-library(philentropy)
+library(philentropy)
# compute the Euclidean Distance with default parameters
distance(x, method = "euclidean")Simple Example# install.packages("microbenchmark")
library(microbenchmark)
-microbenchmark(
+microbenchmark(
distance(x,method = "euclidean", test.na = FALSE),
dist(x,method = "euclidean"),
euclidean(P, Q, FALSE)
@@ -312,7 +312,7 @@ Simple Example
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Information_Theory.html b/docs/articles/Information_Theory.html
index 510e3e0..0539e21 100644
--- a/docs/articles/Information_Theory.html
+++ b/docs/articles/Information_Theory.html
@@ -6,7 +6,7 @@
Information Theory • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -373,7 +373,7 @@ Generalized Jensen-Shannon Diverg
diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html
index 6474437..b7fbdfe 100644
--- a/docs/articles/Introduction.html
+++ b/docs/articles/Introduction.html
@@ -6,7 +6,7 @@
Introduction • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -422,7 +422,7 @@ Information Theory
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Many_Distances.html b/docs/articles/Many_Distances.html
index 9b5b7c4..68ab5b3 100644
--- a/docs/articles/Many_Distances.html
+++ b/docs/articles/Many_Distances.html
@@ -6,7 +6,7 @@
Comparing many probability density functions • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -141,7 +141,7 @@ 2021-08-20
Let’s start testing them by attaching the
philentropy package.
+library(philentropy)
dist_one_one()
@@ -176,11 +176,11 @@
## 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
-## 5986 6396 8233.62 6724.0 7113.5 108691 100
-## 9266 9922 18894.85 10475.5 11931.0 783756 100
-## 820 902 1150.87 943.0 1086.5 3854 100
-## 1189 1271 1756.03 1353.0 1496.5 19680 100
+## min lq mean median uq max neval
+## 5166 5371 6431.26 5658 5883.5 75563 100
+## 7585 7913 12703.03 8036 8241.0 459200 100
+## 492 533 771.62 574 615.0 19352 100
+## 820 861 1093.88 943 1025.0 15375 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.
@@ -219,10 +219,10 @@
## as.matrix(dist(rbind(P, M), method = "euclidean"))[1, ][-1]
## 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
-## 130.831 148.1125 160.26367 157.9935 167.690 263.548 100
-## 9016.515 9735.1630 11155.15536 10312.8735 12742.677 14336.511 100
-## 9.512 10.3730 12.67269 11.8285 13.858 44.526 100
+## min lq mean median uq max neval
+## 65.313 71.4425 77.49861 74.3330 80.8315 152.028 100
+## 6430.850 6534.4570 6748.67462 6621.6845 6945.7895 8020.297 100
+## 7.749 8.8970 9.69158 9.2455 9.6350 30.381 100
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
@@ -265,11 +265,11 @@
)
## Unit: microseconds
## expr min lq
-## many_dists(M1, M2) 958.990 994.5575
-## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 14.104 14.8830
-## mean median uq max neval
-## 1181.08126 1013.458 1081.375 4497.126 100
-## 16.36269 15.375 16.851 37.843 100
+## many_dists(M1, M2) 815.982 859.6265
+## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 12.669 13.7965
+## mean median uq max neval
+## 1018.45107 900.114 992.6305 3761.668 100
+## 15.36475 14.719 16.1745 32.062 100
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
@@ -294,7 +294,7 @@
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b8ef73d..2f170dd 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • philentropy Articles • philentropy
@@ -17,7 +17,7 @@
@@ -87,7 +87,7 @@ All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index bb364f2..83be8d6 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • philentropy Authors and Citation • philentropy
@@ -17,7 +17,7 @@
@@ -63,7 +63,7 @@
diff --git a/docs/index.html b/docs/index.html
index 3d56d12..3b24f29 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
Similarity and Distance Quantification Between Probability Functions • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -89,7 +89,7 @@
-
+ 
Similarity and Distance Quantification between Probability Functions
@@ -104,7 +104,7 @@ Si
Installation
-# install philentropy version 0.8.0 from CRAN
+# install philentropy version 0.9.0 from CRAN
install.packages("philentropy")
@@ -129,7 +129,7 @@ TutorialsExamples
-library(philentropy)
+library(philentropy)
# retrieve available distance metrics
philentropy::getDistMethods()
[1] "euclidean" "manhattan" "minkowski"
@@ -421,7 +421,7 @@ Developers
diff --git a/docs/news/index.html b/docs/news/index.html
index fe02957..13475f1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • philentropy Changelog • philentropy
@@ -17,7 +17,7 @@
@@ -67,7 +67,13 @@ Changelog
+
+Version 0.8.02023-12-02
Updates
Fixing warning on Debian systems:
@@ -112,7 +118,7 @@ Updatesstats::dist() when working with 2 dimensional input matrices (2 vector inputs) (see #29) (Many thanks to Jakub Nowosad (@Nowosad)) Example:
-library(philentropy)
+library(philentropy)
m1 = matrix(c(1, 2), ncol = 1)
@@ -240,7 +246,7 @@ Version 0.0.1
diff --git a/docs/paper.html b/docs/paper.html
index 05106b9..7da9177 100644
--- a/docs/paper.html
+++ b/docs/paper.html
@@ -1,5 +1,5 @@
-Summary • philentropy Summary • philentropy
@@ -17,7 +17,7 @@
@@ -82,7 +82,7 @@
Minkowski : $d = ( \sum_{i = 1}^N | P_i - Q_i |^p)^{1/p}$
-Chebyshev : d = max|Pi−Qi|
+ Chebyshev : d = max|Pi − Qi|
@@ -202,7 +202,7 @@ Information Theory Measures$KL(P || Q) = \sum\limits_{i=1}^n P(p_i) \cdot log_2(\frac{P(p_i) }{P(q_i)}) = H(P, Q) - H(P)$
-Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R)+KL(Q||R))
+ Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R) + KL(Q||R))
Generalized Jensen-Shannon Divergence : $gJSD_{\pi_1,...,\pi_n}(P_1, ..., P_n) = H(\sum_{i = 1}^n \pi_i \cdot P_i) - \sum_{i = 1}^n \pi_i \cdot H(P_i)$
@@ -233,7 +233,7 @@ References
- Site built with pkgdown 2.0.7.
+ Site built with pkgdown 2.0.9.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 70ec28c..e9d6dfb 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,10 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
Distances: Distances.html
Information_Theory: Information_Theory.html
Introduction: Introduction.html
Many_Distances: Many_Distances.html
-last_built: 2024-02-09T18:18Z
+last_built: 2024-11-12T20:43Z
diff --git a/docs/reference/CE.html b/docs/reference/CE.html
index 2d20e6b..eca2096 100644
--- a/docs/reference/CE.html
+++ b/docs/reference/CE.html
@@ -1,5 +1,5 @@
-Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Jensen-Shannon Divergence — JSD • philentropy Jensen-Shannon Divergence — JSD • philentropy
@@ -17,7 +18,7 @@
@@ -68,7 +69,8 @@ Jensen-Shannon Divergence
- This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+ This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the link{sqrt} on the JSD() output.
