Created
August 14, 2018 00:49
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combinations and permutations benchmark for R
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## All functions from other packages will be called | |
## using the double colon (::) (i.e. the scope operator) | |
# 1. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(13) | |
testVector1 <- sort(sample(100, 17)) | |
m <- 9 | |
t1 <- comboGeneral(testVector1, m) ## returns matrix with m columns | |
t3 <- combinat::combn(testVector1, m) ## returns matrix with m rows | |
t4 <- gtools::combinations(17, m, testVector1) ## returns matrix with m columns | |
identical(t(t3), t4) ## must transpose to compare | |
t5 <- combinations(testVector1, m) | |
identical(t1, t5) | |
t6 <- gRbase::combnPrim(testVector1, m) | |
identical(t(t6)[do.call(order, as.data.frame(t(t6))),], t1) | |
gc() | |
microbenchmark(cbRcppAlgos = comboGeneral(testVector1, m), | |
cbGRbase = gRbase::combnPrim(testVector1, m), | |
cbGtools = gtools::combinations(17, m, testVector1), | |
cbCombinat = combinat::combn(testVector1, m), | |
cbArrangements = combinations(17, m, testVector1), | |
unit = "relative") | |
# 2. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(97) | |
testVector2 <- sort(rnorm(10)) | |
m <- 8 | |
t1 <- comboGeneral(testVector2, m, repetition = TRUE) | |
t3 <- gtools::combinations(10, m, testVector2, repeats.allowed = TRUE) | |
identical(t1, t3) | |
## arrangements | |
t4 <- combinations(testVector2, m, replace = TRUE) | |
identical(t1, t4) | |
gc() | |
microbenchmark(cbRcppAlgos = comboGeneral(testVector2, m, TRUE), | |
cbGtools = gtools::combinations(10, m, testVector2, repeats.allowed = TRUE), | |
cbArrangements = combinations(testVector2, m, replace = TRUE), | |
unit = "relative") | |
# 3. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(101) | |
testVector3 <- as.integer(c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29)) | |
## RcppAlgos... permuteGeneral same as comboGeneral above | |
t1 <- permuteGeneral(testVector3, 6) | |
## gtools... permutations same as combinations above | |
t3 <- gtools::permutations(10, 6, testVector3) | |
identical(t1, t3) | |
## arrangements | |
t4 <- permutations(testVector3, 6) | |
identical(t1, t4) | |
gc() | |
microbenchmark(cbRcppAlgos = permuteGeneral(testVector3, 6), | |
cbGtools = gtools::permutations(10, 6, testVector3), | |
cbArrangements = permutations(testVector3, 6), | |
unit = "relative") | |
# 4. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(89) | |
testVector3 <- as.integer(c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29)) | |
testVector3Prime <- testVector3[1:7] | |
## For RcppAlgos, & gtools (see above) | |
## combinat | |
t4 <- combinat::permn(testVector3Prime) ## returns a list of vectors | |
## convert to a matrix | |
t4 <- do.call(rbind, t4) | |
## multicool.. we must first call initMC | |
t5 <- multicool::allPerm(multicool::initMC(testVector3Prime)) ## returns a matrix with n columns | |
all.equal(t4[do.call(order,as.data.frame(t4)),], | |
t5[do.call(order,as.data.frame(t5)),]) | |
gc() | |
microbenchmark(cbRcppAlgos = permuteGeneral(testVector3Prime, 7), | |
cbGtools = gtools::permutations(7, 7, testVector3Prime), | |
cbCombinat = combinat::permn(testVector3Prime), | |
cbMulticool = multicool::allPerm(multicool::initMC(testVector3Prime)), | |
cbArrangements = permutations(x = testVector3Prime, k = 7), | |
unit = "relative") | |
# 5. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(89) | |
t1 <- partitions::perms(7) ## returns an object of type 'partition' with n rows | |
identical(t(as.matrix(t1)), permutations(7,7)) | |
gc() | |
