Initial commit.

Initial testing suite along with some measures implemented.

1 files changed, 88 insertions, 0 deletions

diff --git a/measures.R b/measures.R
new file mode 100644
index 0000000..c3f5021
--- /dev/null
+++ b/measures.R
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+stress <- function(Dx, Dy) {
+  if (any(Dx != t(Dx)) || any(Dy != t(Dy))) {
+    stop("Dx and Dy must be symmetric")
+  }
+
+  Dx <- as.matrix(Dx)
+  Dy <- as.matrix(Dy)
+  if (nrow(Dx) != nrow(Dy)) {
+    stop("Dx and Dy must have the same number of elements")
+  }
+
+  n <- nrow(Dx)
+  s <- vector("numeric", n)
+  for (i in 1:n) {
+    s[i] <- 0
+    for (j in 1:n) {
+      if (i == j) {
+        next
+      }
+
+      s[i] = s[i] + (Dx[i, j] - Dy[i, j])^2 / Dx[i, j]
+    }
+    s[i] = s[i] / sum(D[i, ])
+  }
+
+  s
+}
+
+NP <- function(Dx, Dy, k = 9) {
+  if (any(Dx != t(Dx)) || any(Dy != t(Dy))) {
+    stop("Dx and Dy must be symmetric")
+  }
+
+  Dx <- as.matrix(Dx)
+  Dy <- as.matrix(Dy)
+  if (nrow(Dx) != nrow(Dy)) {
+    stop("Dx and Dy must have the same number of elements")
+  }
+
+  n <- nrow(Dx)
+  if (k >= n) {
+    stop("k must be smaller than the number of elements")
+  }
+
+  preservation <- vector("numeric", n)
+  for (i in 1:n) {
+    nx <- order(Dx[i, ])[1 + 1:k]
+    ny <- order(Dy[i, ])[1 + 1:k]
+    diff <- setdiff(nx, ny)
+    preservation[i] <- (k - length(diff)) / k
+  }
+
+  preservation
+}
+
+d2p <- function(D, sigmas) {
+  if (any(D != t(D))) {
+    stop("D must be symmetric")
+  }
+
+  D <- as.matrix(D)
+  n <- nrow(D)
+  P <- matrix(data=NA, nrow=nrow(D), ncol=ncol(D))
+
+  for (i in 1:n) {
+    denom <- sum(exp(-D[i, ] / sigmas))
+    P[i, ] <- exp(-D[i, ] / sigmas) / denom
+  }
+
+  P
+}
+
+klDivergence <- function(P, Q) {
+  if (nrow(P) != ncol(P) || nrow(Q) != ncol(Q)) {
+    stop("P and Q must be square")
+  }
+  if (nrow(P) != nrow(Q)) {
+    stop("P and Q must have the same number of elements")
+  }
+
+  n <- nrow(P)
+  d <- vector("numeric", n)
+  for (i in 1:n) {
+    d[i] <- sum(P[i, ] * log(P[i, ] / Q[i, ]))
+  }
+
+  d
+}