@@ -98,7 +100,7 @@ Arguments
Value
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
Details
@@ -166,7 +168,7 @@ Examples
#> jensen-shannon
#> 0.03792749
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
@@ -192,7 +194,7 @@ Examples
diff --git a/docs/reference/KL-1.png b/docs/reference/KL-1.png
index 202b9bb..30a7905 100644
Binary files a/docs/reference/KL-1.png and b/docs/reference/KL-1.png differ
diff --git a/docs/reference/KL.html b/docs/reference/KL.html
index 7da42db..a371da0 100644
--- a/docs/reference/KL.html
+++ b/docs/reference/KL.html
@@ -1,5 +1,5 @@
-Kullback-Leibler Divergence — KL • philentropy Kullback-Leibler Divergence — KL • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/avg.html b/docs/reference/avg.html
index cb60568..544da83 100644
--- a/docs/reference/avg.html
+++ b/docs/reference/avg.html
@@ -1,5 +1,5 @@
-AVG distance (lowlevel function) — avg • philentropy AVG distance (lowlevel function) — avg • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/bhattacharyya.html b/docs/reference/bhattacharyya.html
index d813f81..50e66d4 100644
--- a/docs/reference/bhattacharyya.html
+++ b/docs/reference/bhattacharyya.html
@@ -1,5 +1,5 @@
-Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy
@@ -17,7 +17,7 @@
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/binned.kernel.est.html b/docs/reference/binned.kernel.est.html
index 5daba65..657d534 100644
--- a/docs/reference/binned.kernel.est.html
+++ b/docs/reference/binned.kernel.est.html
@@ -1,5 +1,5 @@
-Kernel Density Estimation — binned.kernel.est • philentropy Kernel Density Estimation — binned.kernel.est • philentropy
@@ -17,7 +17,7 @@
@@ -148,7 +148,7 @@ Author
diff --git a/docs/reference/canberra.html b/docs/reference/canberra.html
index b16d474..104893d 100644
--- a/docs/reference/canberra.html
+++ b/docs/reference/canberra.html
@@ -1,5 +1,5 @@
-Canberra distance (lowlevel function) — canberra • philentropy Canberra distance (lowlevel function) — canberra • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/chebyshev.html b/docs/reference/chebyshev.html
index ccaf554..a12bc9d 100644
--- a/docs/reference/chebyshev.html
+++ b/docs/reference/chebyshev.html
@@ -1,5 +1,5 @@
-Chebyshev distance (lowlevel function) — chebyshev • philentropy Chebyshev distance (lowlevel function) — chebyshev • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/clark_sq.html b/docs/reference/clark_sq.html
index 325d8db..09e0cea 100644
--- a/docs/reference/clark_sq.html
+++ b/docs/reference/clark_sq.html
@@ -1,5 +1,5 @@
-Clark squared distance (lowlevel function) — clark_sq • philentropy Clark squared distance (lowlevel function) — clark_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/cosine_dist.html b/docs/reference/cosine_dist.html
index f2a739e..a52a572 100644
--- a/docs/reference/cosine_dist.html
+++ b/docs/reference/cosine_dist.html
@@ -1,5 +1,5 @@
-Cosine distance (lowlevel function) — cosine_dist • philentropy Cosine distance (lowlevel function) — cosine_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/czekanowski.html b/docs/reference/czekanowski.html
index 6b61e36..3c09167 100644
--- a/docs/reference/czekanowski.html
+++ b/docs/reference/czekanowski.html
@@ -1,5 +1,5 @@
-Czekanowski distance (lowlevel function) — czekanowski • philentropy Czekanowski distance (lowlevel function) — czekanowski • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dice_dist.html b/docs/reference/dice_dist.html
index ca45645..4d9df52 100644
--- a/docs/reference/dice_dist.html
+++ b/docs/reference/dice_dist.html
@@ -1,5 +1,5 @@
-Dice distance (lowlevel function) — dice_dist • philentropy Dice distance (lowlevel function) — dice_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dist.diversity.html b/docs/reference/dist.diversity.html
index c57920f..bf390ac 100644
--- a/docs/reference/dist.diversity.html
+++ b/docs/reference/dist.diversity.html
@@ -1,5 +1,5 @@
-Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/dist_one_many.html b/docs/reference/dist_one_many.html
index 82fe0f8..4db596b 100644
--- a/docs/reference/dist_one_many.html
+++ b/docs/reference/dist_one_many.html
@@ -1,5 +1,5 @@
-Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Examples
diff --git a/docs/reference/dist_one_one.html b/docs/reference/dist_one_one.html
index 18f3b01..684dc1f 100644
--- a/docs/reference/dist_one_one.html
+++ b/docs/reference/dist_one_one.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/distance.html b/docs/reference/distance.html
index f8c089f..6b95cbb 100644
--- a/docs/reference/distance.html
+++ b/docs/reference/distance.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Probability Density Functions — distance • philentropy Distances and Similarities between Probability Density Functions — distance • philentropy
@@ -17,7 +17,7 @@
@@ -366,7 +366,7 @@ Examples
diff --git a/docs/reference/divergence_sq.html b/docs/reference/divergence_sq.html
index 0722d20..597a0e0 100644
--- a/docs/reference/divergence_sq.html
+++ b/docs/reference/divergence_sq.html
@@ -1,5 +1,5 @@
-Divergence squared distance (lowlevel function) — divergence_sq • philentropy Divergence squared distance (lowlevel function) — divergence_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/estimate.probability.html b/docs/reference/estimate.probability.html
index e31c183..fac2942 100644
--- a/docs/reference/estimate.probability.html
+++ b/docs/reference/estimate.probability.html
@@ -1,5 +1,5 @@
-Estimate Probability Vectors From Count Vectors — estimate.probability • philentropy
@@ -111,14 +111,11 @@ Author
Examples
-
-# generate a count vector
+ # generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
@@ -133,7 +130,7 @@ Examples
diff --git a/docs/reference/euclidean.html b/docs/reference/euclidean.html
index e7bfdb3..10ba169 100644
--- a/docs/reference/euclidean.html
+++ b/docs/reference/euclidean.html
@@ -1,5 +1,5 @@
-Euclidean distance (lowlevel function) — euclidean • philentropy Euclidean distance (lowlevel function) — euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/fidelity.html b/docs/reference/fidelity.html
index 478f65b..1ada4df 100644
--- a/docs/reference/fidelity.html
+++ b/docs/reference/fidelity.html
@@ -1,5 +1,5 @@
-Fidelity distance (lowlevel function) — fidelity • philentropy Fidelity distance (lowlevel function) — fidelity • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/gJSD.html b/docs/reference/gJSD.html
index 8968a16..bb73703 100644
--- a/docs/reference/gJSD.html
+++ b/docs/reference/gJSD.html
@@ -1,5 +1,5 @@
-Generalized Jensen-Shannon Divergence — gJSD • philentropy Generalized Jensen-Shannon Divergence — gJSD • philentropy
@@ -17,7 +17,7 @@
@@ -174,7 +174,7 @@ Examples
diff --git a/docs/reference/getDistMethods.html b/docs/reference/getDistMethods.html
index 22b6112..62fd3a2 100644
--- a/docs/reference/getDistMethods.html
+++ b/docs/reference/getDistMethods.html
@@ -1,5 +1,5 @@
-Get method names for distance — getDistMethods • philentropy Get method names for distance — getDistMethods • philentropy Gower distance (lowlevel function) — gower • philentropy Gower distance (lowlevel function) — gower • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/harmonic_mean_dist.html b/docs/reference/harmonic_mean_dist.html
index 1b56c5b..74d6368 100644
--- a/docs/reference/harmonic_mean_dist.html
+++ b/docs/reference/harmonic_mean_dist.html
@@ -1,5 +1,5 @@
-Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/hellinger.html b/docs/reference/hellinger.html
index 939f247..1b29a72 100644
--- a/docs/reference/hellinger.html
+++ b/docs/reference/hellinger.html
@@ -1,5 +1,5 @@
-Hellinger distance (lowlevel function) — hellinger • philentropy Hellinger distance (lowlevel function) — hellinger • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 45334af..fc23a81 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • philentropy Function reference • philentropy
@@ -17,7 +17,7 @@
@@ -334,7 +334,7 @@ Other
diff --git a/docs/reference/inner_product.html b/docs/reference/inner_product.html
index 9d62594..47d3480 100644
--- a/docs/reference/inner_product.html
+++ b/docs/reference/inner_product.html
@@ -1,5 +1,5 @@
-Inner product distance (lowlevel function) — inner_product • philentropy Inner product distance (lowlevel function) — inner_product • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/intersection_dist.html b/docs/reference/intersection_dist.html
index 9cdfc44..c890da3 100644
--- a/docs/reference/intersection_dist.html
+++ b/docs/reference/intersection_dist.html
@@ -1,5 +1,5 @@
-Intersection distance (lowlevel function) — intersection_dist • philentropy Intersection distance (lowlevel function) — intersection_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jaccard.html b/docs/reference/jaccard.html
index f38efbd..2dd5aee 100644
--- a/docs/reference/jaccard.html
+++ b/docs/reference/jaccard.html
@@ -1,5 +1,5 @@
-Jaccard distance (lowlevel function) — jaccard • philentropy Jaccard distance (lowlevel function) — jaccard • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jeffreys.html b/docs/reference/jeffreys.html
index d2667a8..b842063 100644
--- a/docs/reference/jeffreys.html
+++ b/docs/reference/jeffreys.html
@@ -1,5 +1,5 @@
-Jeffreys distance (lowlevel function) — jeffreys • philentropy Jeffreys distance (lowlevel function) — jeffreys • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/jensen_difference.html b/docs/reference/jensen_difference.html
index b6c46c7..851f47e 100644
--- a/docs/reference/jensen_difference.html
+++ b/docs/reference/jensen_difference.html
@@ -1,5 +1,5 @@
-Jensen difference (lowlevel function) — jensen_difference • philentropy Jensen difference (lowlevel function) — jensen_difference • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/jensen_shannon.html b/docs/reference/jensen_shannon.html
index e4afc37..3b31c6c 100644
--- a/docs/reference/jensen_shannon.html
+++ b/docs/reference/jensen_shannon.html
@@ -1,5 +1,5 @@
-Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/k_divergence.html b/docs/reference/k_divergence.html
index 6586850..01b895c 100644
--- a/docs/reference/k_divergence.html
+++ b/docs/reference/k_divergence.html
@@ -1,5 +1,5 @@
-K-Divergence (lowlevel function) — k_divergence • philentropy K-Divergence (lowlevel function) — k_divergence • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/kulczynski_d.html b/docs/reference/kulczynski_d.html
index 4a02a9a..d4de785 100644
--- a/docs/reference/kulczynski_d.html
+++ b/docs/reference/kulczynski_d.html
@@ -1,5 +1,5 @@
-Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/kullback_leibler_distance.html b/docs/reference/kullback_leibler_distance.html
index c858e31..269de13 100644
--- a/docs/reference/kullback_leibler_distance.html
+++ b/docs/reference/kullback_leibler_distance.html
@@ -1,5 +1,5 @@
-kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/kumar_hassebrook.html b/docs/reference/kumar_hassebrook.html
index 5f4a665..ffd46e1 100644
--- a/docs/reference/kumar_hassebrook.html
+++ b/docs/reference/kumar_hassebrook.html
@@ -1,5 +1,5 @@
-Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/kumar_johnson.html b/docs/reference/kumar_johnson.html
index eb7c507..8932862 100644
--- a/docs/reference/kumar_johnson.html
+++ b/docs/reference/kumar_johnson.html
@@ -1,5 +1,5 @@
-Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/lin.cor.html b/docs/reference/lin.cor.html
index 2a89ac2..303061a 100644
--- a/docs/reference/lin.cor.html
+++ b/docs/reference/lin.cor.html
@@ -1,5 +1,5 @@
