[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]
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