Rfast

New version
Date release: 05/22/2019


Statistical functions

  1. 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” | ***

  1. New
Function What’s new!

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
AddToNamespace remove unused option
check_usage improved version
nth fix bug

version

1.9.3
Date release: 04/03/2019


Statistical functions

  1. Improved (by speed, correctness or options)
Function What’s new!
omp Time improvement.

  1. 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.

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
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.

version

1.9.2
Date release: 25/10/2018


Statistical functions

  1. 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.

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

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
which_isFactor Removed and replaced by “which.is”.
checkUsage Bix a bug.
colsums Time improvement for integer matrices.
rowsums Time improvement for integer matrices.
group.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.

Comments

  1. From now on the Rfast needs R version > 3.5.x

version

1.9.1
Date release: 10/07/2018


Statistical functions

  1. Improved (by speed, correctness or options)
Function What’s new!
ompr Time improvement.
omp Time improvement .
cholesky Time improvement.

  1. New
Function What’s new!

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
colnth, rownth Add extra options, “na.rm” and “descending” order and “index.return”.
colrow.zero deprecate it and replaced by “colrow.value”.

  1. 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.

version

1.9.0
Date release: 15/05/2018


Statistical functions

  1. 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.

  1. 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.

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
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.

  1. New
Function What’s new!
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
Date release: 10/03/2018


Statistical functions

  1. 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.

  1. New
Function What’s new!
colanovas ANOVA with many categorical variables.
quasi.poison_only Many quasi Poisson univariate regressions.
permcor Permutation based hypothesis test for zero correlation.
boot.ttest2 Bootstrap t-sample independent t-test.
univglms2 Univariate GLMs for data.frames with continuous and categorical predictor variables.
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.

Utility functions

  1. Improved (by speed, correctness or options)
Function What’s new!
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”. time improvement/quite efficient version.
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.
CheckExmaples change option “print.errors”.

  1. New
Function What’s new!
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