-Linear Correlation — lin.cor • philentropy Linear Correlation — lin.cor • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/manhattan.html b/docs/reference/manhattan.html
index f6d96af..e665ee7 100644
--- a/docs/reference/manhattan.html
+++ b/docs/reference/manhattan.html
@@ -1,5 +1,5 @@
-Manhattan distance (lowlevel function) — manhattan • philentropy Manhattan distance (lowlevel function) — manhattan • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/matusita.html b/docs/reference/matusita.html
index ca4085b..aa559e7 100644
--- a/docs/reference/matusita.html
+++ b/docs/reference/matusita.html
@@ -1,5 +1,5 @@
-Matusita distance (lowlevel function) — matusita • philentropy Matusita distance (lowlevel function) — matusita • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/minkowski.html b/docs/reference/minkowski.html
index 8a54d62..6284b61 100644
--- a/docs/reference/minkowski.html
+++ b/docs/reference/minkowski.html
@@ -1,5 +1,5 @@
-Minkowski distance (lowlevel function) — minkowski • philentropy Minkowski distance (lowlevel function) — minkowski • philentropy
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/motyka.html b/docs/reference/motyka.html
index 0828b79..8df784d 100644
--- a/docs/reference/motyka.html
+++ b/docs/reference/motyka.html
@@ -1,5 +1,5 @@
-Motyka distance (lowlevel function) — motyka • philentropy Motyka distance (lowlevel function) — motyka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/neyman_chi_sq.html b/docs/reference/neyman_chi_sq.html
index 688ab07..874906f 100644
--- a/docs/reference/neyman_chi_sq.html
+++ b/docs/reference/neyman_chi_sq.html
@@ -1,5 +1,5 @@
-Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/pearson_chi_sq.html b/docs/reference/pearson_chi_sq.html
index f2290e6..c43d4a3 100644
--- a/docs/reference/pearson_chi_sq.html
+++ b/docs/reference/pearson_chi_sq.html
@@ -1,5 +1,5 @@
-Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/prob_symm_chi_sq.html b/docs/reference/prob_symm_chi_sq.html
index d637fcd..20ea75e 100644
--- a/docs/reference/prob_symm_chi_sq.html
+++ b/docs/reference/prob_symm_chi_sq.html
@@ -1,5 +1,5 @@
-Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/ruzicka.html b/docs/reference/ruzicka.html
index f66c101..b2eb4b1 100644
--- a/docs/reference/ruzicka.html
+++ b/docs/reference/ruzicka.html
@@ -1,5 +1,5 @@
-Ruzicka distance (lowlevel function) — ruzicka • philentropy Ruzicka distance (lowlevel function) — ruzicka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/soergel.html b/docs/reference/soergel.html
index e7407cf..eee7183 100644
--- a/docs/reference/soergel.html
+++ b/docs/reference/soergel.html
@@ -1,5 +1,5 @@
-Soergel distance (lowlevel function) — soergel • philentropy Soergel distance (lowlevel function) — soergel • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/sorensen.html b/docs/reference/sorensen.html
index d7e4710..a42c8c9 100644
--- a/docs/reference/sorensen.html
+++ b/docs/reference/sorensen.html
@@ -1,5 +1,5 @@
-Sorensen distance (lowlevel function) — sorensen • philentropy Sorensen distance (lowlevel function) — sorensen • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chi_sq.html b/docs/reference/squared_chi_sq.html
index 9c4fd48..3c2ae24 100644
--- a/docs/reference/squared_chi_sq.html
+++ b/docs/reference/squared_chi_sq.html
@@ -1,5 +1,5 @@
-Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chord.html b/docs/reference/squared_chord.html
index fb11253..80a1d81 100644
--- a/docs/reference/squared_chord.html
+++ b/docs/reference/squared_chord.html
@@ -1,5 +1,5 @@
-Squared chord distance (lowlevel function) — squared_chord • philentropy Squared chord distance (lowlevel function) — squared_chord • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_euclidean.html b/docs/reference/squared_euclidean.html
index 9adb873..7db57fe 100644
--- a/docs/reference/squared_euclidean.html
+++ b/docs/reference/squared_euclidean.html
@@ -1,5 +1,5 @@
-Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/taneja.html b/docs/reference/taneja.html
index 35e74d8..6ba928b 100644
--- a/docs/reference/taneja.html
+++ b/docs/reference/taneja.html
@@ -1,5 +1,5 @@
-Taneja difference (lowlevel function) — taneja • philentropy Taneja difference (lowlevel function) — taneja • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/tanimoto.html b/docs/reference/tanimoto.html
index bdf88f1..cee92f1 100644
--- a/docs/reference/tanimoto.html
+++ b/docs/reference/tanimoto.html
@@ -1,5 +1,5 @@
-Tanimoto distance (lowlevel function) — tanimoto • philentropy Tanimoto distance (lowlevel function) — tanimoto • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/topsoe.html b/docs/reference/topsoe.html
index d9294b6..e359a23 100644
--- a/docs/reference/topsoe.html
+++ b/docs/reference/topsoe.html
@@ -1,5 +1,5 @@
-Topsoe distance (lowlevel function) — topsoe • philentropy Topsoe distance (lowlevel function) — topsoe • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/wave_hedges.html b/docs/reference/wave_hedges.html
index e420c96..bc62841 100644
--- a/docs/reference/wave_hedges.html
+++ b/docs/reference/wave_hedges.html
@@ -1,5 +1,5 @@
-Wave hedges distance (lowlevel function) — wave_hedges • philentropy Wave hedges distance (lowlevel function) — wave_hedges • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/man/JSD.Rd b/man/JSD.Rd
index 05073b5..60ac6c8 100644
--- a/man/JSD.Rd
+++ b/man/JSD.Rd
@@ -19,10 +19,11 @@ JSD(x, test.na = TRUE, unit = "log2", est.prob = NULL)
}}
}
\value{
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
}
\description{
-This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the \code{link{sqrt}} on the \code{JSD()} output.
}
\details{
Function to compute the Jensen-Shannon Divergence JSD(P || Q) between two
@@ -64,7 +65,7 @@ Q.count <- 20:29
x.count <- rbind(P.count,Q.count)
JSD(x.count, est.prob = "empirical")
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
diff --git a/man/estimate.probability.Rd b/man/estimate.probability.Rd
index 98412a6..c2fafba 100644
--- a/man/estimate.probability.Rd
+++ b/man/estimate.probability.Rd
@@ -27,14 +27,11 @@ The following probability estimation methods are implemented in this function:
}
}
\examples{
-
# generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
}
\author{
Hajk-Georg Drost
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Information_Theory.html b/docs/articles/Information_Theory.html index 510e3e0..0539e21 100644 --- a/docs/articles/Information_Theory.html +++ b/docs/articles/Information_Theory.html @@ -6,7 +6,7 @@Generalized Jensen-Shannon Diverg
diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html
index 6474437..b7fbdfe 100644
--- a/docs/articles/Introduction.html
+++ b/docs/articles/Introduction.html
@@ -6,7 +6,7 @@
Introduction • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -422,7 +422,7 @@ Information Theory
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Many_Distances.html b/docs/articles/Many_Distances.html
index 9b5b7c4..68ab5b3 100644
--- a/docs/articles/Many_Distances.html
+++ b/docs/articles/Many_Distances.html
@@ -6,7 +6,7 @@
Comparing many probability density functions • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -141,7 +141,7 @@ 2021-08-20
Let’s start testing them by attaching the
philentropy package.
+library(philentropy)
dist_one_one()
@@ -176,11 +176,11 @@
## 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
-## 5986 6396 8233.62 6724.0 7113.5 108691 100
-## 9266 9922 18894.85 10475.5 11931.0 783756 100
-## 820 902 1150.87 943.0 1086.5 3854 100
-## 1189 1271 1756.03 1353.0 1496.5 19680 100
+## min lq mean median uq max neval
+## 5166 5371 6431.26 5658 5883.5 75563 100
+## 7585 7913 12703.03 8036 8241.0 459200 100
+## 492 533 771.62 574 615.0 19352 100
+## 820 861 1093.88 943 1025.0 15375 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.
@@ -219,10 +219,10 @@
## as.matrix(dist(rbind(P, M), method = "euclidean"))[1, ][-1]
## 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
-## 130.831 148.1125 160.26367 157.9935 167.690 263.548 100
-## 9016.515 9735.1630 11155.15536 10312.8735 12742.677 14336.511 100
-## 9.512 10.3730 12.67269 11.8285 13.858 44.526 100
+## min lq mean median uq max neval
+## 65.313 71.4425 77.49861 74.3330 80.8315 152.028 100
+## 6430.850 6534.4570 6748.67462 6621.6845 6945.7895 8020.297 100
+## 7.749 8.8970 9.69158 9.2455 9.6350 30.381 100
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
@@ -265,11 +265,11 @@
)
## Unit: microseconds
## expr min lq
-## many_dists(M1, M2) 958.990 994.5575
-## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 14.104 14.8830
-## mean median uq max neval
-## 1181.08126 1013.458 1081.375 4497.126 100
-## 16.36269 15.375 16.851 37.843 100
+## many_dists(M1, M2) 815.982 859.6265
+## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 12.669 13.7965
+## mean median uq max neval
+## 1018.45107 900.114 992.6305 3761.668 100
+## 15.36475 14.719 16.1745 32.062 100
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
@@ -294,7 +294,7 @@
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b8ef73d..2f170dd 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • philentropy Articles • philentropy
@@ -17,7 +17,7 @@
@@ -87,7 +87,7 @@ All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index bb364f2..83be8d6 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • philentropy Authors and Citation • philentropy
@@ -17,7 +17,7 @@
@@ -63,7 +63,7 @@
diff --git a/docs/index.html b/docs/index.html
index 3d56d12..3b24f29 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
Similarity and Distance Quantification Between Probability Functions • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -89,7 +89,7 @@
-
+
Similarity and Distance Quantification between Probability Functions
@@ -104,7 +104,7 @@ Si
Installation
-# install philentropy version 0.8.0 from CRAN
+# install philentropy version 0.9.0 from CRAN
install.packages("philentropy")
@@ -129,7 +129,7 @@ TutorialsExamples
-library(philentropy)
+library(philentropy)
# retrieve available distance metrics
philentropy::getDistMethods()
[1] "euclidean" "manhattan" "minkowski"
@@ -421,7 +421,7 @@ Developers
diff --git a/docs/news/index.html b/docs/news/index.html
index fe02957..13475f1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • philentropy Changelog • philentropy
@@ -17,7 +17,7 @@
@@ -67,7 +67,13 @@ Changelog
+
+Version 0.8.02023-12-02
Updates
Fixing warning on Debian systems:
@@ -112,7 +118,7 @@ Updatesstats::dist() when working with 2 dimensional input matrices (2 vector inputs) (see #29) (Many thanks to Jakub Nowosad (@Nowosad)) Example:
-library(philentropy)
+library(philentropy)
m1 = matrix(c(1, 2), ncol = 1)
@@ -240,7 +246,7 @@ Version 0.0.1
diff --git a/docs/paper.html b/docs/paper.html
index 05106b9..7da9177 100644
--- a/docs/paper.html
+++ b/docs/paper.html
@@ -1,5 +1,5 @@
-Summary • philentropy Summary • philentropy
@@ -17,7 +17,7 @@
@@ -82,7 +82,7 @@
Minkowski : $d = ( \sum_{i = 1}^N | P_i - Q_i |^p)^{1/p}$
-Chebyshev : d = max|Pi−Qi|
+ Chebyshev : d = max|Pi − Qi|
@@ -202,7 +202,7 @@ Information Theory Measures$KL(P || Q) = \sum\limits_{i=1}^n P(p_i) \cdot log_2(\frac{P(p_i) }{P(q_i)}) = H(P, Q) - H(P)$
-Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R)+KL(Q||R))
+ Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R) + KL(Q||R))
Generalized Jensen-Shannon Divergence : $gJSD_{\pi_1,...,\pi_n}(P_1, ..., P_n) = H(\sum_{i = 1}^n \pi_i \cdot P_i) - \sum_{i = 1}^n \pi_i \cdot H(P_i)$
@@ -233,7 +233,7 @@ References
- Site built with pkgdown 2.0.7.
