Sort.int fast sorting integer.

colCumMaxs apply cummax to column.

colCumSums apply cumsum to column.

colCumMins apply cummin to column.

colCumProds apply cumprod to column.

positive apply method to each positive value.

positive.negative apply method to each positive and negative value.

negative apply method to each negative value.

as.Rfast.function convert an R function to Rfast’s equivalent

mat.mult Generic matrix multiplication using parallel.

checkUsage checking usage section in Rd files.

Hash Create Hash object.

Hash.key Search key or multi key.

apply.condition Apply method to each column using a condition. Only integers.

Stack Stack object. See man page.

iterator iterator object. See man page.

Elem access element of an iterator object.

print.environment S3 method for printing environment.

env.copy deep copy environment.

ufactor Untyped factor object. See man page.

Function	What’s new!
topological_sort	Time improvement.
permcor	Fix a bug.
omp	Time improvement.
normlog.regs	Fix a bug.
cova	Added an extra argument.
ompr	Time improvement.
as_integer	Fix a bug.
Round	Fix a bug. digit argument can be up to 15.
matrix.sum	Deprecate it.
countNA	Deprecate it.
sort_unique.length	Deprecate it for numeric numbers.
Rank	Deprecate method=“first”.
Match	Improved.
nth	Improved method for integers.
colshuffle	Fix a bug.
transpose	Now can handle generic matrix using parallel
colshuffle	Fix a bug.

Function	What’s new!
betabinom.mle	MLE of the beta binomial distribution.
betageom.mle	MLE of the beta geometric distribution.
multivt.mle	MLE of the multivariate t distribution.
colpoisson.anovas	Column-wise ANOVA with Poisson distribution.
colquasipoisson.anovas	Column-wise ANOVA with quasi Poisson.
exact.ttest2	Exact permutations 2-sample t-test.
chi2Test	Chi-squared test of independence.
gchi2Test	G-square and Chi-square tests of indepdence.
chi2tests	Many chi-squared tests of independence.
chi2Test_univariate	Matrix with chi-square tests of indepedence.
mvlnorm.mle	MLE of the multivariate lognormal distribution.
poly.cor	Polychoric correlation.
pooled.cov	Pooled covariance matrix.
spatmed.reg	Spatial median (multivariate) regression.
sscov	Spatial sign covariance matrix.
trim.colmeans	Trimmed column-wise means.
trim.rowmeans	Trimmed row-wise means.
eigs.sym	Extract some principal components from a symmetric matrix.
invgauss.regs	Many simple inverse Gaussian regressions with a log link.
invgauss.reg	Inverse Gaussian regression with a log link.
gammaregs	Many simple Gamma regressions with a log link.
gammareg	Gamma regression with a log link.
gammacon	Gamma regression with a constant term only.
Outer	like R’s outer.
RemoveFromNamespace	remove exported functions.
Sort.int	fast sorting integer.
colCumMaxs	apply cummax to column.
colCumSums	apply cumsum to column.
colCumMins	apply cummin to column.
colCumProds	apply cumprod to column.
positive	apply method to each positive value.
positive.negative	apply method to each positive and negative value.
negative	apply method to each negative value.
as.Rfast.function	convert an R function to Rfast’s equivalent
mat.mult	Generic matrix multiplication using parallel.
checkUsage	checking usage section in Rd files.
Hash	Create Hash object.
Hash.key	Search key or multi key.
apply.condition	Apply method to each column using a condition. Only integers.
Stack	Stack object. See man page.
iterator	iterator object. See man page.
Elem	access element of an iterator object.
print.environment	S3 method for printing environment.
env.copy	deep copy environment.
ufactor	Untyped factor object. See man page.

Version 1.8.8

Improved (by speed, correctness or options)

Function What’s new!

rowMedians Fix a bug

mad2 Add option handling NAs and fix a bug

prop.regs Made it more stable.

logistic_only Made it more stable.

multinom.regs Fix a bug and removed parallel for safety reasons.

rint.regs Fix a bug.

univglms Add the option for quasi Poisson regression

hd.eigen Now returns eigen-vectors as well.

ompr Fix a bug.

tobit.mle Made it faster.

standardise Made it faster.

auc Made it faster.

colaucs Made it faster.

pc.skel Made it faster and added more utilities.

cor.fsreg Made it faster and fix a bug.

allttests Made it faster and fix a bug.

data.frame.to_matrix Add option setting colnames and rownames. Fix a bug

nth Add option for handling NAs.

Pmax Add option for handling NAs.

Pmin Add option for handling NAs.

Sort Add option for handling NAs.

