remove redundant_ifelse

KlausVigo · Nov 28, 2024 · 46cacf7 · 46cacf7
1 parent d10b44a
commit 46cacf7
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Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/R/bab.R b/R/bab.R
@@ -179,8 +179,8 @@ bab <- function(data, tree = NULL, trace = 1, ...) {
   if (nTips < 4) return(stree(nTips, tip.label = names(data)))
 
   data <- removeParsimonyUninfomativeSites(data, recursive=recursive)
-  star_tree <- ifelse(attr(data, "nr") == 0, TRUE, FALSE)
-  add_taxa <- ifelse(is.null(attr(data, "duplicated")), FALSE, TRUE)
+  star_tree <- attr(data, "nr") == 0
+  add_taxa <- !is.null(attr(data, "duplicated"))
   p0 <- attr(data, "p0")
 
   nTips <- length(data)

diff --git a/R/fitch64.R b/R/fitch64.R
@@ -265,8 +265,8 @@ optim.fitch <- function(tree, data, trace = 1, rearrangements = "NNI", ...) {
   #  New
   data <- removeParsimonyUninfomativeSites(data, recursive=TRUE)
 
-  star_tree <- ifelse(attr(data, "nr") == 0, TRUE, FALSE)
-  add_taxa <- ifelse(is.null(attr(data, "duplicated")), FALSE, TRUE)
+  star_tree <- attr(data, "nr") == 0
+  add_taxa <- !is.null(attr(data, "duplicated"))
   nTips <- length(data)
   if (nTips < 4L  || star_tree) {
     nam <- names(data)

diff --git a/R/parsimony.R b/R/parsimony.R
@@ -353,8 +353,8 @@ pratchet <- function(data, start = NULL, method = "fitch", maxit = 1000,
   if(!is.null(attr(data, "informative"))) w[attr(data, "informative")] <- TRUE
   else w[] <- TRUE
 
-  star_tree <- ifelse(attr(data, "nr") == 0, TRUE, FALSE)
-  add_taxa <- ifelse(is.null(attr(data, "duplicated")), FALSE, TRUE)
+  star_tree <- attr(data, "nr") == 0
+  add_taxa <- !(is.null(attr(data, "duplicated")))
   nTips <- length(data)
   # check for trivial trees
   if (nTips < (3L + !ROOTED)  || star_tree) {

diff --git a/R/phylo.R b/R/phylo.R
@@ -2067,9 +2067,9 @@ optim.pml <- function(object, optNni = FALSE, optBf = FALSE, optQ = FALSE,
   aLRT <- FALSE
   rearrangement <- match.arg(rearrangement,
                         c("none", "NNI", "ratchet", "stochastic", "multi2di"))
-  optNni <- ifelse(rearrangement ==  "none", FALSE, TRUE)
-  perturbation <- ifelse(rearrangement %in%
-                        c("ratchet", "stochastic", "multi2di"), TRUE, FALSE)
+  optNni <- !(rearrangement ==  "none")
+  perturbation <- rearrangement %in%
+                        c("ratchet", "stochastic", "multi2di")
   if(rearrangement=="ratchet") fbs <- vector("list", ratchet.par$minit)
   extras <- match.call(expand.dots = FALSE)$...
   pmla <- c("wMix", "llMix")

diff --git a/R/splits.R b/R/splits.R
@@ -369,8 +369,8 @@ postprocess.splits <- function (x)
   x <- SHORTwise(x)
   drop <- duplicated(x)
   if (any(drop)) {
-    W <- ifelse (is.null(tmp$weights), FALSE, TRUE)
-    CONF <- ifelse (is.null(tmp$confidences), FALSE, TRUE)
+    W <- !(is.null(tmp$weights))
+    CONF <- !(is.null(tmp$confidences))
     if(W) w <- tmp$weights
     if (CONF) conf <- tmp$confidences
     class(x) <- NULL