Merge branch 'issue-3' into develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rBAPS
 Title: Bayesian Analysis of Population Structure
-Version: 0.0.0.9008
+Version: 0.0.0.9009
 Date: 2020-11-09
 Authors@R:
     c(
@@ -36,7 +36,7 @@ Description: Partial R implementation of the BAPS software
 License: GPL-3
 BugReports: https://github.com/ocbe-uio/rBAPS/issues
 Encoding: UTF-8
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Suggests:
     testthat (>= 2.1.0)
 Imports:

R/computeCounts.R

@@ -0,0 +1,25 @@
+computeCounts <- function(cliques, separators, npops, PARTITION) {
+  ncliq <- size(cliques, 1)
+  nsep <- size(separators, 1)
+
+  cliqPartition <- zeros(ncliq, size(cliques, 2))
+  sepPartition <- zeros(nsep, size(separators, 2))
+
+  apuCliq <- find(cliques > 0)
+  apuSep <- find(separators > 0)
+
+  cliqPartition[apuCliq] <- PARTITION[cliques[apuCliq]]
+  sepPartition[apuSep] <- PARTITION[separators[apuSep]]
+
+  cliqcounts <- zeros(ncliq, npops)
+  for (i in 1:npops) {
+    cliqcounts[, i] <- rowSums(cliqPartition == i)
+  }
+
+  sepcounts <- zeros(nsep, npops)
+  for (i in 1:npops) {
+    sepcounts[, i] <- rowSums(sepPartition == i)
+  }
+
+  return(list(cliqcounts = cliqcounts, sepcounts = sepcounts))
+}

tests/testthat/test-spatialMixture.R

@@ -0,0 +1,9 @@
+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)))
+})