From bd424520a4713a06764a4351bf82f09fb7f3feb6 Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 10:57:22 +0000
Subject: [PATCH 1/6] Declaring capture.output import from utils

---
 R/vec.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/vec.R b/R/vec.R
index f684aa5..0f27cc2 100644
--- a/R/vec.R
+++ b/R/vec.R
@@ -71,7 +71,7 @@ is.coded.vec <- function(x) FALSE
 print.vec <- function(x, detail = FALSE, ...) {
   if (detail) {
     for (i in seq_along(x)) {
-      cat("[[", i, "]] ", capture.output(x[[i]]), "\n", sep = "")
+      cat("[[", i, "]] ", utils::capture.output(x[[i]]), "\n", sep = "")
     }
   } else {
     cat("Vector of type '", type(x),

From 74894d7ce06c885c3b716f6ba1ed78b21e319bf7 Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 10:58:46 +0000
Subject: [PATCH 2/6] Renaming

---
 R/{pc-milne-spectrum.R => milne-pc-spectrum.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename R/{pc-milne-spectrum.R => milne-pc-spectrum.R} (100%)

diff --git a/R/pc-milne-spectrum.R b/R/milne-pc-spectrum.R
similarity index 100%
rename from R/pc-milne-spectrum.R
rename to R/milne-pc-spectrum.R

From bdaa5d94e7af565ca3d12d106e342d59f16a982a Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 11:11:58 +0000
Subject: [PATCH 3/6] Renaming Milne pitch-class spectrum

---
 R/milne-pc-spectrum.R        | 8 ++++----
 man/dot-milne_pc_spectrum.Rd | 4 ++--
 man/is.milne_pc_spectrum.Rd  | 2 +-
 man/milne_pc_spectrum.Rd     | 8 ++++----
 man/new_complex_tone.Rd      | 2 +-
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/milne-pc-spectrum.R b/R/milne-pc-spectrum.R
index e791b2e..3a94ce0 100644
--- a/R/milne-pc-spectrum.R
+++ b/R/milne-pc-spectrum.R
@@ -1,4 +1,4 @@
-#' Constructor function for pitch-class Milne spectrum
+#' Constructor function for Milne pitch-class spectrum
 #'
 #' This function constructs a "milne_pc_spectrum" object.
 #' @param x A numeric vector of pitch-class weights,
@@ -23,11 +23,11 @@
   y
 }
 
-#' Pitch-class Milne spectrum
+#' Milne pitch-class spectrum
 #'
 #' This function represents an input object as a
-#' 'pitch-class Milne spectrum'.
-#' A pitch-class Milne spectrum defines 'perceptual weight'
+#' 'Milne pitch-class spectrum'.
+#' A Milne pitch-class spectrum defines 'perceptual weight'
 #' as a continuous function of 'pitch class'.
 #' @details
 #' This spectrum is typically constructed from musical chords
diff --git a/man/dot-milne_pc_spectrum.Rd b/man/dot-milne_pc_spectrum.Rd
index b7edc45..8433bc2 100644
--- a/man/dot-milne_pc_spectrum.Rd
+++ b/man/dot-milne_pc_spectrum.Rd
@@ -1,8 +1,8 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pc-milne-spectrum.R
+% Please edit documentation in R/milne-pc-spectrum.R
 \name{.milne_pc_spectrum}
 \alias{.milne_pc_spectrum}
-\title{Constructor function for pitch-class Milne spectrum}
+\title{Constructor function for Milne pitch-class spectrum}
 \usage{
 .milne_pc_spectrum(x)
 }
diff --git a/man/is.milne_pc_spectrum.Rd b/man/is.milne_pc_spectrum.Rd
index c3e3083..4163fbc 100644
--- a/man/is.milne_pc_spectrum.Rd
+++ b/man/is.milne_pc_spectrum.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pc-milne-spectrum.R
+% Please edit documentation in R/milne-pc-spectrum.R
 \name{is.milne_pc_spectrum}
 \alias{is.milne_pc_spectrum}
 \title{Check for class "milne_pc_spectrum"}
diff --git a/man/milne_pc_spectrum.Rd b/man/milne_pc_spectrum.Rd
index 1158cf3..c670548 100644
--- a/man/milne_pc_spectrum.Rd
+++ b/man/milne_pc_spectrum.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pc-milne-spectrum.R
+% Please edit documentation in R/milne-pc-spectrum.R
 \name{milne_pc_spectrum}
 \alias{milne_pc_spectrum}
 \alias{milne_pc_spectrum.pc_set}
 \alias{milne_pc_spectrum.default}
-\title{Pitch-class Milne spectrum}
+\title{Milne pitch-class spectrum}
 \usage{
 milne_pc_spectrum(x, ...)
 