+ Site built with pkgdown 2.0.9.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 70ec28c..e9d6dfb 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,10 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
Distances: Distances.html
Information_Theory: Information_Theory.html
Introduction: Introduction.html
Many_Distances: Many_Distances.html
-last_built: 2024-02-09T18:18Z
+last_built: 2024-11-12T20:43Z
diff --git a/docs/reference/CE.html b/docs/reference/CE.html
index 2d20e6b..eca2096 100644
--- a/docs/reference/CE.html
+++ b/docs/reference/CE.html
@@ -1,5 +1,5 @@
-Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Jensen-Shannon Divergence — JSD • philentropy Jensen-Shannon Divergence — JSD • philentropy
@@ -17,7 +18,7 @@
@@ -68,7 +69,8 @@ Jensen-Shannon Divergence
- This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+ This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the link{sqrt} on the JSD() output.
@@ -98,7 +100,7 @@ Arguments
Value
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
Details
@@ -166,7 +168,7 @@ Examples
#> jensen-shannon
#> 0.03792749
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
@@ -192,7 +194,7 @@ Examples
diff --git a/docs/reference/KL-1.png b/docs/reference/KL-1.png
index 202b9bb..30a7905 100644
Binary files a/docs/reference/KL-1.png and b/docs/reference/KL-1.png differ
diff --git a/docs/reference/KL.html b/docs/reference/KL.html
index 7da42db..a371da0 100644
--- a/docs/reference/KL.html
+++ b/docs/reference/KL.html
@@ -1,5 +1,5 @@
-Kullback-Leibler Divergence — KL • philentropy Kullback-Leibler Divergence — KL • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/avg.html b/docs/reference/avg.html
index cb60568..544da83 100644
--- a/docs/reference/avg.html
+++ b/docs/reference/avg.html
@@ -1,5 +1,5 @@
-AVG distance (lowlevel function) — avg • philentropy AVG distance (lowlevel function) — avg • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/bhattacharyya.html b/docs/reference/bhattacharyya.html
index d813f81..50e66d4 100644
--- a/docs/reference/bhattacharyya.html
+++ b/docs/reference/bhattacharyya.html
@@ -1,5 +1,5 @@
-Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy
@@ -17,7 +17,7 @@
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/binned.kernel.est.html b/docs/reference/binned.kernel.est.html
index 5daba65..657d534 100644
--- a/docs/reference/binned.kernel.est.html
+++ b/docs/reference/binned.kernel.est.html
@@ -1,5 +1,5 @@
-Kernel Density Estimation — binned.kernel.est • philentropy Kernel Density Estimation — binned.kernel.est • philentropy
@@ -17,7 +17,7 @@
@@ -148,7 +148,7 @@ Author
diff --git a/docs/reference/canberra.html b/docs/reference/canberra.html
index b16d474..104893d 100644
--- a/docs/reference/canberra.html
+++ b/docs/reference/canberra.html
@@ -1,5 +1,5 @@
-Canberra distance (lowlevel function) — canberra • philentropy Canberra distance (lowlevel function) — canberra • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/chebyshev.html b/docs/reference/chebyshev.html
index ccaf554..a12bc9d 100644
--- a/docs/reference/chebyshev.html
+++ b/docs/reference/chebyshev.html
@@ -1,5 +1,5 @@
-Chebyshev distance (lowlevel function) — chebyshev • philentropy Chebyshev distance (lowlevel function) — chebyshev • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/clark_sq.html b/docs/reference/clark_sq.html
index 325d8db..09e0cea 100644
--- a/docs/reference/clark_sq.html
+++ b/docs/reference/clark_sq.html
@@ -1,5 +1,5 @@
-Clark squared distance (lowlevel function) — clark_sq • philentropy Clark squared distance (lowlevel function) — clark_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/cosine_dist.html b/docs/reference/cosine_dist.html
index f2a739e..a52a572 100644
--- a/docs/reference/cosine_dist.html
+++ b/docs/reference/cosine_dist.html
@@ -1,5 +1,5 @@
-Cosine distance (lowlevel function) — cosine_dist • philentropy Cosine distance (lowlevel function) — cosine_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/czekanowski.html b/docs/reference/czekanowski.html
index 6b61e36..3c09167 100644
--- a/docs/reference/czekanowski.html
+++ b/docs/reference/czekanowski.html
@@ -1,5 +1,5 @@
-Czekanowski distance (lowlevel function) — czekanowski • philentropy Czekanowski distance (lowlevel function) — czekanowski • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dice_dist.html b/docs/reference/dice_dist.html
index ca45645..4d9df52 100644
--- a/docs/reference/dice_dist.html
+++ b/docs/reference/dice_dist.html
@@ -1,5 +1,5 @@
-Dice distance (lowlevel function) — dice_dist • philentropy Dice distance (lowlevel function) — dice_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dist.diversity.html b/docs/reference/dist.diversity.html
index c57920f..bf390ac 100644
--- a/docs/reference/dist.diversity.html
+++ b/docs/reference/dist.diversity.html
@@ -1,5 +1,5 @@
-Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/dist_one_many.html b/docs/reference/dist_one_many.html
index 82fe0f8..4db596b 100644
--- a/docs/reference/dist_one_many.html
+++ b/docs/reference/dist_one_many.html
@@ -1,5 +1,5 @@
-Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Examples
diff --git a/docs/reference/dist_one_one.html b/docs/reference/dist_one_one.html
index 18f3b01..684dc1f 100644
--- a/docs/reference/dist_one_one.html
+++ b/docs/reference/dist_one_one.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/distance.html b/docs/reference/distance.html
index f8c089f..6b95cbb 100644
--- a/docs/reference/distance.html
+++ b/docs/reference/distance.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Probability Density Functions — distance • philentropy Distances and Similarities between Probability Density Functions — distance • philentropy
@@ -17,7 +17,7 @@
@@ -366,7 +366,7 @@ Examples
diff --git a/docs/reference/divergence_sq.html b/docs/reference/divergence_sq.html
index 0722d20..597a0e0 100644
--- a/docs/reference/divergence_sq.html
+++ b/docs/reference/divergence_sq.html
@@ -1,5 +1,5 @@
-Divergence squared distance (lowlevel function) — divergence_sq • philentropy Divergence squared distance (lowlevel function) — divergence_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/estimate.probability.html b/docs/reference/estimate.probability.html
index e31c183..fac2942 100644
--- a/docs/reference/estimate.probability.html
+++ b/docs/reference/estimate.probability.html
@@ -1,5 +1,5 @@
-Estimate Probability Vectors From Count Vectors — estimate.probability • philentropy
@@ -111,14 +111,11 @@ Author
Examples
-
-# generate a count vector
+ # generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
@@ -133,7 +130,7 @@ Examples
diff --git a/docs/reference/euclidean.html b/docs/reference/euclidean.html
index e7bfdb3..10ba169 100644
--- a/docs/reference/euclidean.html
+++ b/docs/reference/euclidean.html
@@ -1,5 +1,5 @@
-Euclidean distance (lowlevel function) — euclidean • philentropy Euclidean distance (lowlevel function) — euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/fidelity.html b/docs/reference/fidelity.html
index 478f65b..1ada4df 100644
--- a/docs/reference/fidelity.html
+++ b/docs/reference/fidelity.html
@@ -1,5 +1,5 @@
-Fidelity distance (lowlevel function) — fidelity • philentropy Fidelity distance (lowlevel function) — fidelity • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/gJSD.html b/docs/reference/gJSD.html
index 8968a16..bb73703 100644
--- a/docs/reference/gJSD.html
+++ b/docs/reference/gJSD.html
@@ -1,5 +1,5 @@
-Generalized Jensen-Shannon Divergence — gJSD • philentropy Generalized Jensen-Shannon Divergence — gJSD • philentropy
@@ -17,7 +17,7 @@
@@ -174,7 +174,7 @@ Examples
diff --git a/docs/reference/getDistMethods.html b/docs/reference/getDistMethods.html
index 22b6112..62fd3a2 100644
--- a/docs/reference/getDistMethods.html
+++ b/docs/reference/getDistMethods.html
@@ -1,5 +1,5 @@
-Get method names for distance — getDistMethods • philentropy Get method names for distance — getDistMethods • philentropy Gower distance (lowlevel function) — gower • philentropy Gower distance (lowlevel function) — gower • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/harmonic_mean_dist.html b/docs/reference/harmonic_mean_dist.html
index 1b56c5b..74d6368 100644
--- a/docs/reference/harmonic_mean_dist.html
+++ b/docs/reference/harmonic_mean_dist.html
@@ -1,5 +1,5 @@
-Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/hellinger.html b/docs/reference/hellinger.html
index 939f247..1b29a72 100644
--- a/docs/reference/hellinger.html
+++ b/docs/reference/hellinger.html
@@ -1,5 +1,5 @@
-Hellinger distance (lowlevel function) — hellinger • philentropy Hellinger distance (lowlevel function) — hellinger • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 45334af..fc23a81 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • philentropy Function reference • philentropy
@@ -17,7 +17,7 @@
@@ -334,7 +334,7 @@ Other
diff --git a/docs/reference/inner_product.html b/docs/reference/inner_product.html
index 9d62594..47d3480 100644
--- a/docs/reference/inner_product.html
+++ b/docs/reference/inner_product.html
@@ -1,5 +1,5 @@
-Inner product distance (lowlevel function) — inner_product • philentropy Inner product distance (lowlevel function) — inner_product • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/intersection_dist.html b/docs/reference/intersection_dist.html
index 9cdfc44..c890da3 100644
--- a/docs/reference/intersection_dist.html
+++ b/docs/reference/intersection_dist.html
@@ -1,5 +1,5 @@
