Improve write.tree. digits < 0 prints no branch lengths. Add digits a…

…rgument to write.nexus.

R/write.nexus.R

@@ -7,7 +7,7 @@
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-write.nexus <- function(..., file = "", translate = TRUE)
+write.nexus <- function(..., file = "", translate = TRUE, digits=10)
 {
     obj <- .getTreesFromDotdotdot(...)
     ntree <- length(obj)
@@ -59,7 +59,7 @@ write.nexus <- function(..., file = "", translate = TRUE)
         if (!inherits(obj[[i]], "phylo")) next
         root.tag <- if (is.rooted(obj[[i]])) "= [&R] " else "= [&U] "
         cat("\tTREE *", title[i], root.tag, file = file, append = TRUE)
-        cat(write.tree(obj[[i]], file = ""),
+        cat(write.tree(obj[[i]], file = "", digits=digits),
             "\n", sep = "", file = file, append = TRUE)
     }
     cat("END;\n", file = file, append = TRUE)

R/write.tree.R

@@ -66,7 +66,7 @@ write.tree <-
 
 .write.tree2 <- function(phy, digits = 10, tree.prefix = "", check_tips)
 {
-    brl <- !is.null(phy$edge.length)
+    brl <- (!is.null(phy$edge.length) && digits >= 0)
     nodelab <- !is.null(phy$node.label)
     if (check_tips) phy$tip.label <- checkLabel(phy$tip.label)
     if (nodelab) {

man/write.nexus.Rd

@@ -2,7 +2,7 @@
 \alias{write.nexus}
 \title{Write Tree File in Nexus Format}
 \usage{
-write.nexus(..., file = "", translate = TRUE)
+write.nexus(..., file = "", translate = TRUE, digits=10)
 }
 \arguments{
   \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
@@ -14,6 +14,8 @@ write.nexus(..., file = "", translate = TRUE)
   \item{translate}{a logical, if \code{TRUE} (the default) a translation
     of the tip labels is done which are replaced in the parenthetic
     representation with tokens.}
+  \item{digits}{a numeric giving the number of digits used for printing
+    branch lengths. For negative numbers no branch lengths are printed.}
 }
 \description{
   This function writes trees in a file with the NEXUS format.

man/write.tree.Rd

@@ -14,7 +14,7 @@ write.tree(phy, file = "", append = FALSE,
     without erasing the data possibly existing in the file, otherwise
     the file (if it exists) is overwritten (\code{FALSE} the default).}
   \item{digits}{a numeric giving the number of digits used for printing
-    branch lengths.}
+    branch lengths. For negative numbers no branch lengths are printed.}
   \item{tree.names}{either a logical or a vector of mode character. If
     \code{TRUE} then any tree names will be written prior to the tree on
     each line. If character, specifies the name of \code{"phylo"}
@@ -54,7 +54,7 @@ write.tree(phy, file = "", append = FALSE,
 
 \author{Emmanuel Paradis, Daniel Lawson
   \email{dan.lawson@bristol.ac.uk}, and Klaus Schliep
-  \email{kschliep@snv.jussieu.fr}}
+  \email{klaus.schliep@gmail.com}}
 \seealso{
   \code{\link{read.tree}}, \code{\link{read.nexus}},
   \code{\link{write.nexus}}, \code{\link{write.phyloXML}}