diff --git a/docs/404.html b/docs/404.html index 52a1438..c461b65 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5bd101e..417f4a7 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/articles/Distances.html b/docs/articles/Distances.html index 64f5ee0..5cdda8f 100644 --- a/docs/articles/Distances.html +++ b/docs/articles/Distances.html @@ -33,7 +33,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/articles/Information_Theory.html b/docs/articles/Information_Theory.html index 2dc8724..9a748dc 100644 --- a/docs/articles/Information_Theory.html +++ b/docs/articles/Information_Theory.html @@ -33,7 +33,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html index 376abf1..448c94c 100644 --- a/docs/articles/Introduction.html +++ b/docs/articles/Introduction.html @@ -33,7 +33,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/articles/Many_Distances.html b/docs/articles/Many_Distances.html index 97d6168..8b16dc2 100644 --- a/docs/articles/Many_Distances.html +++ b/docs/articles/Many_Distances.html @@ -33,7 +33,7 @@ philentropy - 0.6.0 + 0.7.0 @@ -136,11 +136,11 @@

## distance(rbind(P, Q), method = "euclidean", test.na = FALSE, mute.message = TRUE) ## euclidean(P, Q, FALSE) ## dist_one_one(P, Q, method = "euclidean", testNA = FALSE) -## min lq mean median uq max neval -## 21.016 22.3740 27.45797 23.6795 24.5565 247.423 100 -## 32.988 33.9510 58.44587 35.2450 36.3600 2240.296 100 -## 2.614 2.9625 3.26110 3.1680 3.5900 4.531 100 -## 3.830 4.2605 5.44420 4.7645 5.1170 55.625 100 +## min lq mean median uq max neval +## 19.903 21.5385 26.00382 22.9865 23.664 255.003 100 +## 31.201 33.3315 62.20181 34.9810 36.704 2471.859 100 +## 2.570 2.9630 3.87179 3.2285 4.172 18.975 100 +## 3.773 4.5095 5.92168 5.0945 6.236 55.923 100

All of them return the same, single value. However, as you can see in the benchmark above, some are more flexible, and others are faster.

@@ -168,9 +168,9 @@

## distance(rbind(P, M), method = "euclidean", test.na = FALSE, mute.message = TRUE)[1, ][-1] ## dist_one_many(P, M, method = "euclidean", testNA = FALSE) ## min lq mean median uq max neval -## 339.026 474.2515 608.66055 567.8230 691.9940 1476.378 100 -## 30725.401 34468.9615 40857.68863 38995.6490 45964.6625 61617.448 100 -## 32.912 39.4340 49.49877 46.6725 52.4215 148.652 100 +## 342.898 439.3615 599.57320 554.0085 674.9135 1592.482 100 +## 28980.090 31848.4475 38114.88579 37076.4105 42270.6595 59766.128 100 +## 30.311 36.4575 48.53632 44.6115 50.4490 176.593 100

The dist_one_many() returns a vector of values. It is, in this case, much faster than distance(), and visibly faster than dist() while allowing for more possible distance measures to be used.

@@ -204,11 +204,11 @@

)

## Unit: microseconds
 ##                                                          expr      min       lq
-##                                            many_dists(M1, M2) 3142.744 3969.297
-##  dist_many_many(M1, M2, method = "euclidean", testNA = FALSE)   45.014   61.359
-##        mean    median        uq       max neval
-##  4763.85534 4215.9530 4640.7525 15319.268   100
-##    70.07327   66.5805   73.6285   128.969   100
+## many_dists(M1, M2) 2857.283 3417.215 +## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 42.186 52.127 +## mean median uq max neval +## 4488.08550 3903.0475 4318.614 15350.761 100 +## 60.53488 57.2035 65.507 115.167 100

Both many_dists()and dist_many_many() return a matrix. The above benchmark concludes that dist_many_many() is about 30 times faster than our custom many_dists() approach.

