[Adephylo-commits] r30 - in pkg: R man

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

Author: jombart
Date: 2008-11-25 18:55:45 +0100 (Tue, 25 Nov 2008)
New Revision: 30

Modified:
   pkg/R/distances.R
   pkg/R/utils.R
   pkg/man/distTips.Rd
Log:
Fixes for distTips.


Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R	2008-11-25 17:16:37 UTC (rev 29)
+++ pkg/R/distances.R	2008-11-25 17:55:45 UTC (rev 30)
@@ -9,9 +9,10 @@
     ## handle arguments
     x <- as(x, "phylo4")
     method <- match.arg(method)
+    N <- nTips(x)
+    if(tips[1]=="all") { tips <- 1:N }
     tips <- getnodes(x, tips)
-    N <- nTips(x)
-    if(tips=="all") { tips <- 1:N }
+    tips.names <- names(tips)
 
     ## some checks
     if (is.character(checkval <- check_phylo4(x))) stop(checkval)
@@ -54,12 +55,10 @@
         edge.idx <- lapply(allPath, function(e) getedges(x, e) ) # list of indices of edges
         allEdgeLength <- edgeLength(x)
         res <- lapply(edge.idx, function(idx) sum(allEdgeLength[idx], na.rm=TRUE) )
-        return(res)
     } # end brlength
 
     if(method=="nNodes"){
         res <- lapply(allPath, length)
-        return(res)
     } # end nNodes
 
     if(method=="Abouheif"){
@@ -69,7 +68,6 @@
             return(prod(temp))
         }
         res <- lapply(allPath, f1)
-        return(res)
     } # end Abouheif
 
     if(method=="sumDD"){
@@ -79,18 +77,23 @@
             return(sum(temp))
         }
         res <- lapply(allPath, f1)
-        return(res)
-
     } # end sumDD
 
+    ## convert res to a dist object
+    res <- unlist(res)
+    class(res) <- "dist"
+    attr(res, "Size") <- length(res)
+    attr(res, "Diag") <- FALSE
+    attr(res, "Upper") <- FALSE
+    attr(res, "method") <- paste("Phylogenetic: ",method,sep="")
+    attr(res, "call") <- match.call()
+    attr(res, "Labels") <- tips.names
+
+    return(res)
+
 } # end distNodes
 
 
-## examples
-# source("/home/master/dev/adephylo/pkg/R/distances.R")
- x <- as(rtree(10),"phylo4")
-     plot(x, show.node=TRUE)
-     axisPhylo()
 
 
 

Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2008-11-25 17:16:37 UTC (rev 29)
+++ pkg/R/utils.R	2008-11-25 17:55:45 UTC (rev 30)
@@ -102,14 +102,14 @@
 # examples
 # source("/home/master/dev/adephylo/pkg/R/utils.R")
 #phy <- as(rtree(15),"phylo4")
-plot(phy,show.n=T)
-tip1 <- "t1"
-tip2 <- "t2"
+## plot(phy,show.n=T)
+## tip1 <- "t1"
+## tip2 <- "t2"
 
 
-sp.tips(phy, "t1", "t2")
-sp.tips(phy, rep(1,15), 1:15)
-sp.tips(phy, rep(1, 15), 1:15, TRUE)
+## sp.tips(phy, "t1", "t2")
+## sp.tips(phy, rep(1,15), 1:15)
+## sp.tips(phy, rep(1, 15), 1:15, TRUE)
 
 ## heavier tree
 # x <- as(rtree(1000), "phylo4")

Modified: pkg/man/distTips.Rd
===================================================================
--- pkg/man/distTips.Rd	2008-11-25 17:16:37 UTC (rev 29)
+++ pkg/man/distTips.Rd	2008-11-25 17:55:45 UTC (rev 30)
@@ -1,14 +1,14 @@
-\name{distNodes}
-\alias{distNodes}
+\name{distTips}
+\alias{distTips}
 \title{Compute some phylogenetic distance between two nodes}
 \description{
-  The function \code{distNodes} computes a given distance between two
-  nodes of a phylogeny. This distance corresponds to the shortest path
-  between the two nodes. Several distances can be used, defaulting to the
+  The function \code{distTips} computes a given distance between a set
+  of tips of a phylogeny. This distance is computed from the shortest path
+  between the nodes. Several distances can be used, defaulting to the
   sum of branch lengths (see argument \code{method}).
 }
 \usage{
-distNodes(x, node1, node2, method=c("brlength","nNodes","Abouheif","sumDD"))
+distTips(x, tips, method=c("brlength","nNodes","Abouheif","sumDD"))
 }
 \arguments{
   \item{x}{a tree of  class \code{\link[pkg:ape]{phylo}},
@@ -54,10 +54,10 @@
 plot(x, show.node=TRUE)
 axisPhylo()
 ## compute different distances
-distNodes(x, "t1", "t2")
-distNodes(x, "t1", "t2", "nNodes")
-distNodes(x, "t1", "t2", "Abouheif")
-distNodes(x, "t1", "t2", "sumDD")
+distTips(x, 1:3)
+distTips(x, 1:3, "nNodes")
+distTips(x, 1:3, "Abouheif")
+distTips(x, 1:3, "sumDD")
 }
 }
 \keyword{manip}