small improvements

KlausVigo · Dec 29, 2024 · a91c088 · a91c088
1 parent a2f33ed
commit a91c088
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/R/plotBS.R b/R/plotBS.R
@@ -11,7 +11,7 @@ support <- function(tree, trees, method="FBP", tol=2e-8, scale=TRUE){
   if("MCC" %in% method){
     trees <- .uncompressTipLabel(trees) # check if needed
     if(any(!is.rooted(trees)))
-      stop("All trees need to be rooted for method 'MCC'!")
+      stop("All trees need to be rooted!")
     x <- prop.clades(tree, trees)
     x <- (x / length(trees))
     if(!scale) x <- x * 100

diff --git a/R/treeRearrangement.R b/R/treeRearrangement.R
@@ -59,6 +59,7 @@ nnin <- function(tree, n) {
 #' @rdname nni
 #' @export nni
 nni <- function(tree) {
+  stopifnot(Ntip(tree) > 3-is.rooted(tree))
   tip.label <- tree$tip.label
   attr(tree, "order") <- NULL
   k <- min(tree$edge[, 1]) - 1
@@ -211,8 +212,7 @@ kSPR <- function(tree, k = NULL) {
 
 
 oneOf4 <- function(tree, ind1, ind2, from = 1, to = 1, root) {
-  if (!is.binary(tree))
-    stop("trees must be binary")
+  if (!is.binary(tree))  stop("tree must be binary")
   tree <- reroot(tree, ind2, FALSE)
   kids1 <- Children(tree, ind1)
   anc <- Ancestors(tree, ind1, "all")