Translated computeLogml

R/computeLogml.R

@@ -0,0 +1,27 @@
+computeLogml <- function(counts, sumcounts, noalle, data, rowsFromInd) {
+	nloci  <- size(counts, 2)
+	npops  <- size(counts, 3)
+	adjnoalle  <- zeros(max(noalle), nloci)
+	for (j in 1:nloci) {
+		adjnoalle[1:noalle[j], j] <- noalle(j)
+		if ((noalle(j)<max(noalle))) {
+			adjnoalle[noalle[j] + 1:ncol(adjnoalle), j] <- 1
+		}
+	}
+
+	rowsInG <- size(data, 1) + rowsFromInd
+
+	logml <- sum(
+		sum(
+			sum(
+				GAMMA_LN[
+					counts + 1 +
+						repmat(rowsInG * (adjnoalle - 1), c(1, 1, npops))
+				]
+			)
+		)
+	) -
+		npops * sum(sum(GAMMA_LN[1, adjnoalle])) -
+		sum(sum(GAMMA_LN[sumcounts + 1, 1]))
+	return(logml)
+}

R/globals.R

@@ -1 +1,3 @@
-utils::globalVariables(c("PARTITION", "COUNTS", "SUMCOUNTS", "LOGDIFF", "POP_LOGML"))
+utils::globalVariables(
+	c("PARTITION", "COUNTS", "SUMCOUNTS", "LOGDIFF", "POP_LOGML", "GAMMA_LN")
+)