microbenchmark(cbRcppAlgos = permuteGeneral(7, 7), | |
cbGtools = gtools::permutations(7, 7), | |
cbCombinat = combinat::permn(7), | |
cbMulticool = multicool::allPerm(multicool::initMC(1:7)), | |
cbPartitions = partitions::perms(7), | |
cbArrangements = permutations(7, 7), | |
unit = "relative") | |
# 6. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(34) | |
testVector3 <- as.integer(c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29)) | |
t1 <- permuteGeneral(testVector3, 5, repetition = TRUE) | |
t3 <- gtools::permutations(10, 5, testVector3, repeats.allowed = TRUE) | |
t4 <- permutations(x = testVector3, k = 5, replace = TRUE) | |
microbenchmark(cbRcppAlgos = permuteGeneral(testVector3, 5, TRUE), | |
cbGtools = gtools::permutations(10, 5, testVector3, repeats.allowed = TRUE), | |
cbArrangements = permutations(x = testVector3, k = 5, replace = TRUE), | |
unit = "relative") | |
# 7. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(496) | |
myFreqs <- sample(1:5, 10, replace = TRUE) | |
## This is how many times each element will be repeated | |
myFreqs | |
testVector4 <- as.integer(c(1, 2, 3, 5, 8, 13, 21, 34, 55, 89)) | |
t1 <- comboGeneral(testVector4, 12, freqs = myFreqs) | |
t3 <- combinations(freq = myFreqs, k = 12, x = testVector4) | |
identical(t1, t3) | |
microbenchmark(cbRcppAlgos = comboGeneral(testVector4, 12, freqs = myFreqs), | |
cbArrangements = combinations(freq = myFreqs, k = 12, x = testVector4), | |
unit = "relative") | |
# 8. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(8128) | |
myFreqs <- sample(1:3, 5, replace = TRUE) | |
testVector5 <- sort(runif(5)) | |
myFreqs | |
t1 <- permuteGeneral(testVector5, 7, freqs = myFreqs) | |
t3 <- permutations(freq = myFreqs, k = 7, x = testVector5) | |
identical(t1, t3) | |
microbenchmark(cbRcppAlgos = permuteGeneral(testVector5, 7, freqs = myFreqs), | |
cbArrangements = permutations(freq = myFreqs, k = 7, x = testVector5), | |
unit = "relative") | |
# 9. | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(8128) | |
myFreqs2 <- c(2,1,2,1,2) | |
testVector6 <- (1:5)^3 | |
## For multicool, you must have the elements explicitly repeated | |
testVector6Prime <- rep(testVector6, times = myFreqs2) | |
t3 <- multicool::allPerm(multicool::initMC(testVector6Prime)) | |
## for comparison | |
t1 <- permuteGeneral(testVector6, freqs = myFreqs2) | |
identical(t1[do.call(order,as.data.frame(t1)),], | |
t3[do.call(order,as.data.frame(t3)),]) | |
microbenchmark(cbRcppAlgos = permuteGeneral(testVector6, freqs = myFreqs2), | |
cbMulticool = multicool::allPerm(multicool::initMC(testVector6Prime)), | |
cbArrangements = permutations(freq = myFreqs2, x = testVector6), | |
unit = "relative") | |
# Summary | |
# arrangements | |
library(arrangements) | |
icomb <- icombinations(1000, 7) | |
icomb$getnext(d = 5) | |
# RcppAlogs | |
library(RcppAlgos) | |
comboGeneral(1000, 7, upper = 5) | |
library(RcppAlgos) | |
system.time(parallel::mclapply(seq(1,6397478649,4390857), function(x) { | |
a <- comboGeneral(25, 15, freqs = c(rep(1:5, 5)), lower = x, upper = x + 4390856) | |
## do something | |
x | |
}, mc.cores = 7)) | |
library(RcppAlgos) | |
library(arrangements) | |
library(microbenchmark) | |
options(digits = 4) | |
set.seed(2187) | |
testVector7 <- sort(sample(10^7, 10^3)) | |
system.time(utils::combn(testVector7, 3)) | |
system.time(RcppAlgos::comboGeneral(testVector7, 3)) | |
system.time(arrangements::combinations(x = testVector7, k = 3)) | |
system.time(RcppAlgos::permuteGeneral(testVector7[1:500], 3)) | |
system.time(arrangements::permutations(x = testVector7[1:500], k = 3)) |
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