Table Add option for handling NAs, add option for second argument, deprecate argument as.vector and replaced from “names”.

Round Fix a bug.

Norm Fix a bug.

colsums Add option for sum using specific indices.

rowsums Add option for sum using specific indices and option for parallel.

is_element Fix a bug.

eachrow Deprecate argument suma and replaced from argument method.

permutation Deprecate argument all and replaced from nperm.

permutation.next Deprecate argument all.next and replaced from nperm.

permutation.prev Deprecate argument all.prev and replaced from nperm.

data.frame.to_matrix Fix a bug and time improvement.

Rank Fix a bug for method=“first”.

Match fix bug and time improvement.

bc Estimate the optimal lambda in the Box-Cox transformation.

ar1 AR(1) model.

colar1 Many column-wise AR(1) models.

bc Estimate the optimal lambda in the Box-Cox transformation.

rbing Random values generation from a special case of the Bingham distribution.

rbingham Random values generation from the Bingham distribution.

omp Orthogonal Matching Pursuit allowing many regression models.

yule Yule’s coefficient of colligation.

col.yule Many column-wise Yule’s coefficients of colligation.

cox.poisrat Test for the ratio of two Poisson means.

col.coxpoisrat Many column-wise tests for the ratio of two Poisson means.

colPmax column-wise parallel maxima

colPmin column-wise parallel minima

freq.max maximum frequency of a number

freq.min minimum frequency of a number

Pmin_Pmax parallel minima-maxima values

Table.sign counting the positive, negative, zeros and NA values.

topological_sort Topological sort of a Directed Acyclic Graph (DAG)

countNA count the NAs

columns get specific columns from a matrix

rows get specific rows from a matrix

eachcol.apply apply a function to each col after the operation

checkTF checking man files for missing TRUE/FALSE values in examples

Function	What’s new!
rowMedians	Fix a bug
mad2	Add option handling NAs and fix a bug
prop.regs	Made it more stable.
logistic_only	Made it more stable.
multinom.regs	Fix a bug and removed parallel for safety reasons.
rint.regs	Fix a bug.
univglms	Add the option for quasi Poisson regression
hd.eigen	Now returns eigen-vectors as well.
ompr	Fix a bug.
tobit.mle	Made it faster.
standardise	Made it faster.
auc	Made it faster.
colaucs	Made it faster.
pc.skel	Made it faster and added more utilities.
cor.fsreg	Made it faster and fix a bug.
allttests	Made it faster and fix a bug.
data.frame.to_matrix	Add option setting colnames and rownames. Fix a bug
nth	Add option for handling NAs.
Pmax	Add option for handling NAs.
Pmin	Add option for handling NAs.
Sort	Add option for handling NAs.
Table	Add option for handling NAs, add option for second argument, deprecate argument as.vector and replaced from “names”.
Round	Fix a bug.
Norm	Fix a bug.
colsums	Add option for sum using specific indices.
rowsums	Add option for sum using specific indices and option for parallel.
is_element	Fix a bug.
eachrow	Deprecate argument suma and replaced from argument method.
permutation	Deprecate argument all and replaced from nperm.
permutation.next	Deprecate argument all.next and replaced from nperm.
permutation.prev	Deprecate argument all.prev and replaced from nperm.
data.frame.to_matrix	Fix a bug and time improvement.
Rank	Fix a bug for method=“first”.
Match	fix bug and time improvement.
bc	Estimate the optimal lambda in the Box-Cox transformation.
ar1	AR(1) model.
colar1	Many column-wise AR(1) models.
bc	Estimate the optimal lambda in the Box-Cox transformation.
rbing	Random values generation from a special case of the Bingham distribution.
rbingham	Random values generation from the Bingham distribution.
omp	Orthogonal Matching Pursuit allowing many regression models.
yule	Yule’s coefficient of colligation.
col.yule	Many column-wise Yule’s coefficients of colligation.
cox.poisrat	Test for the ratio of two Poisson means.
col.coxpoisrat	Many column-wise tests for the ratio of two Poisson means.
colPmax	column-wise parallel maxima
colPmin	column-wise parallel minima
freq.max	maximum frequency of a number
freq.min	minimum frequency of a number
Pmin_Pmax	parallel minima-maxima values
Table.sign	counting the positive, negative, zeros and NA values.
topological_sort	Topological sort of a Directed Acyclic Graph (DAG)
countNA	count the NAs
columns	get specific columns from a matrix
rows	get specific rows from a matrix
eachcol.apply	apply a function to each col after the operation
checkTF	checking man files for missing TRUE/FALSE values in examples