-Intersection distance (lowlevel function) — intersection_dist • philentropy Intersection distance (lowlevel function) — intersection_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jaccard.html b/docs/reference/jaccard.html
index f38efbd..2dd5aee 100644
--- a/docs/reference/jaccard.html
+++ b/docs/reference/jaccard.html
@@ -1,5 +1,5 @@
-Jaccard distance (lowlevel function) — jaccard • philentropy Jaccard distance (lowlevel function) — jaccard • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jeffreys.html b/docs/reference/jeffreys.html
index d2667a8..b842063 100644
--- a/docs/reference/jeffreys.html
+++ b/docs/reference/jeffreys.html
@@ -1,5 +1,5 @@
-Jeffreys distance (lowlevel function) — jeffreys • philentropy Jeffreys distance (lowlevel function) — jeffreys • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/jensen_difference.html b/docs/reference/jensen_difference.html
index b6c46c7..851f47e 100644
--- a/docs/reference/jensen_difference.html
+++ b/docs/reference/jensen_difference.html
@@ -1,5 +1,5 @@
-Jensen difference (lowlevel function) — jensen_difference • philentropy Jensen difference (lowlevel function) — jensen_difference • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/jensen_shannon.html b/docs/reference/jensen_shannon.html
index e4afc37..3b31c6c 100644
--- a/docs/reference/jensen_shannon.html
+++ b/docs/reference/jensen_shannon.html
@@ -1,5 +1,5 @@
-Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/k_divergence.html b/docs/reference/k_divergence.html
index 6586850..01b895c 100644
--- a/docs/reference/k_divergence.html
+++ b/docs/reference/k_divergence.html
@@ -1,5 +1,5 @@
-K-Divergence (lowlevel function) — k_divergence • philentropy K-Divergence (lowlevel function) — k_divergence • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/kulczynski_d.html b/docs/reference/kulczynski_d.html
index 4a02a9a..d4de785 100644
--- a/docs/reference/kulczynski_d.html
+++ b/docs/reference/kulczynski_d.html
@@ -1,5 +1,5 @@
-Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/kullback_leibler_distance.html b/docs/reference/kullback_leibler_distance.html
index c858e31..269de13 100644
--- a/docs/reference/kullback_leibler_distance.html
+++ b/docs/reference/kullback_leibler_distance.html
@@ -1,5 +1,5 @@
-kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/kumar_hassebrook.html b/docs/reference/kumar_hassebrook.html
index 5f4a665..ffd46e1 100644
--- a/docs/reference/kumar_hassebrook.html
+++ b/docs/reference/kumar_hassebrook.html
@@ -1,5 +1,5 @@
-Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/kumar_johnson.html b/docs/reference/kumar_johnson.html
index eb7c507..8932862 100644
--- a/docs/reference/kumar_johnson.html
+++ b/docs/reference/kumar_johnson.html
@@ -1,5 +1,5 @@
-Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/lin.cor.html b/docs/reference/lin.cor.html
index 2a89ac2..303061a 100644
--- a/docs/reference/lin.cor.html
+++ b/docs/reference/lin.cor.html
@@ -1,5 +1,5 @@
-Linear Correlation — lin.cor • philentropy Linear Correlation — lin.cor • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/manhattan.html b/docs/reference/manhattan.html
index f6d96af..e665ee7 100644
--- a/docs/reference/manhattan.html
+++ b/docs/reference/manhattan.html
@@ -1,5 +1,5 @@
-Manhattan distance (lowlevel function) — manhattan • philentropy Manhattan distance (lowlevel function) — manhattan • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/matusita.html b/docs/reference/matusita.html
index ca4085b..aa559e7 100644
--- a/docs/reference/matusita.html
+++ b/docs/reference/matusita.html
@@ -1,5 +1,5 @@
-Matusita distance (lowlevel function) — matusita • philentropy Matusita distance (lowlevel function) — matusita • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/minkowski.html b/docs/reference/minkowski.html
index 8a54d62..6284b61 100644
--- a/docs/reference/minkowski.html
+++ b/docs/reference/minkowski.html
@@ -1,5 +1,5 @@
-Minkowski distance (lowlevel function) — minkowski • philentropy Minkowski distance (lowlevel function) — minkowski • philentropy
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/motyka.html b/docs/reference/motyka.html
index 0828b79..8df784d 100644
--- a/docs/reference/motyka.html
+++ b/docs/reference/motyka.html
@@ -1,5 +1,5 @@
-Motyka distance (lowlevel function) — motyka • philentropy Motyka distance (lowlevel function) — motyka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/neyman_chi_sq.html b/docs/reference/neyman_chi_sq.html
index 688ab07..874906f 100644
--- a/docs/reference/neyman_chi_sq.html
+++ b/docs/reference/neyman_chi_sq.html
@@ -1,5 +1,5 @@
-Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/pearson_chi_sq.html b/docs/reference/pearson_chi_sq.html
index f2290e6..c43d4a3 100644
--- a/docs/reference/pearson_chi_sq.html
+++ b/docs/reference/pearson_chi_sq.html
@@ -1,5 +1,5 @@
-Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/prob_symm_chi_sq.html b/docs/reference/prob_symm_chi_sq.html
index d637fcd..20ea75e 100644
--- a/docs/reference/prob_symm_chi_sq.html
+++ b/docs/reference/prob_symm_chi_sq.html
@@ -1,5 +1,5 @@
-Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/ruzicka.html b/docs/reference/ruzicka.html
index f66c101..b2eb4b1 100644
--- a/docs/reference/ruzicka.html
+++ b/docs/reference/ruzicka.html
@@ -1,5 +1,5 @@
-Ruzicka distance (lowlevel function) — ruzicka • philentropy Ruzicka distance (lowlevel function) — ruzicka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/soergel.html b/docs/reference/soergel.html
index e7407cf..eee7183 100644
--- a/docs/reference/soergel.html
+++ b/docs/reference/soergel.html
@@ -1,5 +1,5 @@
-Soergel distance (lowlevel function) — soergel • philentropy Soergel distance (lowlevel function) — soergel • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/sorensen.html b/docs/reference/sorensen.html
index d7e4710..a42c8c9 100644
--- a/docs/reference/sorensen.html
+++ b/docs/reference/sorensen.html
@@ -1,5 +1,5 @@
-Sorensen distance (lowlevel function) — sorensen • philentropy Sorensen distance (lowlevel function) — sorensen • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chi_sq.html b/docs/reference/squared_chi_sq.html
index 9c4fd48..3c2ae24 100644
--- a/docs/reference/squared_chi_sq.html
+++ b/docs/reference/squared_chi_sq.html
@@ -1,5 +1,5 @@
-Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chord.html b/docs/reference/squared_chord.html
index fb11253..80a1d81 100644
--- a/docs/reference/squared_chord.html
+++ b/docs/reference/squared_chord.html
@@ -1,5 +1,5 @@
-Squared chord distance (lowlevel function) — squared_chord • philentropy Squared chord distance (lowlevel function) — squared_chord • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_euclidean.html b/docs/reference/squared_euclidean.html
index 9adb873..7db57fe 100644
--- a/docs/reference/squared_euclidean.html
+++ b/docs/reference/squared_euclidean.html
@@ -1,5 +1,5 @@
-Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/taneja.html b/docs/reference/taneja.html
index 35e74d8..6ba928b 100644
--- a/docs/reference/taneja.html
+++ b/docs/reference/taneja.html
@@ -1,5 +1,5 @@
-Taneja difference (lowlevel function) — taneja • philentropy Taneja difference (lowlevel function) — taneja • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/tanimoto.html b/docs/reference/tanimoto.html
index bdf88f1..cee92f1 100644
--- a/docs/reference/tanimoto.html
+++ b/docs/reference/tanimoto.html
@@ -1,5 +1,5 @@
-Tanimoto distance (lowlevel function) — tanimoto • philentropy Tanimoto distance (lowlevel function) — tanimoto • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/topsoe.html b/docs/reference/topsoe.html
index d9294b6..e359a23 100644
--- a/docs/reference/topsoe.html
+++ b/docs/reference/topsoe.html
@@ -1,5 +1,5 @@
-Topsoe distance (lowlevel function) — topsoe • philentropy Topsoe distance (lowlevel function) — topsoe • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/wave_hedges.html b/docs/reference/wave_hedges.html
index e420c96..bc62841 100644
--- a/docs/reference/wave_hedges.html
+++ b/docs/reference/wave_hedges.html
@@ -1,5 +1,5 @@
-Wave hedges distance (lowlevel function) — wave_hedges • philentropy Wave hedges distance (lowlevel function) — wave_hedges • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/man/JSD.Rd b/man/JSD.Rd
index 05073b5..60ac6c8 100644
--- a/man/JSD.Rd
+++ b/man/JSD.Rd
@@ -19,10 +19,11 @@ JSD(x, test.na = TRUE, unit = "log2", est.prob = NULL)
}}
}
\value{
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
}
\description{
-This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the \code{link{sqrt}} on the \code{JSD()} output.
}
\details{
Function to compute the Jensen-Shannon Divergence JSD(P || Q) between two
@@ -64,7 +65,7 @@ Q.count <- 20:29
x.count <- rbind(P.count,Q.count)
JSD(x.count, est.prob = "empirical")
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
diff --git a/man/estimate.probability.Rd b/man/estimate.probability.Rd
index 98412a6..c2fafba 100644
--- a/man/estimate.probability.Rd
+++ b/man/estimate.probability.Rd
@@ -27,14 +27,11 @@ The following probability estimation methods are implemented in this function:
}
}
\examples{
-
# generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
}
\author{
Hajk-Georg Drost
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Many_Distances.html b/docs/articles/Many_Distances.html index 9b5b7c4..68ab5b3 100644 --- a/docs/articles/Many_Distances.html +++ b/docs/articles/Many_Distances.html @@ -6,7 +6,7 @@2021-08-20
Let’s start testing them by attaching the philentropy package.
