syntax tidy

ms609 · May 28, 2024 · 6674ed4 · 6674ed4
1 parent c783b01
commit 6674ed4
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/R/Concordance.R b/R/Concordance.R
@@ -100,7 +100,7 @@ QuartetConcordance <- function (tree, dataset = NULL) {
 
 #' @importFrom TreeDist Entropy
 .Entropy <- function (...) {
-  Entropy (c(...) / sum(...))
+  Entropy(c(...) / sum(...))
 }
 
 #' @rdname SiteConcordance

diff --git a/R/PlotCharacter.R b/R/PlotCharacter.R
@@ -88,19 +88,19 @@ PlotCharacter <- function (tree, dataset, char = 1L,
   right <- left
   parentOf <- integer(nNode + nTip)
   for (e in seq_len(dim(edge)[1])) {
-    pa <- parent[e]
-    ch <- child[e]
-    parentOf[ch] <- pa
-    if (right[pa]) {
-      left[pa] <- ch
+    pa <- parent[[e]]
+    ch <- child[[e]]
+    parentOf[[ch]] <- pa
+    if (right[[pa]]) {
+      left[[pa]] <- ch
     } else {
-      right[pa] <- ch
+      right[[pa]] <- ch
     }
   }
   preOrderNodes <- unique(rev(parent)) # Root guaranteed first
   postOrderNodes <- rev(preOrderNodes)
-  rootNode <- preOrderNodes[1]
-  parentOf[rootNode] <- rootNode
+  rootNode <- preOrderNodes[[1]]
+  parentOf[[rootNode]] <- rootNode
   tips <- seq_len(nTip)
 
   # Read states