[Phylobase-commits] r633 - in pkg: R inst inst/doc inst/unitTests

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Sep 11 03:58:16 CEST 2009


Author: francois
Date: 2009-09-11 03:58:15 +0200 (Fri, 11 Sep 2009)
New Revision: 633

Modified:
   pkg/R/checkdata.R
   pkg/R/methods-phylo4.R
   pkg/inst/
   pkg/inst/doc/
   pkg/inst/doc/phylobase.pdf
   pkg/inst/doc/technotes.pdf
   pkg/inst/unitTests/runit.methods-phylo4d.R
Log:
removed direct calls to slots in methods-phylo4, fixed mispelling in error message in checkPhylo4, created RUnit tests for tdata and tdata<-

Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2009-09-10 06:53:11 UTC (rev 632)
+++ pkg/R/checkdata.R	2009-09-11 01:58:15 UTC (rev 633)
@@ -31,7 +31,7 @@
       ## presumably we shouldn't allow NAs mixed
       ## with numeric branch lengths except at the root
       if (sum(is.na(object at edge.length)) > 1)
-        return("NAs in edge lenghts")
+        return("NAs in edge lengths")
       ## Strip root edge branch lenght (if set to NA)
       if (any(object at edge.length[!is.na(object at edge.length)] < 0))
         return("edge lengths must be non-negative")

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-09-10 06:53:11 UTC (rev 632)
+++ pkg/R/methods-phylo4.R	2009-09-11 01:58:15 UTC (rev 633)
@@ -187,7 +187,7 @@
 
 setReplaceMethod("edgeLength", "phylo4", function(x, use.names=TRUE, ..., value) {
     if(use.names && !is.null(names(value))) {
-        if(!all(names(value) %in% names(x at edge.length)))
+        if(!all(names(value) %in% names(edgeLength(x))))
             stop("Names provided don't match internal edge labels")
         x at edge.length[match(names(value), names(x at edge.length))] <- value
     }
@@ -238,16 +238,20 @@
     type <- match.arg(type)
     ## [JR: below, using match for ordering rather than direct character
     ## indexing b/c the latter is slow for vectors of a certain size]
-    if (type=="all") {
-        all <- c(object at tip.label, object at node.label)
-        return(all[match(nodeId(object, "all"), names(all))])
-    } else if (type=="tip") {
-        tip <- object at tip.label
-        return(tip[match(nodeId(object, "tip"), names(tip))])
-    } else if (type=="internal") {
-        int <- object at node.label
-        return(int[match(nodeId(object, "internal"), names(int))])
-    }
+    lbl <- switch(type,
+                  all={
+                      all <- c(object at tip.label, object at node.label)
+                      all[match(nodeId(object, "all"), names(all))]
+                  },
+                  tip={
+                      tip <- object at tip.label
+                      tip[match(nodeId(object, "tip"), names(tip))]
+                  },
+                  internal={
+                      int <- object at node.label
+                      int[match(nodeId(object, "internal"), names(int))]
+                  })
+    return(lbl)
 })
 
 setReplaceMethod("labels",
@@ -368,7 +372,7 @@
 
 ### print
 printphylo4 <- function(x, edgeOrder=c("pretty", "real"), printall=TRUE) {
-    if(!nrow(x at edge)) {
+    if(!nrow(edges(x))) {
         msg <- paste("Empty \'", class(x), "\' object\n", sep="")
         cat(msg)
     }
@@ -507,7 +511,7 @@
     order <- match.arg(order)
 
     ## get a root node free edge matrix
-    edge <- phy at edge[!is.na(phy at edge[, 1]), ]
+    edge <- edges(phy)[!is.na(edges(phy)[, 1]), ]
     ## Sort edges -- ensures that starting order of edge matrix doesn't
     ## affect the order of reordered trees
     edge <- edge[order(edge[, 2]), ]
@@ -581,7 +585,7 @@
     ##} else {stop(paste("Method for", order, "not implemented"))}
 
     ## match the new node order to the old order to get an index
-    index <- match(descendantReord, phy at edge[, 2])
+    index <- match(descendantReord, edges(phy)[, 2])
 
 }
 


Property changes on: pkg/inst
___________________________________________________________________
Name: svn:ignore
   + 



Property changes on: pkg/inst/doc
___________________________________________________________________
Name: svn:ignore
   + technotes.pdf
phylobase.pdf


Modified: pkg/inst/doc/phylobase.pdf
===================================================================
--- pkg/inst/doc/phylobase.pdf	2009-09-10 06:53:11 UTC (rev 632)
+++ pkg/inst/doc/phylobase.pdf	2009-09-11 01:58:15 UTC (rev 633)
@@ -100,24 +100,22 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 633


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