+library(philentropy)
dist_one_one()
@@ -176,11 +176,11 @@
## 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
-## 5986 6396 8233.62 6724.0 7113.5 108691 100
-## 9266 9922 18894.85 10475.5 11931.0 783756 100
-## 820 902 1150.87 943.0 1086.5 3854 100
-## 1189 1271 1756.03 1353.0 1496.5 19680 100
+## min lq mean median uq max neval
+## 5166 5371 6431.26 5658 5883.5 75563 100
+## 7585 7913 12703.03 8036 8241.0 459200 100
+## 492 533 771.62 574 615.0 19352 100
+## 820 861 1093.88 943 1025.0 15375 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.
## as.matrix(dist(rbind(P, M), method = "euclidean"))[1, ][-1] ## 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 -## 130.831 148.1125 160.26367 157.9935 167.690 263.548 100 -## 9016.515 9735.1630 11155.15536 10312.8735 12742.677 14336.511 100 -## 9.512 10.3730 12.67269 11.8285 13.858 44.526 100 +## min lq mean median uq max neval +## 65.313 71.4425 77.49861 74.3330 80.8315 152.028 100 +## 6430.850 6534.4570 6748.67462 6621.6845 6945.7895 8020.297 100 +## 7.749 8.8970 9.69158 9.2455 9.6350 30.381 100
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
@@ -265,11 +265,11 @@
)
## Unit: microseconds
## expr min lq
-## many_dists(M1, M2) 958.990 994.5575
-## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 14.104 14.8830
-## mean median uq max neval
-## 1181.08126 1013.458 1081.375 4497.126 100
-## 16.36269 15.375 16.851 37.843 100
+## many_dists(M1, M2) 815.982 859.6265
+## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 12.669 13.7965
+## mean median uq max neval
+## 1018.45107 900.114 992.6305 3761.668 100
+## 15.36475 14.719 16.1745 32.062 100
## Unit: microseconds
## expr min lq
-## many_dists(M1, M2) 958.990 994.5575
-## dist_many_many(M1, M2, method = "euclidean", testNA = FALSE) 14.104 14.8830
-## mean median uq max neval
-## 1181.08126 1013.458 1081.375 4497.126 100
-## 16.36269 15.375 16.851 37.843 100Both 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
@@ -294,7 +294,7 @@
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b8ef73d..2f170dd 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • philentropy Articles • philentropy
@@ -17,7 +17,7 @@
@@ -87,7 +87,7 @@ All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index bb364f2..83be8d6 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • philentropy Authors and Citation • philentropy
@@ -17,7 +17,7 @@
@@ -63,7 +63,7 @@
diff --git a/docs/index.html b/docs/index.html
index 3d56d12..3b24f29 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
Similarity and Distance Quantification Between Probability Functions • philentropy
-
+
@@ -33,7 +33,7 @@
@@ -89,7 +89,7 @@
-
+
Similarity and Distance Quantification between Probability Functions
@@ -104,7 +104,7 @@ Si
Installation
-# install philentropy version 0.8.0 from CRAN
+# install philentropy version 0.9.0 from CRAN
install.packages("philentropy")
@@ -129,7 +129,7 @@ TutorialsExamples
-library(philentropy)
+library(philentropy)
# retrieve available distance metrics
philentropy::getDistMethods()
[1] "euclidean" "manhattan" "minkowski"
@@ -421,7 +421,7 @@ Developers
diff --git a/docs/news/index.html b/docs/news/index.html
index fe02957..13475f1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • philentropy Changelog • philentropy
@@ -17,7 +17,7 @@
@@ -67,7 +67,13 @@ Changelog
+
+Version 0.8.02023-12-02
Updates
Fixing warning on Debian systems:
@@ -112,7 +118,7 @@ Updatesstats::dist() when working with 2 dimensional input matrices (2 vector inputs) (see #29) (Many thanks to Jakub Nowosad (@Nowosad)) Example:
-library(philentropy)
+library(philentropy)
m1 = matrix(c(1, 2), ncol = 1)
@@ -240,7 +246,7 @@ Version 0.0.1
diff --git a/docs/paper.html b/docs/paper.html
index 05106b9..7da9177 100644
--- a/docs/paper.html
+++ b/docs/paper.html
@@ -1,5 +1,5 @@
-Summary • philentropy Summary • philentropy
@@ -17,7 +17,7 @@
@@ -82,7 +82,7 @@
Minkowski : $d = ( \sum_{i = 1}^N | P_i - Q_i |^p)^{1/p}$
-Chebyshev : d = max|Pi−Qi|
+ Chebyshev : d = max|Pi − Qi|
@@ -202,7 +202,7 @@ Information Theory Measures$KL(P || Q) = \sum\limits_{i=1}^n P(p_i) \cdot log_2(\frac{P(p_i) }{P(q_i)}) = H(P, Q) - H(P)$
-Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R)+KL(Q||R))
+ Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R) + KL(Q||R))
Generalized Jensen-Shannon Divergence : $gJSD_{\pi_1,...,\pi_n}(P_1, ..., P_n) = H(\sum_{i = 1}^n \pi_i \cdot P_i) - \sum_{i = 1}^n \pi_i \cdot H(P_i)$
@@ -233,7 +233,7 @@ References
- Site built with pkgdown 2.0.7.
+ Site built with pkgdown 2.0.9.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 70ec28c..e9d6dfb 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,10 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
Distances: Distances.html
Information_Theory: Information_Theory.html
Introduction: Introduction.html
Many_Distances: Many_Distances.html
-last_built: 2024-02-09T18:18Z
+last_built: 2024-11-12T20:43Z
diff --git a/docs/reference/CE.html b/docs/reference/CE.html
index 2d20e6b..eca2096 100644
--- a/docs/reference/CE.html
+++ b/docs/reference/CE.html
@@ -1,5 +1,5 @@
-Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Conditional-Entropy \(H(X | Y)\) — CE • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Entropy \(H(X)\) — H • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Shannon's Joint-Entropy \(H(X,Y)\) — JE • philentropy Jensen-Shannon Divergence — JSD • philentropy Jensen-Shannon Divergence — JSD • philentropy
@@ -17,7 +18,7 @@
@@ -68,7 +69,8 @@ Jensen-Shannon Divergence
- This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+ This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the link{sqrt} on the JSD() output.
@@ -98,7 +100,7 @@ Arguments
Value
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
Details
@@ -166,7 +168,7 @@ Examples
#> jensen-shannon
#> 0.03792749
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
@@ -192,7 +194,7 @@ Examples
diff --git a/docs/reference/KL-1.png b/docs/reference/KL-1.png
index 202b9bb..30a7905 100644
Binary files a/docs/reference/KL-1.png and b/docs/reference/KL-1.png differ
diff --git a/docs/reference/KL.html b/docs/reference/KL.html
index 7da42db..a371da0 100644
--- a/docs/reference/KL.html
+++ b/docs/reference/KL.html
@@ -1,5 +1,5 @@
-Kullback-Leibler Divergence — KL • philentropy Kullback-Leibler Divergence — KL • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Shannon's Mutual Information \(I(X,Y)\) — MI • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy Additive symmetric chi-squared distance (lowlevel function) — additive_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/avg.html b/docs/reference/avg.html
index cb60568..544da83 100644
--- a/docs/reference/avg.html
+++ b/docs/reference/avg.html
@@ -1,5 +1,5 @@
-AVG distance (lowlevel function) — avg • philentropy AVG distance (lowlevel function) — avg • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/bhattacharyya.html b/docs/reference/bhattacharyya.html
index d813f81..50e66d4 100644
--- a/docs/reference/bhattacharyya.html
+++ b/docs/reference/bhattacharyya.html
@@ -1,5 +1,5 @@
-Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy Bhattacharyya distance (lowlevel function) — bhattacharyya • philentropy
@@ -17,7 +17,7 @@
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/binned.kernel.est.html b/docs/reference/binned.kernel.est.html
index 5daba65..657d534 100644
--- a/docs/reference/binned.kernel.est.html
+++ b/docs/reference/binned.kernel.est.html
@@ -1,5 +1,5 @@
-Kernel Density Estimation — binned.kernel.est • philentropy Kernel Density Estimation — binned.kernel.est • philentropy
@@ -17,7 +17,7 @@
@@ -148,7 +148,7 @@ Author
diff --git a/docs/reference/canberra.html b/docs/reference/canberra.html
index b16d474..104893d 100644
--- a/docs/reference/canberra.html
+++ b/docs/reference/canberra.html
@@ -1,5 +1,5 @@
-Canberra distance (lowlevel function) — canberra • philentropy Canberra distance (lowlevel function) — canberra • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/chebyshev.html b/docs/reference/chebyshev.html
index ccaf554..a12bc9d 100644
--- a/docs/reference/chebyshev.html
+++ b/docs/reference/chebyshev.html
@@ -1,5 +1,5 @@
-Chebyshev distance (lowlevel function) — chebyshev • philentropy Chebyshev distance (lowlevel function) — chebyshev • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/clark_sq.html b/docs/reference/clark_sq.html
index 325d8db..09e0cea 100644
--- a/docs/reference/clark_sq.html
+++ b/docs/reference/clark_sq.html
@@ -1,5 +1,5 @@
-Clark squared distance (lowlevel function) — clark_sq • philentropy Clark squared distance (lowlevel function) — clark_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/cosine_dist.html b/docs/reference/cosine_dist.html
index f2a739e..a52a572 100644
--- a/docs/reference/cosine_dist.html
+++ b/docs/reference/cosine_dist.html
@@ -1,5 +1,5 @@
-Cosine distance (lowlevel function) — cosine_dist • philentropy Cosine distance (lowlevel function) — cosine_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/czekanowski.html b/docs/reference/czekanowski.html
index 6b61e36..3c09167 100644
--- a/docs/reference/czekanowski.html
+++ b/docs/reference/czekanowski.html
@@ -1,5 +1,5 @@
-Czekanowski distance (lowlevel function) — czekanowski • philentropy Czekanowski distance (lowlevel function) — czekanowski • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dice_dist.html b/docs/reference/dice_dist.html
index ca45645..4d9df52 100644
--- a/docs/reference/dice_dist.html
+++ b/docs/reference/dice_dist.html
@@ -1,5 +1,5 @@
-Dice distance (lowlevel function) — dice_dist • philentropy Dice distance (lowlevel function) — dice_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/dist.diversity.html b/docs/reference/dist.diversity.html
