From 22cea5b2238584621c0e9ce22051dc060eda7106 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Thu, 19 Nov 2020 10:46:37 +0100
Subject: [PATCH] Translated computeLogml

---
 R/computeLogml.R | 27 +++++++++++++++++++++++++++
 R/globals.R      |  4 +++-
 2 files changed, 30 insertions(+), 1 deletion(-)
 create mode 100644 R/computeLogml.R

diff --git a/R/computeLogml.R b/R/computeLogml.R
new file mode 100644
index 0000000..795925c
--- /dev/null
+++ b/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)
+}
diff --git a/R/globals.R b/R/globals.R
index 143c664..b994258 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -1 +1,3 @@
-utils::globalVariables(c("PARTITION", "COUNTS", "SUMCOUNTS", "LOGDIFF", "POP_LOGML"))
\ No newline at end of file
+utils::globalVariables(
+	c("PARTITION", "COUNTS", "SUMCOUNTS", "LOGDIFF", "POP_LOGML", "GAMMA_LN")
+)
\ No newline at end of file