New

Function What’s new! coeff Coefficient matrix.

(Improved)by speed, correctness or options

Function What’s new! cor.fsreg Bug fix in the adjusted R-squared computation. ompr Bug fix in the adjusted R-squared computation. rmdp Support parallel. colMads Supports data.frame eachrow Fix bug. colMedians Fix bug about data.frame. rowMedians Fix bug. colVars Fix bug about data.frame. Dist(…,method = “minimum”) Bug fix. Dist(…,method = “bhattacharyya”) Bug fix . Dist(…,method = “itakura_saito”) Bug fix. Supports parallel. Dist(…,method = “canberra1”) Depricated. Dist(…,method = “canberra2”) Depricated. Dist(…,method = “jensen_shannon”) Supports parallel. Dist(…,method = “kullback_leibler”) Supports parallel. Dist New methods (“canberra”,“chi_square”,“soergel”,“sorensen”,“cosine”,“wave_hedges”,“motyka”,“harmonic_mean”,“jeffries_matusita”,“gower”,“kulczynski”) dista All the methods from the Dist function are now supported. total.dist All the methods from the Dist function are now supported. total.dista All the methods from the Dist function are now supported. Sort Supports parallel. Available only in Windows and most unix. Order Supports parallel. Available only in Windows and most unix. Rank Supports parallel. Available only in Windows and most unix. Add extra option for stable algorithm. checkUsage checking if usage lines are wider than 90 characters.

(LinkingTo)by speed, correctness or options

Function/Structure What’s new! colMads Supports data.frame

(Improved)by speed, correctness or options

Function What’s new! colMads Supports data.frame colShuffle Supports data.frame colMedian Supports data.frame colRanks Supports data.frame and fix bug about method “min”. colSort Supports data.frame colMaxs Supports data.frame colMins Supports data.frame colMinsMaxs Supports data.frame and add extra option for parallelism. colrange Supports data.frame and add extra option for parallelism. checkExamples Add extra option for running examples inside environment. Treat special functions with new export attribute. sort_mat Depricated.

(LinkingTo)by speed, correctness or options

Function/Structure What’s new! colMads Supports data.frame colShuffle Supports data.frame colMedian Supports data.frame colSort Supports data.frame colMaxs Supports data.frame colMins Supports data.frame colMinsMaxs Supports data.frame and add extra option for parallelism. NA A structure for manage R’s NA values. Supports {int, double, bool, string}. Type A structure for manage R’s types. Supports {REAL,INT,CHAR,FACTOR,LIST,DATAFRAME}.

Comments

From now on all the function will be inside namespace Rfast. Sub-namespaces “vector” and “matrix” have been removed.

(Improved)by speed, correctness or options

Function What’s new! colVars Supports data.frame colmeans Supports data.frame invdir.mle A small optimization

(Improved)by speed, correctness or options

Function What’s new! Dist(method = “bhattacharyya”) Minor optimization.

(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.

(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.

(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.

(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 “//[[Rcppdepends(Rfast)]]”.
Include in your cpp files the header “Rfast.h” and enjoy!

(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.

(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 “Rfast2colGroup(…,method=”var“)” sort_mat Deprecated and replaced by “colSort” and “rowSort” AddToNamespace remove unused option nth fix bug

(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.

(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

(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.

(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.

(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