index c57920f..bf390ac 100644
--- a/docs/reference/dist.diversity.html
+++ b/docs/reference/dist.diversity.html
@@ -1,5 +1,5 @@
-Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distance Diversity between Probability Density Functions — dist.diversity • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy Distances and Similarities between Many Probability Density Functions — dist_many_many • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/dist_one_many.html b/docs/reference/dist_one_many.html
index 82fe0f8..4db596b 100644
--- a/docs/reference/dist_one_many.html
+++ b/docs/reference/dist_one_many.html
@@ -1,5 +1,5 @@
-Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy Distances and Similarities between One and Many Probability Density Functions — dist_one_many • philentropy
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Examples
diff --git a/docs/reference/dist_one_one.html b/docs/reference/dist_one_one.html
index 18f3b01..684dc1f 100644
--- a/docs/reference/dist_one_one.html
+++ b/docs/reference/dist_one_one.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy Distances and Similarities between Two Probability Density Functions — dist_one_one • philentropy
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/distance.html b/docs/reference/distance.html
index f8c089f..6b95cbb 100644
--- a/docs/reference/distance.html
+++ b/docs/reference/distance.html
@@ -1,5 +1,5 @@
-Distances and Similarities between Probability Density Functions — distance • philentropy Distances and Similarities between Probability Density Functions — distance • philentropy
@@ -17,7 +17,7 @@
@@ -366,7 +366,7 @@ Examples
diff --git a/docs/reference/divergence_sq.html b/docs/reference/divergence_sq.html
index 0722d20..597a0e0 100644
--- a/docs/reference/divergence_sq.html
+++ b/docs/reference/divergence_sq.html
@@ -1,5 +1,5 @@
-Divergence squared distance (lowlevel function) — divergence_sq • philentropy Divergence squared distance (lowlevel function) — divergence_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/estimate.probability.html b/docs/reference/estimate.probability.html
index e31c183..fac2942 100644
--- a/docs/reference/estimate.probability.html
+++ b/docs/reference/estimate.probability.html
@@ -1,5 +1,5 @@
-Estimate Probability Vectors From Count Vectors — estimate.probability • philentropy
@@ -111,14 +111,11 @@ Author
Examples
-
-# generate a count vector
+ # generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
@@ -133,7 +130,7 @@ Examples
diff --git a/docs/reference/euclidean.html b/docs/reference/euclidean.html
index e7bfdb3..10ba169 100644
--- a/docs/reference/euclidean.html
+++ b/docs/reference/euclidean.html
@@ -1,5 +1,5 @@
-Euclidean distance (lowlevel function) — euclidean • philentropy Euclidean distance (lowlevel function) — euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/fidelity.html b/docs/reference/fidelity.html
index 478f65b..1ada4df 100644
--- a/docs/reference/fidelity.html
+++ b/docs/reference/fidelity.html
@@ -1,5 +1,5 @@
-Fidelity distance (lowlevel function) — fidelity • philentropy Fidelity distance (lowlevel function) — fidelity • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/gJSD.html b/docs/reference/gJSD.html
index 8968a16..bb73703 100644
--- a/docs/reference/gJSD.html
+++ b/docs/reference/gJSD.html
@@ -1,5 +1,5 @@
-Generalized Jensen-Shannon Divergence — gJSD • philentropy Generalized Jensen-Shannon Divergence — gJSD • philentropy
@@ -17,7 +17,7 @@
@@ -174,7 +174,7 @@ Examples
diff --git a/docs/reference/getDistMethods.html b/docs/reference/getDistMethods.html
index 22b6112..62fd3a2 100644
--- a/docs/reference/getDistMethods.html
+++ b/docs/reference/getDistMethods.html
@@ -1,5 +1,5 @@
-Get method names for distance — getDistMethods • philentropy Get method names for distance — getDistMethods • philentropy Gower distance (lowlevel function) — gower • philentropy Gower distance (lowlevel function) — gower • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/harmonic_mean_dist.html b/docs/reference/harmonic_mean_dist.html
index 1b56c5b..74d6368 100644
--- a/docs/reference/harmonic_mean_dist.html
+++ b/docs/reference/harmonic_mean_dist.html
@@ -1,5 +1,5 @@
-Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy Harmonic mean distance (lowlevel function) — harmonic_mean_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/hellinger.html b/docs/reference/hellinger.html
index 939f247..1b29a72 100644
--- a/docs/reference/hellinger.html
+++ b/docs/reference/hellinger.html
@@ -1,5 +1,5 @@
-Hellinger distance (lowlevel function) — hellinger • philentropy Hellinger distance (lowlevel function) — hellinger • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 45334af..fc23a81 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • philentropy Function reference • philentropy
@@ -17,7 +17,7 @@
@@ -334,7 +334,7 @@ Other
diff --git a/docs/reference/inner_product.html b/docs/reference/inner_product.html
index 9d62594..47d3480 100644
--- a/docs/reference/inner_product.html
+++ b/docs/reference/inner_product.html
@@ -1,5 +1,5 @@
-Inner product distance (lowlevel function) — inner_product • philentropy Inner product distance (lowlevel function) — inner_product • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/intersection_dist.html b/docs/reference/intersection_dist.html
index 9cdfc44..c890da3 100644
--- a/docs/reference/intersection_dist.html
+++ b/docs/reference/intersection_dist.html
@@ -1,5 +1,5 @@
-Intersection distance (lowlevel function) — intersection_dist • philentropy Intersection distance (lowlevel function) — intersection_dist • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jaccard.html b/docs/reference/jaccard.html
index f38efbd..2dd5aee 100644
--- a/docs/reference/jaccard.html
+++ b/docs/reference/jaccard.html
@@ -1,5 +1,5 @@
-Jaccard distance (lowlevel function) — jaccard • philentropy Jaccard distance (lowlevel function) — jaccard • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/jeffreys.html b/docs/reference/jeffreys.html
index d2667a8..b842063 100644
--- a/docs/reference/jeffreys.html
+++ b/docs/reference/jeffreys.html
@@ -1,5 +1,5 @@
-Jeffreys distance (lowlevel function) — jeffreys • philentropy Jeffreys distance (lowlevel function) — jeffreys • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/jensen_difference.html b/docs/reference/jensen_difference.html
index b6c46c7..851f47e 100644
--- a/docs/reference/jensen_difference.html
+++ b/docs/reference/jensen_difference.html
@@ -1,5 +1,5 @@
-Jensen difference (lowlevel function) — jensen_difference • philentropy Jensen difference (lowlevel function) — jensen_difference • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/jensen_shannon.html b/docs/reference/jensen_shannon.html
index e4afc37..3b31c6c 100644
--- a/docs/reference/jensen_shannon.html
+++ b/docs/reference/jensen_shannon.html
@@ -1,5 +1,5 @@
-Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy Jensen-Shannon distance (lowlevel function) — jensen_shannon • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/k_divergence.html b/docs/reference/k_divergence.html
index 6586850..01b895c 100644
--- a/docs/reference/k_divergence.html
+++ b/docs/reference/k_divergence.html
@@ -1,5 +1,5 @@
-K-Divergence (lowlevel function) — k_divergence • philentropy K-Divergence (lowlevel function) — k_divergence • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/kulczynski_d.html b/docs/reference/kulczynski_d.html
index 4a02a9a..d4de785 100644
--- a/docs/reference/kulczynski_d.html
+++ b/docs/reference/kulczynski_d.html
@@ -1,5 +1,5 @@
-Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy Kulczynski_d distance (lowlevel function) — kulczynski_d • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/kullback_leibler_distance.html b/docs/reference/kullback_leibler_distance.html
index c858e31..269de13 100644
--- a/docs/reference/kullback_leibler_distance.html
+++ b/docs/reference/kullback_leibler_distance.html
@@ -1,5 +1,5 @@
-kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy kullback-Leibler distance (lowlevel function) — kullback_leibler_distance • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/kumar_hassebrook.html b/docs/reference/kumar_hassebrook.html
index 5f4a665..ffd46e1 100644
--- a/docs/reference/kumar_hassebrook.html
+++ b/docs/reference/kumar_hassebrook.html
@@ -1,5 +1,5 @@
-Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy Kumar hassebrook distance (lowlevel function) — kumar_hassebrook • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/kumar_johnson.html b/docs/reference/kumar_johnson.html
index eb7c507..8932862 100644
--- a/docs/reference/kumar_johnson.html
+++ b/docs/reference/kumar_johnson.html
@@ -1,5 +1,5 @@
-Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy Kumar-Johnson distance (lowlevel function) — kumar_johnson • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/lin.cor.html b/docs/reference/lin.cor.html
index 2a89ac2..303061a 100644
--- a/docs/reference/lin.cor.html
+++ b/docs/reference/lin.cor.html
@@ -1,5 +1,5 @@
-Linear Correlation — lin.cor • philentropy Linear Correlation — lin.cor • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy Lorentzian distance (lowlevel function) — lorentzian • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/manhattan.html b/docs/reference/manhattan.html
index f6d96af..e665ee7 100644
--- a/docs/reference/manhattan.html
+++ b/docs/reference/manhattan.html
@@ -1,5 +1,5 @@
-Manhattan distance (lowlevel function) — manhattan • philentropy Manhattan distance (lowlevel function) — manhattan • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/matusita.html b/docs/reference/matusita.html
