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RcppAlgos

CRAN status Codacy Badge Dependencies R-CMD-check Codecov test coverage

A collection of high performance functions and iterators implemented in C++ for solving problems in combinatorics and computational mathematics.

Featured Functions

  • {combo|permute}General: Generate all combinations/permutations of a vector (including multisets) meeting specific criteria.
  • {partitions|compositions}General: Efficient algorithms for partitioning numbers under various constraints
  • {combo|permute|partitions|compositions}Sample: Generate reproducible random samples
  • {combo|permute|partitions|compositions}Iter: Flexible iterators allow for bidirectional iteration as well as random access.
  • primeSieve: Fast prime number generator
  • primeCount: Prime counting function using Legendre's formula

The primeSieve function and the primeCount function are both based off of the excellent work by Kim Walisch. The respective repos can be found here: kimwalisch/primesieve; kimwalisch/primecount

Additionally, many of the sieving functions make use of the fast integer division library libdivide by ridiculousfish.

Benchmarks

Installation

install.packages("RcppAlgos")

## install the development version
devtools::install_github("jwood000/RcppAlgos")

Basic Usage

Combinatorics

## Find all 3-tuples combinations of 1:4
comboGeneral(4, 3)
#>      [,1] [,2] [,3]
#> [1,]   1    2    3
#> [2,]   1    2    4
#> [3,]   1    3    4
#> [4,]   2    3    4


## Alternatively, iterate over combinations
a = comboIter(4, 3)
a@nextIter()
#> [1] 1 2 3

a@back()
#> [1] 2 3 4

a[[2]]
#> [1] 1 2 4


## Pass any atomic type vector
permuteGeneral(letters, 3, upper = 4)
#>      [,1] [,2] [,3]
#> [1,] "a"  "b"  "c"
#> [2,] "a"  "b"  "d"
#> [3,] "a"  "b"  "e"
#> [4,] "a"  "b"  "f"


## Flexible partitioning algorithms
partitionsGeneral(0:5, 3, freqs = rep(1:2, 3), target = 6)
#>      [,1] [,2] [,3]
#> [1,]    0    1    5
#> [2,]    0    2    4
#> [3,]    0    3    3
#> [4,]    1    1    4
#> [5,]    1    2    3


## And compositions
compositionsGeneral(0:3, repetition = TRUE)
#>      [,1] [,2] [,3]
#> [1,]    0    0    3
#> [2,]    0    1    2
#> [3,]    0    2    1
#> [4,]    1    1    1


## Generate a reproducible sample
comboSample(10, 8, TRUE, n = 5, seed = 84)
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    3    3    3    6    6   10   10   10
#> [2,]    1    3    3    4    4    7    9   10
#> [3,]    3    7    7    7    9   10   10   10
#> [4,]    3    3    3    9   10   10   10   10
#> [5,]    1    2    2    3    3    4    4    7


## Get combinations such that the product is between
## 3600 and 4000 (including 3600 but not 4000)
comboGeneral(5, 7, TRUE, constraintFun = "prod",
             comparisonFun = c(">=","<"),
             limitConstraints = c(3600, 4000),
             keepResults = TRUE)
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    1    2    3    5    5    5    5 3750
#> [2,]    1    3    3    4    4    5    5 3600
#> [3,]    1    3    4    4    4    4    5 3840
#> [4,]    2    2    3    3    4    5    5 3600
#> [5,]    2    2    3    4    4    4    5 3840
#> [6,]    3    3    3    3    3    3    5 3645
#> [7,]    3    3    3    3    3    4    4 3888


## We can even iterate over constrained cases. These are
## great when we don't know how many results there are upfront.
## Save on memory and still at the speed of C++!!
p = permuteIter(5, 7, TRUE, constraintFun = "prod",
                comparisonFun = c(">=","<"),
                limitConstraints = c(3600, 4000),
                keepResults = TRUE)

## Get the next n results
t <- p@nextNIter(1048)

## N.B. keepResults = TRUE adds the 8th column
tail(t)
#>         [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1043,]    5    4    4    3    4    1    4 3840
#> [1044,]    5    4    4    3    4    4    1 3840
#> [1045,]    5    4    4    4    1    3    4 3840
#> [1046,]    5    4    4    4    1    4    3 3840
#> [1047,]    5    4    4    4    3    1    4 3840
#> [1048,]    5    4    4    4    3    4    1 3840

## Continue iterating from where we left off
p@nextIter()
#> [1]    5    4    4    4    4    1    3 3840

p@nextIter()
#> [1]    5    4    4    4    4    3    1 3840

p@nextIter()
#> [1]    2    2    3    3    4    5    5 3600

## N.B. totalResults and totalRemaining are NA because there is no
## closed form solution for determining this.
p@summary()
#> $description
#> [1] "Permutations with repetition of 5 choose 7 where the prod is between 3600 and 4000"
#> 
#> $currentIndex
#> [1] 1051
#> 
#> $totalResults
#> [1] NA
#> 
#> $totalRemaining
#> [1] NA

Computational Mathematics

## Generate prime numbers
primeSieve(50)
#> [1]  2  3  5  7 11 13 17 19 23 29 31 37 41 43 47

## Many of the functions can produce results in
## parallel for even greater performance
p = primeSieve(1e15, 1e15 + 1e8, nThreads = 4)

head(p)
#> [1] 1000000000000037 1000000000000091 1000000000000159
#> [4] 1000000000000187 1000000000000223 1000000000000241
tail(p)
#> [1] 1000000099999847 1000000099999867 1000000099999907
#> [4] 1000000099999919 1000000099999931 1000000099999963


## Count prime numbers less than n
primeCount(1e10)
#> [1] 455052511

## Get the prime factorization
set.seed(24028)
primeFactorize(sample(1e15, 3), namedList = TRUE)
#> $`701030825091514`
#> [1]             2           149 2352452433193
#> 
#> $`83054168594779`
#> [1]  3098071 26808349
#> 
#> $`397803024735610`
#> [1]            2            5           13           13 235386405169

Further Reading

Why RcppAlgos but no Rcpp?

Previous versions of RcppAlgos relied on Rcpp to ease the burden of exposing C++ to R. While the current version of RcppAlgos does not utilize Rcpp, it would not be possible without the myriad of excellent contributions to Rcpp.

Contact

If you would like to report a bug, have a question, or have suggestions for possible improvements, please file an issue.