From 84e0eb61d8e2f0a1970a0badc44f2844e6f4a2e6 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Thu, 28 Jul 2022 14:23:35 +0200
Subject: [PATCH 1/2] Translated `computeDiffInCliqCounts()` (#3)

---
 R/computeDiffInCliqCounts.R          | 15 +++++++++++++++
 tests/testthat/test-spatialMixture.R | 15 ++++++++++-----
 2 files changed, 25 insertions(+), 5 deletions(-)
 create mode 100644 R/computeDiffInCliqCounts.R

diff --git a/R/computeDiffInCliqCounts.R b/R/computeDiffInCliqCounts.R
new file mode 100644
index 0000000..cf49d57
--- /dev/null
+++ b/R/computeDiffInCliqCounts.R
@@ -0,0 +1,15 @@
+computeDiffInCliqCounts <- function(cliques, inds) {
+  # Laskee muutoksen CLIQCOUNTS:ssa (tai SEPCOUNTS:ssa, jos syצtteen?
+  # separators) kun yksilצt inds siirretההn. diffInCliqcounts on ncliq*1 taulu,
+  # joka on CLIQCOUNTS:n sarakkeesta josta yksilצt inds siirretההn ja
+  # lisהttהv?sarakkeeseen, johon yksilצt siirretההn.
+  ncliq <- size(cliques, 1)
+  diffInCliqCounts <- zeros(ncliq, 1)
+  ninds <- length(inds)
+  for (i in 1:ninds) {
+    ind <- inds[i]
+    rivit <- rowSums(cliques == ind)
+    diffInCliqCounts <- diffInCliqCounts + rivit
+  }
+  return(diffInCliqCounts)
+}
diff --git a/tests/testthat/test-spatialMixture.R b/tests/testthat/test-spatialMixture.R
index 969c2a0..133ee33 100644
--- a/tests/testthat/test-spatialMixture.R
+++ b/tests/testthat/test-spatialMixture.R
@@ -1,9 +1,14 @@
 context("Spatial mixture")
 
 test_that("functions work with basic input", {
-  x <- c(1, 3, 0, 2)
-  y <- array(c(1, 3, 2, 4, 5, 7, 6, 8), c(2, 2, 2))
-  z <- computeCounts(x, 4, 5, y)
-  expect_equal(z$cliqcounts, t(c(1, 1, 1, 0, 0)))
-  expect_equal(z$sepcounts, t(c(0, 0, 0, 1, 0)))
+  q <- c(1, 3, 0, 2)
+  w <- array(c(1, 3, 2, 4, 5, 7, 6, 8), c(2, 2, 2))
+  e <- computeCounts(q, 4, 5, w)
+  r <- matrix(c(5, 3, 3, 6, 4, 4, 7, 9, 1), 3)
+  expect_equal(e$cliqcounts, t(c(1, 1, 1, 0, 0)))
+  expect_equal(e$sepcounts, t(c(0, 0, 0, 1, 0)))
+  expect_equal(computeDiffInCliqCounts(r, 4), matrix(c(0, 1, 1)))
+  expect_equal(computeDiffInCliqCounts(r, 3), matrix(c(0, 1, 1)))
+  expect_equal(computeDiffInCliqCounts(r, 5), matrix(c(1, 0, 0)))
+  expect_equal(computeDiffInCliqCounts(r, 0), matrix(c(0, 0, 0)))
 })

From 86a5dda6d6d20de681f24c5be0fe2e61d7b0564a Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Thu, 28 Jul 2022 14:43:04 +0200
Subject: [PATCH 2/2] Translated `mysetdiff()` (#3)

---
 R/mysetdiff.R                        | 18 ++++++++++++++++++
 tests/testthat/test-spatialMixture.R |  3 +++
 2 files changed, 21 insertions(+)
 create mode 100644 R/mysetdiff.R

diff --git a/R/mysetdiff.R b/R/mysetdiff.R
new file mode 100644
index 0000000..2e4112f
--- /dev/null
+++ b/R/mysetdiff.R
@@ -0,0 +1,18 @@
+mysetdiff <- function(A, B) {
+ # MYSETDIFF Set difference of two sets of positive integers (much faster than
+ # built - in setdiff)
+ # C <- mysetdiff(A, B)
+ # C <- A \ B = { things in A that are not in B }
+ # MATLAB Original by Kevin Murphy, modified by Leon Peshkin
+  if (is.null(A)) {
+    return(vector())
+  } else if (is.null(B)) {
+    return(A)
+  } else { # both non-empty
+    bits <- zeros(1, base::max(base::max(A), base::max(B)))
+    bits[A] <- 1
+    bits[B] <- 0
+    C <- A[as.logical(bits[A])]
+  }
+    return(C)
+}
diff --git a/tests/testthat/test-spatialMixture.R b/tests/testthat/test-spatialMixture.R
index 133ee33..0b638c6 100644
--- a/tests/testthat/test-spatialMixture.R
+++ b/tests/testthat/test-spatialMixture.R
@@ -5,10 +5,13 @@ test_that("functions work with basic input", {
   w <- array(c(1, 3, 2, 4, 5, 7, 6, 8), c(2, 2, 2))
   e <- computeCounts(q, 4, 5, w)
   r <- matrix(c(5, 3, 3, 6, 4, 4, 7, 9, 1), 3)
+  t <- 1:5
+  y <- c(4, 3, 1, 4, 8)
   expect_equal(e$cliqcounts, t(c(1, 1, 1, 0, 0)))
   expect_equal(e$sepcounts, t(c(0, 0, 0, 1, 0)))
   expect_equal(computeDiffInCliqCounts(r, 4), matrix(c(0, 1, 1)))
   expect_equal(computeDiffInCliqCounts(r, 3), matrix(c(0, 1, 1)))
   expect_equal(computeDiffInCliqCounts(r, 5), matrix(c(1, 0, 0)))
   expect_equal(computeDiffInCliqCounts(r, 0), matrix(c(0, 0, 0)))
+  expect_equal(mysetdiff(t, y), c(2, 5))
 })