[Adephylo-commits] r39 - in pkg: R man

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

Author: jombart
Date: 2008-11-26 15:58:26 +0100 (Wed, 26 Nov 2008)
New Revision: 39

Modified:
   pkg/R/distances.R
   pkg/man/distRoot.Rd
   pkg/man/distTips.Rd
   pkg/man/sp.tips.Rd
Log:
Some doc fixes. 
findAllPairs fixed in distTips.


Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R	2008-11-26 14:10:34 UTC (rev 38)
+++ pkg/R/distances.R	2008-11-26 14:58:26 UTC (rev 39)
@@ -23,7 +23,7 @@
         res <- list(i=NULL,j=NULL)
         k <- 0
         for(i in 1:(length(vec)-1)){
-            for(j in 2:length(vec)){
+            for(j in (i+1):length(vec)){
                 k <- k+1
                 res[[1]][k] <- i
                 res[[2]][k] <- j
@@ -39,7 +39,8 @@
     if(method != "brlength") {
         allPath <- sp.tips(x, allPairs$i, allPairs$j, useTipNames=TRUE, quiet=TRUE)
     } else {
-        allPath <- sp.tips(x, allPairs$i, allPairs$j, useTipNames=TRUE, quiet=TRUE, include.mrca=FALSE)
+        allPath <- sp.tips(x, allPairs$i, allPairs$j, useTipNames=TRUE, quiet=TRUE,
+                           include.mrca=FALSE)
     }
 
     ## compute distances
@@ -47,7 +48,8 @@
         if(!hasEdgeLength(x)) stop("x does not have branch length")
         ## add tip1 and tip2 to the paths, so that these edges are counted
         allPath.names <- names(allPath)
-        allPath <- lapply(1:length(allPath), function(i) c(allPath[[i]], allPairs[i,]) )
+        allPath <- lapply(1:length(allPath), function(i)
+                          c(allPath[[i]], allPairs[i,1], allPairs[i,2]) )
         names(allPath) <- allPath.names
 
         edge.idx <- lapply(allPath, function(e) getedges(x, e) ) # list of indices of edges

Modified: pkg/man/distRoot.Rd
===================================================================
--- pkg/man/distRoot.Rd	2008-11-26 14:10:34 UTC (rev 38)
+++ pkg/man/distRoot.Rd	2008-11-26 14:58:26 UTC (rev 39)
@@ -11,6 +11,8 @@
 \arguments{
   \item{x}{a tree of  class \code{\link[pkg:ape]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
+  \item{tips}{A vector of integers identifying tips by their numbers, or
+    a vector of characters identifying tips by their names.}
   \item{method}{a character string (full or abbreviated without
     ambiguity) specifying the method used to compute distances ;
     possible values are:\cr

Modified: pkg/man/distTips.Rd
===================================================================
--- pkg/man/distTips.Rd	2008-11-26 14:10:34 UTC (rev 38)
+++ pkg/man/distTips.Rd	2008-11-26 14:58:26 UTC (rev 39)
@@ -3,8 +3,10 @@
 \title{Compute some phylogenetic distance between two nodes}
 \description{
   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
+  of tips of a phylogeny. A vector of tips is supplied: distances
+  between all possible pairs of these tips are computed.
+  The distances are computed from the shortest path
+  between the tips. Several distances can be used, defaulting to the
   sum of branch lengths (see argument \code{method}).
 }
 \usage{
@@ -13,6 +15,9 @@
 \arguments{
   \item{x}{a tree of  class \code{\link[pkg:ape]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
+  \item{tips}{A vector of integers identifying tips by their numbers, or
+    a vector of characters identifying tips by their names. Distances
+    will be computed between all possible pairs of tips.}
   \item{method}{a character string (full or abbreviated without
     ambiguity) specifying the method used to compute distances ;
     possible values are:\cr

Modified: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd	2008-11-26 14:10:34 UTC (rev 38)
+++ pkg/man/sp.tips.Rd	2008-11-26 14:58:26 UTC (rev 39)
@@ -8,7 +8,7 @@
   \linkS4class{phylo4d}. Several tips can be provided at a time.
 }
 \usage{
-sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE)
+sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE, include.mrca=TRUE)
 }
 \arguments{
   \item{x}{A tree of  class \code{\link[pkg:ape]{phylo}},