index ca4085b..aa559e7 100644
--- a/docs/reference/matusita.html
+++ b/docs/reference/matusita.html
@@ -1,5 +1,5 @@
-Matusita distance (lowlevel function) — matusita • philentropy Matusita distance (lowlevel function) — matusita • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/minkowski.html b/docs/reference/minkowski.html
index 8a54d62..6284b61 100644
--- a/docs/reference/minkowski.html
+++ b/docs/reference/minkowski.html
@@ -1,5 +1,5 @@
-Minkowski distance (lowlevel function) — minkowski • philentropy Minkowski distance (lowlevel function) — minkowski • philentropy
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/motyka.html b/docs/reference/motyka.html
index 0828b79..8df784d 100644
--- a/docs/reference/motyka.html
+++ b/docs/reference/motyka.html
@@ -1,5 +1,5 @@
-Motyka distance (lowlevel function) — motyka • philentropy Motyka distance (lowlevel function) — motyka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/neyman_chi_sq.html b/docs/reference/neyman_chi_sq.html
index 688ab07..874906f 100644
--- a/docs/reference/neyman_chi_sq.html
+++ b/docs/reference/neyman_chi_sq.html
@@ -1,5 +1,5 @@
-Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy Neyman chi-squared distance (lowlevel function) — neyman_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/pearson_chi_sq.html b/docs/reference/pearson_chi_sq.html
index f2290e6..c43d4a3 100644
--- a/docs/reference/pearson_chi_sq.html
+++ b/docs/reference/pearson_chi_sq.html
@@ -1,5 +1,5 @@
-Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy Pearson chi-squared distance (lowlevel function) — pearson_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/prob_symm_chi_sq.html b/docs/reference/prob_symm_chi_sq.html
index d637fcd..20ea75e 100644
--- a/docs/reference/prob_symm_chi_sq.html
+++ b/docs/reference/prob_symm_chi_sq.html
@@ -1,5 +1,5 @@
-Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy Probability symmetric chi-squared distance (lowlevel function) — prob_symm_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/ruzicka.html b/docs/reference/ruzicka.html
index f66c101..b2eb4b1 100644
--- a/docs/reference/ruzicka.html
+++ b/docs/reference/ruzicka.html
@@ -1,5 +1,5 @@
-Ruzicka distance (lowlevel function) — ruzicka • philentropy Ruzicka distance (lowlevel function) — ruzicka • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/soergel.html b/docs/reference/soergel.html
index e7407cf..eee7183 100644
--- a/docs/reference/soergel.html
+++ b/docs/reference/soergel.html
@@ -1,5 +1,5 @@
-Soergel distance (lowlevel function) — soergel • philentropy Soergel distance (lowlevel function) — soergel • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/sorensen.html b/docs/reference/sorensen.html
index d7e4710..a42c8c9 100644
--- a/docs/reference/sorensen.html
+++ b/docs/reference/sorensen.html
@@ -1,5 +1,5 @@
-Sorensen distance (lowlevel function) — sorensen • philentropy Sorensen distance (lowlevel function) — sorensen • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chi_sq.html b/docs/reference/squared_chi_sq.html
index 9c4fd48..3c2ae24 100644
--- a/docs/reference/squared_chi_sq.html
+++ b/docs/reference/squared_chi_sq.html
@@ -1,5 +1,5 @@
-Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy Squared chi-squared distance (lowlevel function) — squared_chi_sq • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_chord.html b/docs/reference/squared_chord.html
index fb11253..80a1d81 100644
--- a/docs/reference/squared_chord.html
+++ b/docs/reference/squared_chord.html
@@ -1,5 +1,5 @@
-Squared chord distance (lowlevel function) — squared_chord • philentropy Squared chord distance (lowlevel function) — squared_chord • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/squared_euclidean.html b/docs/reference/squared_euclidean.html
index 9adb873..7db57fe 100644
--- a/docs/reference/squared_euclidean.html
+++ b/docs/reference/squared_euclidean.html
@@ -1,5 +1,5 @@
-Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy Squared euclidean distance (lowlevel function) — squared_euclidean • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/taneja.html b/docs/reference/taneja.html
index 35e74d8..6ba928b 100644
--- a/docs/reference/taneja.html
+++ b/docs/reference/taneja.html
@@ -1,5 +1,5 @@
-Taneja difference (lowlevel function) — taneja • philentropy Taneja difference (lowlevel function) — taneja • philentropy
@@ -17,7 +17,7 @@
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/tanimoto.html b/docs/reference/tanimoto.html
index bdf88f1..cee92f1 100644
--- a/docs/reference/tanimoto.html
+++ b/docs/reference/tanimoto.html
@@ -1,5 +1,5 @@
-Tanimoto distance (lowlevel function) — tanimoto • philentropy Tanimoto distance (lowlevel function) — tanimoto • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/topsoe.html b/docs/reference/topsoe.html
index d9294b6..e359a23 100644
--- a/docs/reference/topsoe.html
+++ b/docs/reference/topsoe.html
@@ -1,5 +1,5 @@
-Topsoe distance (lowlevel function) — topsoe • philentropy Topsoe distance (lowlevel function) — topsoe • philentropy
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/wave_hedges.html b/docs/reference/wave_hedges.html
index e420c96..bc62841 100644
--- a/docs/reference/wave_hedges.html
+++ b/docs/reference/wave_hedges.html
@@ -1,5 +1,5 @@
-Wave hedges distance (lowlevel function) — wave_hedges • philentropy Wave hedges distance (lowlevel function) — wave_hedges • philentropy
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Examples
diff --git a/man/JSD.Rd b/man/JSD.Rd
index 05073b5..60ac6c8 100644
--- a/man/JSD.Rd
+++ b/man/JSD.Rd
@@ -19,10 +19,11 @@ JSD(x, test.na = TRUE, unit = "log2", est.prob = NULL)
}}
}
\value{
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
}
\description{
-This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the \code{link{sqrt}} on the \code{JSD()} output.
}
\details{
Function to compute the Jensen-Shannon Divergence JSD(P || Q) between two
@@ -64,7 +65,7 @@ Q.count <- 20:29
x.count <- rbind(P.count,Q.count)
JSD(x.count, est.prob = "empirical")
-# Example: Distance Matrix using JSD-Distance
+# Example: Divergence Matrix using JSD-Divergence
Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39))
diff --git a/man/estimate.probability.Rd b/man/estimate.probability.Rd
index 98412a6..c2fafba 100644
--- a/man/estimate.probability.Rd
+++ b/man/estimate.probability.Rd
@@ -27,14 +27,11 @@ The following probability estimation methods are implemented in this function:
}
}
\examples{
-
# generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-
}
\author{
Hajk-Georg Drost
Similarity and Distance Quantification between Probability Functions
@@ -104,7 +104,7 @@Si
Installation
-# install philentropy version 0.8.0 from CRAN
+# install philentropy version 0.9.0 from CRAN
install.packages("philentropy")
-# install philentropy version 0.8.0 from CRAN
+# install philentropy version 0.9.0 from CRAN
install.packages("philentropy")
@@ -129,7 +129,7 @@
@@ -67,7 +67,13 @@ TutorialsExamples
-library(philentropy)
+library(philentropy)
# retrieve available distance metrics
philentropy::getDistMethods() [1] "euclidean" "manhattan" "minkowski"
@@ -421,7 +421,7 @@ Developers
diff --git a/docs/news/index.html b/docs/news/index.html
index fe02957..13475f1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • philentropy Changelog • philentropy
@@ -17,7 +17,7 @@
Changelog
Version 0.8.02023-12-02
Updates
Fixing warning on Debian systems:
@@ -112,7 +118,7 @@Updatesstats::dist() when working with 2 dimensional input matrices (2 vector inputs) (see #29) (Many thanks to Jakub Nowosad (@Nowosad)) Example:
-library(philentropy)
+library(philentropy)
m1 = matrix(c(1, 2), ncol = 1)
@@ -240,7 +246,7 @@ Version 0.0.1
diff --git a/docs/paper.html b/docs/paper.html
index 05106b9..7da9177 100644
--- a/docs/paper.html
+++ b/docs/paper.html
@@ -1,5 +1,5 @@
-Summary • philentropy Summary • philentropy
@@ -17,7 +17,7 @@
-library(philentropy)
+library(philentropy)
m1 = matrix(c(1, 2), ncol = 1)
@@ -240,7 +246,7 @@ Version 0.0.1
Information Theory Measures$KL(P || Q) = \sum\limits_{i=1}^n P(p_i) \cdot log_2(\frac{P(p_i) }{P(q_i)}) = H(P, Q) - H(P)$
-Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R)+KL(Q||R))
+ Jensen-Shannon Divergence : JSD(P||Q) = 0.5 * (KL(P||R) + KL(Q||R))
Generalized Jensen-Shannon Divergence : $gJSD_{\pi_1,...,\pi_n}(P_1, ..., P_n) = H(\sum_{i = 1}^n \pi_i \cdot P_i) - \sum_{i = 1}^n \pi_i \cdot H(P_i)$
@@ -233,7 +233,7 @@ References
- Site built with pkgdown 2.0.7.
+ Site built with pkgdown 2.0.9.
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
This function computes a distance matrix or distance value based on the Jensen-Shannon Divergence with equal weights.
+This function computes a divergence matrix or divergence value based on the Jensen-Shannon Divergence with equal weights.
+Please be aware that when aiming to compute the Jensen-Shannon Distance (rather than Divergence), you will need to apply the link{sqrt} on the JSD() output.
Arguments
Value
-a distance value or matrix based on JSD computations.
+a divergence value or matrix based on JSD computations.
Details
@@ -166,7 +168,7 @@Examples
#> jensen-shannon #> 0.03792749 -# Example: Distance Matrix using JSD-Distance +# Example: Divergence Matrix using JSD-Divergence Prob <- rbind(1:10/sum(1:10), 20:29/sum(20:29), 30:39/sum(30:39)) @@ -192,7 +194,7 @@Examples
Examples
-
-# generate a count vector
+ # generate a count vector
x <- runif(100)
-
# generate a probability vector from corresponding counts
# method = "empirical"
x.prob <- estimate.probability(x, method = "empirical")
-