diff --git a/docs/articles/index.html b/docs/articles/index.html index efc03c4..5b64b40 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/authors.html b/docs/authors.html index 4e968e2..0d94987 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/index.html b/docs/index.html index 60686a2..5aea173 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/news/index.html b/docs/news/index.html index fa40224..7dd7165 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/paper.html b/docs/paper.html index c084c2b..102a896 100644 --- a/docs/paper.html +++ b/docs/paper.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 92d7cbd..9525b23 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: Information_Theory: Information_Theory.html Introduction: Introduction.html Many_Distances: Many_Distances.html -last_built: 2022-11-04T14:50Z +last_built: 2022-11-04T15:53Z diff --git a/docs/reference/CE.html b/docs/reference/CE.html index 6ccc6db..827203a 100644 --- a/docs/reference/CE.html +++ b/docs/reference/CE.html @@ -19,7 +19,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/H.html b/docs/reference/H.html index 8a58a62..3e270a0 100644 --- a/docs/reference/H.html +++ b/docs/reference/H.html @@ -18,7 +18,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/JE.html b/docs/reference/JE.html index bca63e1..90071d8 100644 --- a/docs/reference/JE.html +++ b/docs/reference/JE.html @@ -18,7 +18,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/JSD.html b/docs/reference/JSD.html index f5e4741..bc225b4 100644 --- a/docs/reference/JSD.html +++ b/docs/reference/JSD.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/KL.html b/docs/reference/KL.html index e2fd2ea..b7c96ef 100644 --- a/docs/reference/KL.html +++ b/docs/reference/KL.html @@ -18,7 +18,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/MI.html b/docs/reference/MI.html index ea87525..33e5d7f 100644 --- a/docs/reference/MI.html +++ b/docs/reference/MI.html @@ -19,7 +19,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/additive_symm_chi_sq.html b/docs/reference/additive_symm_chi_sq.html index 2417b7f..d16dc2e 100644 --- a/docs/reference/additive_symm_chi_sq.html +++ b/docs/reference/additive_symm_chi_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/avg.html b/docs/reference/avg.html index b7bf097..f531e0f 100644 --- a/docs/reference/avg.html +++ b/docs/reference/avg.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/bhattacharyya.html b/docs/reference/bhattacharyya.html index ca20c71..ee3a29b 100644 --- a/docs/reference/bhattacharyya.html +++ b/docs/reference/bhattacharyya.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/binned.kernel.est.html b/docs/reference/binned.kernel.est.html index e4b28fd..4c6749c 100644 --- a/docs/reference/binned.kernel.est.html +++ b/docs/reference/binned.kernel.est.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/canberra.html b/docs/reference/canberra.html index 9936ef8..f684d33 100644 --- a/docs/reference/canberra.html +++ b/docs/reference/canberra.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/chebyshev.html b/docs/reference/chebyshev.html index 38dd43a..aa616e3 100644 --- a/docs/reference/chebyshev.html +++ b/docs/reference/chebyshev.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/clark_sq.html b/docs/reference/clark_sq.html index 65535bf..e348514 100644 --- a/docs/reference/clark_sq.html +++ b/docs/reference/clark_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/cosine_dist.html b/docs/reference/cosine_dist.html index a1b6aac..bcd0a3a 100644 --- a/docs/reference/cosine_dist.html +++ b/docs/reference/cosine_dist.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/czekanowski.html b/docs/reference/czekanowski.html index 9c7062c..db6c61c 100644 --- a/docs/reference/czekanowski.html +++ b/docs/reference/czekanowski.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/dice_dist.html b/docs/reference/dice_dist.html index 80f237a..cf30a56 100644 --- a/docs/reference/dice_dist.html +++ b/docs/reference/dice_dist.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/dist.diversity.html b/docs/reference/dist.diversity.html index fc2c06d..ae4b75d 100644 --- a/docs/reference/dist.diversity.html +++ b/docs/reference/dist.diversity.html @@ -18,7 +18,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/dist_many_many.html b/docs/reference/dist_many_many.html index 43023b9..1e5be88 100644 --- a/docs/reference/dist_many_many.html +++ b/docs/reference/dist_many_many.