[Phylobase-commits] r846 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: francois
Date: 2014-02-12 19:45:24 +0100 (Wed, 12 Feb 2014)
New Revision: 846

Modified:
   pkg/R/readNCL.R
   pkg/man/readNCL.Rd
Log:
adding option convert.edge.length to readNCL to convert negative branch lengths to 0 so that objects can be imported into phylobase

Modified: pkg/R/readNCL.R
===================================================================
--- pkg/R/readNCL.R	2014-02-12 18:34:20 UTC (rev 845)
+++ pkg/R/readNCL.R	2014-02-12 18:45:24 UTC (rev 846)
@@ -8,11 +8,12 @@
                     levels.uniform=FALSE, quiet=TRUE,
                     check.node.labels=c("keep", "drop", "asdata"),
                     return.labels=TRUE, file.format=c("nexus", "newick"),
-                    check.names=TRUE, ...) {
+                    check.names=TRUE, convert.edge.length=FALSE, ...) {
 
   ## turn on to TRUE to test new way of building trees in NCL
  experimental <- FALSE
 
+ file <- path.expand(file)
  type <- match.arg(type)
  check.node.labels <- match.arg(check.node.labels)
  file.format <- match.arg(file.format)
@@ -144,6 +145,9 @@
          tr$tip.label <- ncl$taxaNames[as.numeric(tr$tip.label)]     
        }
        else stop("phylobase doesn't deal with multiple taxa block at this time.")
+       if (convert.edge.length) {
+         tr$edge.length[tr$edge.length < 0] <- 0
+       }
        if (is.null(tr$node.label)) {
          if (check.node.labels == "asdata") {
            warning("Could not use value \"asdata\" for ",
@@ -169,6 +173,9 @@
      edgeMat <- cbind(ncl$parentVector, c(1:length(ncl$parentVector)))
      edgeLgth <- ncl$branchLengthVector
      edgeLgth[edgeLgth == -1] <- NA
+     if (convert.edge.length) {
+       edgeLgth[edgeLgth < 0] <- 0
+     }
      if (length(ncl$taxaNames) != min(ncl$parentVector)-1) {
        stop("phylobase doesn't deal with multiple taxa block at this time.")
      }
@@ -224,18 +231,21 @@
                        char.all=FALSE, polymorphic.convert=TRUE,
                        levels.uniform=FALSE, quiet=TRUE,
                        check.node.labels=c("keep", "drop", "asdata"),
-                       return.labels=TRUE, check.names=TRUE, ...) {
+                       return.labels=TRUE, check.names=TRUE, convert.edge.length=FALSE,
+                       ...) {
 
   return(readNCL(file=file, simplify=simplify, type=type, char.all=char.all,
           polymorphic.convert=polymorphic.convert, levels.uniform=levels.uniform,
           quiet=quiet, check.node.labels=check.node.labels,
           return.labels=return.labels, file.format="nexus",
-          check.names=check.names, ...))
+          check.names=check.names, convert.edge.length=convert.edge.length, ...))
 }
 
 readNewick <- function(file, simplify=FALSE, quiet=TRUE,
-                       check.node.labels=c("keep", "drop", "asdata"), ...) {
+                       check.node.labels=c("keep", "drop", "asdata"),
+                       convert.edge.length=FALSE, ...) {
 
   return(readNCL(file=file, simplify=simplify, quiet=quiet,
-                 check.node.labels=check.node.labels, file.format="newick", ...))
+                 check.node.labels=check.node.labels, file.format="newick",
+                 convert.edge.length=convert.edge.length, ...))
 }

Modified: pkg/man/readNCL.Rd
===================================================================
--- pkg/man/readNCL.Rd	2014-02-12 18:34:20 UTC (rev 845)
+++ pkg/man/readNCL.Rd	2014-02-12 18:45:24 UTC (rev 846)
@@ -19,10 +19,12 @@
 readNexus(file, simplify=FALSE, type=c("all", "tree", "data"),
           char.all=FALSE, polymorphic.convert=TRUE, levels.uniform=FALSE,
           quiet=TRUE, check.node.labels=c("keep", "drop", "asdata"),
-          return.labels=TRUE, check.names=TRUE, ...)
+          return.labels=TRUE, check.names=TRUE, convert.edge.length=FALSE,
+          ...)
 
 readNewick(file, simplify=FALSE, quiet=TRUE,
-           check.node.labels=c("keep", "drop", "asdata"), ...)
+           check.node.labels=c("keep", "drop", "asdata"),
+           convert.edge.length=FALSE, ...)
 
 }
 
@@ -63,6 +65,12 @@
           are syntactically valid variable names and are not duplicated.
           If necessary they are adjusted (by \sQuote{make.names}) so
           that they are.}
+
+  \item{convert.edge.length}{logical. If \sQuote{TRUE} negative edge
+    lengths are replaced with 0. At this time \code{phylobase} does not
+    accept objects with negative branch lengths, this workaround allows
+    to still use trees with negative branch lengths are an artifact of
+    the method used to build the tree.}
   
   \item{\dots}{Additional arguments to be passed to phylo4 or phylo4d
     constructor (see Details)}