a few changes...

[ape.git] / R / dist.topo.R

diff --git a/R/dist.topo.R b/R/dist.topo.R
index d94866adfe1c65f9c46946567573196b6a4e51a9..525178f2528ed1ba66321e178d8c79d2cf0c91ed 100644 (file)
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,4 +1,4 @@
-## dist.topo.R (2011-02-21)
+## dist.topo.R (2011-07-13)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
@@ -71,23 +71,26 @@ dist.topo <- function(x, y, method = "PH85")
     if (any(table(ref) != 1))
         stop("some tip labels are duplicated in tree no. 1")
     n <- length(ref)
-    for (i in 2:length(x)) {
-        label <- x[[i]]$tip.label
-        if (!identical(label, ref)) {
-            if (length(label) != length(ref))
-                stop(paste("tree no.", i, "has a different number of tips"))
-            ilab <- match(label, ref)
-            ## can use tabulate here because 'ilab' contains integers
-            if (any(is.na(ilab)))
-                stop(paste("tree no.", i, "has different tip labels"))
+    Ntree <- length(x)
+    if (Ntree > 1) {
+        for (i in 2:Ntree) {
+            label <- x[[i]]$tip.label
+            if (!identical(label, ref)) {
+                if (length(label) != length(ref))
+                    stop(paste("tree no.", i, "has a different number of tips"))
+                ilab <- match(label, ref)
+                ## can use tabulate here because 'ilab' contains integers
+                if (any(is.na(ilab)))
+                    stop(paste("tree no.", i, "has different tip labels"))
 ### <FIXME> the test below does not seem useful anymore
 ###            if (any(tabulate(ilab) > 1))
 ###                stop(paste("some tip labels are duplicated in tree no.", i))
 ### </FIXME>
-            ie <- match(1:n, x[[i]]$edge[, 2])
-            x[[i]]$edge[ie, 2] <- ilab
+                ie <- match(1:n, x[[i]]$edge[, 2])
+                x[[i]]$edge[ie, 2] <- ilab
+            }
+            x[[i]]$tip.label <- NULL
         }
-        x[[i]]$tip.label <- NULL
     }
     x[[1]]$tip.label <- NULL
     attr(x, "TipLabel") <- ref
@@ -181,7 +184,8 @@ prop.clades <- function(phy, ..., part = NULL)
     n
 }
 
-boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo <- function(phy, x, FUN, B = 100, block = 1,
+                       trees = FALSE, quiet = FALSE)
 {
     if (is.list(x) && !is.data.frame(x)) {
         if (inherits(x, "DNAbin")) x <- as.matrix(x)
@@ -195,6 +199,7 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
         }
     }
     boot.tree <- vector("list", B)
+    if (!quiet) progbar <- utils::txtProgressBar(style = 3) # suggestion by Alastair Potts
     for (i in 1:B) {
         if (block > 1) {
             y <- seq(block, ncol(x), block)
@@ -205,11 +210,14 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
               boot.samp[y - j] <- boot.i - j
         } else boot.samp <- sample(ncol(x), replace = TRUE)
         boot.tree[[i]] <- FUN(x[, boot.samp])
+        if (!quiet) utils::setTxtProgressBar(progbar, i/B)
     }
+    if (!quiet) close(progbar)
     for (i in 1:B) storage.mode(boot.tree[[i]]$Nnode) <- "integer"
     storage.mode(phy$Nnode) <- "integer"
-    ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
-                      B + 1, FALSE, PACKAGE = "ape"), "number") - 1
+    ans <- prop.clades(phy, boot.tree)
+    ##ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
+    ##                  B + 1, FALSE, PACKAGE = "ape"), "number") - 1
     if (trees) {
         class(boot.tree) <- "multiPhylo"
         ans <- list(BP = ans, trees = boot.tree)
@@ -260,6 +268,7 @@ consensus <- function(..., p = 1, check.labels = TRUE)
     ## Get all observed partitions and their frequencies:
     pp <- prop.part(obj, check.labels = FALSE)
     ## Drop the partitions whose frequency is less than 'p':
+    if (p == 0.5) p <- 0.5000001 # avoid incompatible splits
     pp <- pp[attr(pp, "number") >= p * ntree]
     ## Get the order of the remaining partitions by decreasing size:
     ind <- sort(unlist(lapply(pp, length)), decreasing = TRUE,