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/dist_one_many.html b/docs/reference/dist_one_many.html index e175288..b27f7be 100644 --- a/docs/reference/dist_one_many.html +++ b/docs/reference/dist_one_many.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/dist_one_one.html b/docs/reference/dist_one_one.html index e752a1c..afabb16 100644 --- a/docs/reference/dist_one_one.html +++ b/docs/reference/dist_one_one.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/distance.html b/docs/reference/distance.html index a21d2f4..56661d3 100644 --- a/docs/reference/distance.html +++ b/docs/reference/distance.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/divergence_sq.html b/docs/reference/divergence_sq.html index 49891a8..4b83842 100644 --- a/docs/reference/divergence_sq.html +++ b/docs/reference/divergence_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/estimate.probability.html b/docs/reference/estimate.probability.html index 9ebef88..ba56dd0 100644 --- a/docs/reference/estimate.probability.html +++ b/docs/reference/estimate.probability.html @@ -25,7 +25,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/euclidean.html b/docs/reference/euclidean.html index bdc7a2a..5c39fd3 100644 --- a/docs/reference/euclidean.html +++ b/docs/reference/euclidean.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/fidelity.html b/docs/reference/fidelity.html index 08df2c7..386502f 100644 --- a/docs/reference/fidelity.html +++ b/docs/reference/fidelity.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/gJSD.html b/docs/reference/gJSD.html index 8e86972..5af4449 100644 --- a/docs/reference/gJSD.html +++ b/docs/reference/gJSD.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/getDistMethods.html b/docs/reference/getDistMethods.html index 8f0c35f..d25c6f6 100644 --- a/docs/reference/getDistMethods.html +++ b/docs/reference/getDistMethods.html @@ -19,7 +19,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/gower.html b/docs/reference/gower.html index 6d7a96b..e63a6d3 100644 --- a/docs/reference/gower.html +++ b/docs/reference/gower.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/harmonic_mean_dist.html b/docs/reference/harmonic_mean_dist.html index 15d73eb..070aeab 100644 --- a/docs/reference/harmonic_mean_dist.html +++ b/docs/reference/harmonic_mean_dist.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/hellinger.html b/docs/reference/hellinger.html index 0429074..3fe269d 100644 --- a/docs/reference/hellinger.html +++ b/docs/reference/hellinger.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 0d13458..1a4d699 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/inner_product.html b/docs/reference/inner_product.html index 3a85495..5a5d029 100644 --- a/docs/reference/inner_product.html +++ b/docs/reference/inner_product.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/intersection_dist.html b/docs/reference/intersection_dist.html index 712a4b1..784a242 100644 --- a/docs/reference/intersection_dist.html +++ b/docs/reference/intersection_dist.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/jaccard.html b/docs/reference/jaccard.html index 5edc131..8545ec5 100644 --- a/docs/reference/jaccard.html +++ b/docs/reference/jaccard.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/jeffreys.html b/docs/reference/jeffreys.html index 6151dc4..311b73f 100644 --- a/docs/reference/jeffreys.html +++ b/docs/reference/jeffreys.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/jensen_difference.html b/docs/reference/jensen_difference.html index 7504281..99917e7 100644 --- a/docs/reference/jensen_difference.html +++ b/docs/reference/jensen_difference.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/jensen_shannon.html b/docs/reference/jensen_shannon.html index 8a7fda6..1935138 100644 --- a/docs/reference/jensen_shannon.html +++ b/docs/reference/jensen_shannon.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/k_divergence.html b/docs/reference/k_divergence.html index b53c61b..c5f3cc4 100644 --- a/docs/reference/k_divergence.html +++ b/docs/reference/k_divergence.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/kulczynski_d.html b/docs/reference/kulczynski_d.html index 6bd3866..5a4f1b3 100644 --- a/docs/reference/kulczynski_d.html +++ b/docs/reference/kulczynski_d.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/kullback_leibler_distance.html b/docs/reference/kullback_leibler_distance.html index 8a76bfe..afc4e04 100644 --- a/docs/reference/kullback_leibler_distance.html +++ b/docs/reference/kullback_leibler_distance.