bug fix

KlausVigo · Sep 11, 2024 · 80baa4e · 80baa4e
1 parent f191bb4
commit 80baa4e
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/parsimony.R b/R/parsimony.R
@@ -362,7 +362,7 @@ pratchet <- function(data, start = NULL, method = "fitch", maxit = 1000,
     else tree <- stree(nTips, tip.label = nam)
     if(add_taxa) tree <- addTaxa(tree, attr(data, "duplicated"))
     if(!ROOTED) tree <- unroot(tree)
-    tree <- relabel(result, ref)
+    tree <- relabel(tree, ref)
     return(tree)
   }
 

diff --git a/R/superTree.R b/R/superTree.R
@@ -180,6 +180,7 @@ superTree <- function(tree, method = "MRP", rooted = FALSE, trace = 0,
     tree <- tree_tmp
   }
 
+# start <- allCompat(tree) ??
 
   if (method != "MRP") rooted <- FALSE
   if (!rooted) tree <- unroot(tree)
@@ -192,7 +193,7 @@ superTree <- function(tree, method = "MRP", rooted = FALSE, trace = 0,
     }
     res <- my.supertree(tree, trace = trace, ...)
     if (rooted) {
-#      if (inherits(res, "multiPhylo")) { # root
+#      if (inherits(res, "multiPhylo")) {
 #        res <- lapply(res, root, "ZZZ")
 #        res <- lapply(res, drop.tip, "ZZZ")
 #        class(res) <- "multiPhylo"