@@ -49,8 +49,8 @@ An object of class \code{milne_pc_spectrum}.
 }
 \description{
 This function represents an input object as a
-'pitch-class Milne spectrum'.
-A pitch-class Milne spectrum defines 'perceptual weight'
+'Milne pitch-class spectrum'.
+A Milne pitch-class spectrum defines 'perceptual weight'
 as a continuous function of 'pitch class'.
 }
 \details{
diff --git a/man/new_complex_tone.Rd b/man/new_complex_tone.Rd
index 131fcaf..0159926 100644
--- a/man/new_complex_tone.Rd
+++ b/man/new_complex_tone.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pc-milne-spectrum.R
+% Please edit documentation in R/milne-pc-spectrum.R
 \name{new_complex_tone}
 \alias{new_complex_tone}
 \title{Make complex tone}

From c824f32bd3e29db4e720e039c30c736e6cde818c Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 11:30:49 +0000
Subject: [PATCH 4/6] Adding milne_pc_spec_dist

---
 NAMESPACE                                 |  2 +
 R/cosine-similarity.R                     | 14 ++++
 R/milne-pc-spec-dist.R                    | 24 ++++++
 man/cosine_similarity.Rd                  | 19 +++++
 man/milne_pc_spec_dist.Rd                 | 27 +++++++
 tests/testthat/test-milne_pc_spec_dist.R  | 95 +++++++++++++++++++++++
 tests/testthat/test-r-cosine-similarity.R | 25 ++++++
 7 files changed, 206 insertions(+)
 create mode 100644 R/cosine-similarity.R
 create mode 100644 R/milne-pc-spec-dist.R
 create mode 100644 man/cosine_similarity.Rd
 create mode 100644 man/milne_pc_spec_dist.Rd
 create mode 100644 tests/testthat/test-milne_pc_spec_dist.R
 create mode 100644 tests/testthat/test-r-cosine-similarity.R

