[Phylobase-commits] r680 - in pkg: R inst/unitTests

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

Author: regetz
Date: 2009-09-29 23:13:52 +0200 (Tue, 29 Sep 2009)
New Revision: 680

Modified:
   pkg/R/methods-phylo4.R
   pkg/inst/unitTests/runit.methods-phylo4.R
Log:
changed edgeLength<- method to use .createEdge helper function, so now
it gets the order right (edgeId order) if names are missing; added tests


Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-09-29 20:30:46 UTC (rev 679)
+++ pkg/R/methods-phylo4.R	2009-09-29 21:13:52 UTC (rev 680)
@@ -203,13 +203,13 @@
 
 setReplaceMethod("edgeLength", signature(x="phylo4"),
  function(x, use.names=TRUE, ..., value) {
-    if(use.names && !is.null(names(value))) {
-        if(!all(names(value) %in% edgeId(x, "all")))
-            stop("Names provided don't match internal edge labels")
-        x at edge.length[match(names(value), names(x at edge.length))] <- value
+    len <- .createEdge(value, x at edge, type="lengths", use.names)
+    ## return empty vector if all values are NA
+    if (all(is.na(len))) {
+        x at edge.length <- numeric()
+    } else {
+        x at edge.length <- len
     }
-    else
-        x at edge.length[1:nEdges(x)] <- value
     if(is.character(checkval <- checkPhylo4(x))) stop(checkval)
     x
 })

Modified: pkg/inst/unitTests/runit.methods-phylo4.R
===================================================================
--- pkg/inst/unitTests/runit.methods-phylo4.R	2009-09-29 20:30:46 UTC (rev 679)
+++ pkg/inst/unitTests/runit.methods-phylo4.R	2009-09-29 21:13:52 UTC (rev 680)
@@ -110,7 +110,56 @@
 }
 
 test.Replace.edgeLength.phylo4 <- function() {
+
   #TODO function(x, use.names=TRUE, ..., value)
+  ## dropping all should produce empty slot
+  edgeLength(phy.alt) <- numeric()
+  checkIdentical(edgeLength(phy.alt), setNames(rep(NA_real_, 9), eid))
+  checkIdentical(phy.alt at edge.length, numeric())
+  edgeLength(phy.alt) <- NA_real_
+  checkIdentical(edgeLength(phy.alt), setNames(rep(NA_real_, 9), eid))
+  checkIdentical(phy.alt at edge.length, numeric())
+
+  #
+  # complete replacement
+  #
+
+  # vector with reversed names, which get matched by default
+  edgeLength(phy.alt) <- numeric()
+  edgeLength(phy.alt) <- setNames(elen, rev(eid))
+  checkIdentical(edgeLength(phy.alt), setNames(rev(elen), eid))
+  # vector with reversed names, but specify no matching
+  edgeLength(phy.alt) <- numeric()
+  edgeLength(phy.alt, use.names=FALSE) <- setNames(elen, rev(eid))
+  checkIdentical(edgeLength(phy.alt), setNames(elen, eid))
+  # vector with no names, should match to edgeId order
+  edgeLength(phy.alt) <- numeric()
+  edgeLength(phy.alt) <- elen
+  checkIdentical(edgeLength(phy.alt), setNames(elen, eid))
+
+  # recycling applies if fewer the nEdges elements are supplied
+  # (duplicate edge length are okay)
+  edgeLength(phy.alt) <- 1
+  checkIdentical(edgeLength(phy.alt), setNames(rep(1, 9), eid))
+
+  #
+  # partial replacement
+  #
+
+  edgeLength(phy.alt) <- elen
+  # replace an edge length using numeric index
+  edgeLength(phy.alt)[9] <- 83
+  checkIdentical(edgeLength(phy.alt), setNames(c(elen[1:8], 83), eid))
+  # and back again, now using character index
+  edgeLength(phy.alt)["8-3"] <- 0.3
+  checkIdentical(edgeLength(phy.alt), setNames(elen, eid))
+  # error to add length for edges that don't exist
+  checkException(edgeLength(phy.alt)["fake"] <- 999)
+  checkException(edgeLength(phy.alt)[999] <- 999)
+  # NAs permitted only for root edge (or for *all* edges)
+  edgeLength(phy.alt)[edgeId(phy.alt, "root")] <- NA
+  checkIdentical(edgeLength(phy.alt), setNames(c(NA, elen[2:9]), eid))
+  checkException(edgeLength(phy.alt)["8-3"] <- NA)
 }
 
 test.sumEdgeLength.phylo4 <- function() {
@@ -293,7 +342,7 @@
 
 test.Replace.edgeLabels.phylo4 <- function() {
 
-  ## dropping all should produce default tip labels, no internal labels
+  ## dropping all should produce empty slot
   edgeLabels(phy.alt) <- character()
   checkIdentical(edgeLabels(phy.alt), setNames(rep(NA_character_, 9), eid))