Added poistaLiianPienet

R/poistaLiianPienet.R

@@ -0,0 +1,49 @@
+#' @title Remove too small
+#' @description Muokkaa tulokset muotoon, jossa outlier yksilöt on poistettu.
+#' Tarkalleen ottaen poistaa ne populaatiot, joissa on vähemmän kuin
+#' 'alaraja':n verran yksilöit?
+#' @param npops npops
+#' @param rowsFromInd rowsFromInd
+#' @param alaraja alaraja
+#' @export
+poistaLiianPienet <- function (npops, rowsFromInd, alaraja,
+    PARTITION = matrix(NA, 0, 0), COUNTS = matrix(NA, 0, 0),
+    SUMCOUNTS = NA) {
+
+    popSize <- zeros(1,npops)
+    if (npops > 0) {
+        for (i in 1:npops) {
+            popSize[i] <- length(which(PARTITION == i))
+        }
+    }
+    miniPops <- which(popSize < alaraja)
+
+    if (length(miniPops) == 0) {
+        return(npops)
+    }
+
+    outliers <- matrix(NA, 0, 0)
+    for (pop in miniPops) {
+        inds <- which(PARTITION == pop)
+        cat('Removed individuals: ')
+        cat(as.character(inds))
+        outliers = matrix(c(outliers, inds), ncol=1)
+    }
+
+    ninds <- length(PARTITION)
+    PARTITION[outliers] <- 0
+    korit <- unique(PARTITION(which(PARTITION > 0)))
+    for (n in 1:length(korit)) {
+        kori <- korit[n]
+        yksilot <- which(PARTITION == kori)
+        PARTITION[yksilot] == n
+    }
+
+    # TODO: add COUNTS, SUMCOUNTS and PARTITION to return or use <<-
+    COUNTS[, , miniPops] <- NA
+    SUMCOUNTS[miniPops, ] <- NA
+
+    npops <- npops - length(miniPops)
+
+    return(npops)
+}