From 0de70264301fbc984a72f4ca4244fa4333d1c6df Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Fri, 15 Jan 2021 09:36:50 +0100
Subject: [PATCH] Fixed handling of global

---
 R/computePersonalAllFreqs.R |  9 ++++++---
 R/laskeMuutokset12345.R     |  6 +++++-
 R/suoritaMuutos.R           | 18 +++++++++++-------
 R/zeros_ones.R              |  4 ++--
 4 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/R/computePersonalAllFreqs.R b/R/computePersonalAllFreqs.R
index 7ccd4e9..4a301cd 100644
--- a/R/computePersonalAllFreqs.R
+++ b/R/computePersonalAllFreqs.R
@@ -10,11 +10,14 @@
 #' @export
 
 computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) {
-    nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2])
-    npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+    if (is.null(dim(COUNTS))) {
+        nloci <- npops <- 1
+    } else {
+        nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2])
+        npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+    }
 
     rows <- as.matrix(t(data))[computeRows(rowsFromInd, ind, 1), , drop = FALSE]
-
     omaFreqs <- zeros(npops, rowsFromInd * nloci)
     pointer <- 1
     for (loc in 1:dim(rows)[2]) {
diff --git a/R/laskeMuutokset12345.R b/R/laskeMuutokset12345.R
index 4d14e0f..d9ae738 100644
--- a/R/laskeMuutokset12345.R
+++ b/R/laskeMuutokset12345.R
@@ -9,7 +9,11 @@
 #' @param logml log maximum likelihood
 #' @export
 laskeMuutokset4 <- function (osuus, osuusTaulu, omaFreqs, logml) {
-	npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+	if (is.null(dim(COUNTS))) {
+		npops <- 1
+	} else {
+		npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+	}
 	notEmpty <- which(osuusTaulu > 0.005)
 	muutokset <- zeros(npops)
 	empties <- !notEmpty
diff --git a/R/suoritaMuutos.R b/R/suoritaMuutos.R
index bb39850..9f94434 100644
--- a/R/suoritaMuutos.R
+++ b/R/suoritaMuutos.R
@@ -5,14 +5,18 @@
 #' @param indeksi index
 #' @export
 suoritaMuutos <- function (osuusTaulu, osuus, indeksi) {
-    npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+	if (is.null(dim(COUNTS))) {
+		npops <- 1
+	} else {
+		npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
+	}
 
-    i1 <- indeksi %% npops
-    if (is.na(i1) | i1 == 0) i1 <- npops
-    i2 <- ceiling(indeksi / npops)
+	i1 <- indeksi %% npops
+	if (is.na(i1) | i1 == 0) i1 <- npops
+	i2 <- ceiling(indeksi / npops)
 
-    osuusTaulu[i1] <- osuusTaulu[i1] - osuus
-    osuusTaulu[i2] <- osuusTaulu[i2] + osuus
+	osuusTaulu[i1] <- osuusTaulu[i1] - osuus
+	osuusTaulu[i2] <- osuusTaulu[i2] + osuus
 
-    return (osuusTaulu)
+	return (osuusTaulu)
 }
\ No newline at end of file
diff --git a/R/zeros_ones.R b/R/zeros_ones.R
index c4487bf..954754c 100644
--- a/R/zeros_ones.R
+++ b/R/zeros_ones.R
@@ -20,7 +20,7 @@ zeros_or_ones <- function(n, x) {
 }
 
 #' @title Matrix of zeros
-#' @description wrapper of `zeros_or_ones()` that replicates the behavior of 
+#' @description wrapper of `zeros_or_ones()` that replicates the behavior of
 #' the `zeros()` function on Matlab
 #' @param n1 number of rows
 #' @param n2 number of columns
@@ -35,7 +35,7 @@ zeros <- function(n1, n2 = n1, ...) {
 }
 
 #' @title Matrix of ones
-#' @description wrapper of `zeros_or_ones()` that replicates the behavior of 
+#' @description wrapper of `zeros_or_ones()` that replicates the behavior of
 #' the `ones()` function on Matlab
 #' @param n1 number of rows
 #' @param n2 number of columns