From d10b44aa861c84677700c02533ac4ec68954c054 Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Thu, 28 Nov 2024 09:55:51 +0100
Subject: [PATCH] fix redundant ifelse (flint)

---
 R/distSeq.R           | 2 +-
 R/plotBS.R            | 4 ++--
 R/read.nexus.splits.R | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/distSeq.R b/R/distSeq.R
index de1c0cdf..79145a3a 100644
--- a/R/distSeq.R
+++ b/R/distSeq.R
@@ -379,7 +379,7 @@ read.nexus.dist <- function(file){
     semico <- grep(";", X)
     X <- gsub("\\[(.*?)\\]", "", X) # get rid of comments
     i1 <- grep("TAXLABELS", X, ignore.case = TRUE)
-    taxlab <- ifelse(length(i1) > 0, TRUE, FALSE)
+    taxlab <- length(i1) > 0
     if (taxlab) {
       end <- semico[semico >= i1][1]
       x <- X[(i1):end] # assumes not a 'new line' after "TRANSLATE"
diff --git a/R/plotBS.R b/R/plotBS.R
index 1d2ce7d7..5e5534fb 100644
--- a/R/plotBS.R
+++ b/R/plotBS.R
@@ -1,8 +1,8 @@
 support <- function(tree, trees, method="FBP", tol=2e-8, scale=TRUE){
   trees <- keep.tip(trees, tree$tip.label)
   method <- match.arg(method, c("FBP", "TBE", "MCC"), several.ok=TRUE)
-  multi <- ifelse(length(method)>1, TRUE, FALSE)
-  tip2root <- ifelse(method=="MCC", TRUE, FALSE)
+  multi <- length(method)>1
+  tip2root <- method=="MCC"
   if(all(sapply(trees, \(x)!is.null(x$edge.length)))){
     trees <- di2multi(trees, tol=tol) # , tip2root=tip2root)
   }
diff --git a/R/read.nexus.splits.R b/R/read.nexus.splits.R
index e0abc759..c90eb460 100644
--- a/R/read.nexus.splits.R
+++ b/R/read.nexus.splits.R
@@ -51,7 +51,7 @@ read.nexus.splits <- function(file) {
   sp <- grep("SPLITS;", X, ignore.case = TRUE)
   i1 <- i1[i1 < sp]
   if(length(i1)>1)i1 <- i1[length(i1)]
-  taxlab <- ifelse(length(i1) > 0, TRUE, FALSE)
+  taxlab <- length(i1) > 0
   if (taxlab) {
     end <- semico[semico >= i1][1]
     x <- X[(i1):end] # assumes not a 'new line' after "TRANSLATE"