[Adephylo-commits] r20 - in pkg: . R

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

Author: jombart
Date: 2008-11-25 12:04:59 +0100 (Tue, 25 Nov 2008)
New Revision: 20

Modified:
   pkg/R/distances.R
   pkg/R/utils.R
   pkg/TODO
Log:
Updated TODO.


Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R	2008-11-21 15:43:42 UTC (rev 19)
+++ pkg/R/distances.R	2008-11-25 11:04:59 UTC (rev 20)
@@ -47,7 +47,7 @@
         temp <- table(E[,1])[as.character(path)] # number of dd per node
         res <- sum(temp)
         return(res)
- } # end Abouheif
+ } # end sumDD
 
 } # end distNodes
 

Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2008-11-21 15:43:42 UTC (rev 19)
+++ pkg/R/utils.R	2008-11-25 11:04:59 UTC (rev 20)
@@ -1,36 +1,35 @@
-###############
-# shortestPath -> moved to phylobase
-###############
-## shortestPath <- function(x, node1, node2){
-##     if(!require(phylobase)) stop("phylobase package is not installed")
+##############
+# pathTwoTips
+##############
+pathTwoTips <- function(phy, tip1, tip2){
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
-##     ## conversion from phylo, phylo4 and phylo4d
-##     x <- as(x, "phylo4")
+    ## conversion from phylo, phylo4 and phylo4d
+    x <- as(phy, "phylo4")
 
-##     ## come checks
-##     if (is.character(checkval <- check_phylo4(x))) stop(checkval)
-##     t1 <- getnodes(x, node1)
-##     t2 <- getnodes(x, node2)
-##     if(any(is.na(c(t1,t2)))) stop("wrong node specified")
-##     if(t1==t2) return(NULL)
+    ## come checks
+    if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+    t1 <- getnodes(x, node1)
+    t2 <- getnodes(x, node2)
+    if(any(is.na(c(t1,t2)))) stop("wrong node specified")
+    # if(t1==t2) return(NULL)
 
-##     ## main computations
-##     comAnc <- MRCA(x, t1, t2) # common ancestor
-##     desComAnc <- descendants(x, comAnc, which="all")
-##     ancT1 <- ancestors(x, t1, which="all")
-##     path1 <- intersect(desComAnc, ancT1) # path: common anc -> t1
+    ## main computations
+    comAnc <- MRCA(x, t1, t2) # common ancestor
+    desComAnc <- descendants(x, comAnc, which="all")
+    ancT1 <- ancestors(x, t1, which="all")
+    path1 <- intersect(desComAnc, ancT1) # path: common anc -> t1
 
-##     ancT2 <- ancestors(x, t2, which="all")
-##     path2 <- intersect(desComAnc, ancT2) # path: common anc -> t2
+    ancT2 <- ancestors(x, t2, which="all")
+    path2 <- intersect(desComAnc, ancT2) # path: common anc -> t2
 
-##     res <- union(path1, path2) # union of the path
-##     ## add the common ancestor if it differs from t1 or t2
-##     if(!comAnc %in% c(t1,t2)){
-##         res <- c(comAnc,res)
-##     }
+    res <- union(path1, path2) # union of the path
+    ## add the common ancestor if it differs from t1 or t2
+    if(!comAnc %in% c(t1,t2)){
+        res <- c(comAnc,res)
+    }
 
-##     res <- getnodes(x, res)
+    res <- getnodes(x, res)
 
-##     return(res)
-## } # end shortestPath
-
+    return(res)
+} # end shortestPath

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-21 15:43:42 UTC (rev 19)
+++ pkg/TODO	2008-11-25 11:04:59 UTC (rev 20)
@@ -36,6 +36,7 @@
 # NEW IMPLEMENTATIONS:
 =====================
 * plot methods from phylobase ('old' version) -- done (TJ)
+* implement a pathTwoTips method, which has to go fast to find shortest path between two tips.
 * basic stuff existing in phylog objects (while option=TRUE), e.g. distance to the root for tips, etc.
 * proximities between OTUs like Abouheif, etc.
 * distances between OTUs (like sum of branch lengths)