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/kumar_hassebrook.html b/docs/reference/kumar_hassebrook.html index 4032937..88a719c 100644 --- a/docs/reference/kumar_hassebrook.html +++ b/docs/reference/kumar_hassebrook.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/kumar_johnson.html b/docs/reference/kumar_johnson.html index 4e2895f..d3c4eb2 100644 --- a/docs/reference/kumar_johnson.html +++ b/docs/reference/kumar_johnson.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/lin.cor.html b/docs/reference/lin.cor.html index 7f486a0..edc7d69 100644 --- a/docs/reference/lin.cor.html +++ b/docs/reference/lin.cor.html @@ -18,7 +18,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/lorentzian.html b/docs/reference/lorentzian.html index 6e61127..f380fd2 100644 --- a/docs/reference/lorentzian.html +++ b/docs/reference/lorentzian.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/manhattan.html b/docs/reference/manhattan.html index 0f96eb1..20e9068 100644 --- a/docs/reference/manhattan.html +++ b/docs/reference/manhattan.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/matusita.html b/docs/reference/matusita.html index 59e3ae5..08ce85e 100644 --- a/docs/reference/matusita.html +++ b/docs/reference/matusita.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/minkowski.html b/docs/reference/minkowski.html index 189c5a2..b549603 100644 --- a/docs/reference/minkowski.html +++ b/docs/reference/minkowski.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/motyka.html b/docs/reference/motyka.html index 27338dd..a48f330 100644 --- a/docs/reference/motyka.html +++ b/docs/reference/motyka.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/neyman_chi_sq.html b/docs/reference/neyman_chi_sq.html index 479ef44..f3cbd32 100644 --- a/docs/reference/neyman_chi_sq.html +++ b/docs/reference/neyman_chi_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/pearson_chi_sq.html b/docs/reference/pearson_chi_sq.html index c6b1503..3707563 100644 --- a/docs/reference/pearson_chi_sq.html +++ b/docs/reference/pearson_chi_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/prob_symm_chi_sq.html b/docs/reference/prob_symm_chi_sq.html index ace1b3e..f0e4b90 100644 --- a/docs/reference/prob_symm_chi_sq.html +++ b/docs/reference/prob_symm_chi_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/ruzicka.html b/docs/reference/ruzicka.html index 090031c..d6e6cce 100644 --- a/docs/reference/ruzicka.html +++ b/docs/reference/ruzicka.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/soergel.html b/docs/reference/soergel.html index 3f55d92..4b34ba3 100644 --- a/docs/reference/soergel.html +++ b/docs/reference/soergel.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/sorensen.html b/docs/reference/sorensen.html index c157a8b..7a1dac4 100644 --- a/docs/reference/sorensen.html +++ b/docs/reference/sorensen.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/squared_chi_sq.html b/docs/reference/squared_chi_sq.html index c807f3c..44b6c56 100644 --- a/docs/reference/squared_chi_sq.html +++ b/docs/reference/squared_chi_sq.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/squared_chord.html b/docs/reference/squared_chord.html index 34a1300..183f251 100644 --- a/docs/reference/squared_chord.html +++ b/docs/reference/squared_chord.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/squared_euclidean.html b/docs/reference/squared_euclidean.html index a81515f..f94bf4a 100644 --- a/docs/reference/squared_euclidean.html +++ b/docs/reference/squared_euclidean.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/taneja.html b/docs/reference/taneja.html index 7a76c14..fdf82ef 100644 --- a/docs/reference/taneja.html +++ b/docs/reference/taneja.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/tanimoto.html b/docs/reference/tanimoto.html index f54dfcb..c631b31 100644 --- a/docs/reference/tanimoto.html +++ b/docs/reference/tanimoto.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/topsoe.html b/docs/reference/topsoe.html index b1fb41f..4075348 100644 --- a/docs/reference/topsoe.html +++ b/docs/reference/topsoe.html @@ -17,7 +17,7 @@ philentropy - 0.6.0 + 0.7.0 diff --git a/docs/reference/wave_hedges.html b/docs/reference/wave_hedges.html index 94b3181..9b60c91 100644 --- a/docs/reference/wave_hedges.html +++ b/docs/reference/wave_hedges.html @@ -17,7 +17,7 @@ philentropy - 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