diff --git a/NAMESPACE b/NAMESPACE
index 2a010bd..484f97c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -203,6 +203,7 @@ export(amplitude_to_dB)
 export(ascending_pc_dist)
 export(coded_vec)
 export(corpus)
+export(cosine_similarity)
 export(dB_to_amplitude)
 export(decode)
 export(encode)
@@ -232,6 +233,7 @@ export(lower)
 export(map_pc_chord_id_to_pc_set_id)
 export(metadata)
 export(midi_to_freq)
+export(milne_pc_spec_dist)
 export(milne_pc_spectrum)
 export(num_elements)
 export(num_sequences)
diff --git a/R/cosine-similarity.R b/R/cosine-similarity.R
new file mode 100644
index 0000000..656dffa
--- /dev/null
+++ b/R/cosine-similarity.R
@@ -0,0 +1,14 @@
+#' Cosine similarity
+#'
+#' Computes the cosine similarity between two numeric vectors.
+#' @param x Numeric vector 1.
+#' @param y Numeric vector 2.
+#' @return Cosine similarity, as a numeric scalar.
+#' @export
+cosine_similarity <- function(x, y) {
+  numerator <- sum(x * y)
+  denominator <-
+    sqrt(sum(x ^ 2)) *
+    sqrt(sum(y ^ 2))
+  numerator / denominator
+}
diff --git a/R/milne-pc-spec-dist.R b/R/milne-pc-spec-dist.R
new file mode 100644
index 0000000..80d1dea
--- /dev/null
+++ b/R/milne-pc-spec-dist.R
@@ -0,0 +1,24 @@
+#' Milne's pitch-class spectral distance
+#'
+#' Computes Milne's pitch-class spectral distance measure between two sonorities.
+#'
+#' @param x First sonority, passed to \code{\link{milne_pc_spectrum}}.
+#' @param y Second sonority, passed to \code{\link{milne_pc_spectrum}}.
+#' @param ... Further arguments passed to \code{\link{milne_pc_spectrum}}.
+#'
+#' @return
+#' A numeric scalar where greater values indicate greater distance.
+#' 0 is the minimum possible distance.
+#' 1 corresponds to two uncorrelated spectra;
+#' values greater than 1 are possible if the spectra are inversely correlated.
+#'
+#' @details
+#' See \insertCite{Milne2016;textual}{hrep} for details.
+#'
+#' @export
+milne_pc_spec_dist <- function(x, y, ...) {
+  1 - cosine_similarity(
+    milne_pc_spectrum(x, ...),
+    milne_pc_spectrum(y, ...)
+  )
+}
diff --git a/man/cosine_similarity.Rd b/man/cosine_similarity.Rd
new file mode 100644
index 0000000..277818f
--- /dev/null
+++ b/man/cosine_similarity.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cosine-similarity.R
+\name{cosine_similarity}
+\alias{cosine_similarity}
+\title{Cosine similarity}
+\usage{
+cosine_similarity(x, y)
+}
+\arguments{
+\item{x}{Numeric vector 1.}
+
+\item{y}{Numeric vector 2.}
+}
+\value{
+Cosine similarity, as a numeric scalar.
+}
+\description{
+Computes the cosine similarity between two numeric vectors.
+}
diff --git a/man/milne_pc_spec_dist.Rd b/man/milne_pc_spec_dist.Rd
new file mode 100644
index 0000000..60105ed
--- /dev/null
+++ b/man/milne_pc_spec_dist.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/milne-pc-spec-dist.R
+\name{milne_pc_spec_dist}
+\alias{milne_pc_spec_dist}
+\title{Milne's pitch-class spectral distance}
+\usage{
+milne_pc_spec_dist(x, y, ...)
+}
+\arguments{
+\item{x}{First sonority, passed to \code{\link{milne_pc_spectrum}}.}
+
+\item{y}{Second sonority, passed to \code{\link{milne_pc_spectrum}}.}
+
+\item{...}{Further arguments passed to \code{\link{milne_pc_spectrum}}.}
+}
+\value{
+A numeric scalar where greater values indicate greater distance.
+0 is the minimum possible distance.
+1 corresponds to two uncorrelated spectra;
+values greater than 1 are possible if the spectra are inversely correlated.
+}
+\description{
+Computes Milne's pitch-class spectral distance measure between two sonorities.
+}
+\details{
+See \insertCite{Milne2016;textual}{hrep} for details.
+}
diff --git a/tests/testthat/test-milne_pc_spec_dist.R b/tests/testthat/test-milne_pc_spec_dist.R
new file mode 100644
index 0000000..076f516
--- /dev/null
+++ b/tests/testthat/test-milne_pc_spec_dist.R
@@ -0,0 +1,95 @@
+context("test-milne_pc_spec_dist")
+
+test_that("examples", {
+  approx_equal <- function(x, y, digits = 4) {
+    all.equal(
+      round(x, digits = digits),
+      round(y, digits = digits)
+    )
+  }
+
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(0, 4, 7)
+      ),
+      0
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(0, 3, 7)
+      ),
+      0.2597
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(0, 2, 7)
+      ),
+      0.2201
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(1, 5, 8)
+      ),
+      0.8527
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(2, 7, 11)
+      ),
+      0.4155
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(0, 4, 7),
+        c(0, 5, 9)
+      ),
+      0.4155
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(2, 7, 8),
+        c(3, 4, 8, 9)
+      ),
+      0.5619
+    )
+  )
+  expect_true(
+    approx_equal(
+      milne_pc_spec_dist(
+        c(2, 6, 8, 9),
+        c(1, 4)
+      ),
+      0.5940
+    )
+  )
+})
+
+test_that("coercion", {
+  expect_equal(
+    milne_pc_spec_dist(c(0, 4, 7), c(0, 3, 7)),
+    milne_pc_spec_dist(c(60, 64, 67), c(60, 63, 67))
+  )
+
+  expect_equal(
+    milne_pc_spec_dist(c(0, 4, 7), c(0, 3, 7)),
+    milne_pc_spec_dist(pi_chord(c(60, 64, 67)), pi_chord(c(60, 63, 67)))
+  )
+})
diff --git a/tests/testthat/test-r-cosine-similarity.R b/tests/testthat/test-r-cosine-similarity.R
new file mode 100644
index 0000000..b43c5fd
--- /dev/null
+++ b/tests/testthat/test-r-cosine-similarity.R
@@ -0,0 +1,25 @@
+context("test-r-cosine-similarity")
+
+test_that("examples", {
+  expect_equal(cosine_similarity(rep(1, times = 10),
+                                 rep(2, times = 10)),
+               1)
+  expect_equal(cosine_similarity(rep(1, times = 10),
+                                 rep(-2, times = 10)),
+               -1)
+  expect_equal(
+    cosine_similarity(
+      c(0, 3, 0, 0, 2, 0, 0, 2, 0, 5),
+      c(1, 2, 0, 0, 1, 1, 0, 1, 0, 3)
+    ),
+    0.94,
+    tolerance = 1e-2
+  )
+  expect_equal(
+    cosine_similarity(
+      c(0, 3, 0, 0, 2, 0, 0, 2, 0, 5),
+      c(1, 2, 0, 0, 1, 1, 0, 1, 0, 3)
+    ),
+    0.9356015
+  )
+})

From 5c7d7a3a74189bc5a721baee70ce8bb9268a12ff Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 11:35:46 +0000
Subject: [PATCH 5/6] Added NEWS.md

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 NEWS.md

diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000..9501360
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,2 @@
+- Added a `NEWS.md` file to track changes to the package.
+- Added `milne_pc_spec_dist` for computing spectral distances between sonorities.

From a5453dee33a35f80d74afd2766de916f5a91c95c Mon Sep 17 00:00:00 2001
From: Peter M C Harrison <pmc.harrison@gmail.com>
Date: Tue, 26 Feb 2019 11:36:00 +0000
Subject: [PATCH 6/6] Increment version number

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2c0ce46..b7663fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hrep
 Title: Harmony Representations
-Version: 0.5.1
+Version: 0.6.0
 Authors@R: person("Peter", "Harrison", email = "pmc.harrison@gmail.com", role = c("aut", "cre"))
 Description: This package provides methods for representing and manipulating chord sequences.
 Depends: R (>= 3.4.0)
diff --git a/NEWS.md b/NEWS.md
index 9501360..27d1058 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,2 +1,4 @@
+# hrep 0.6.0
+
 - Added a `NEWS.md` file to track changes to the package.
 - Added `milne_pc_spec_dist` for computing spectral distances between sonorities.