[Phylobase-commits] r411 - in pkg: R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 30 19:42:00 CET 2008
Author: francois
Date: 2008-12-30 19:42:00 +0100 (Tue, 30 Dec 2008)
New Revision: 411
Modified:
pkg/R/checkdata.R
pkg/R/class-phylo4d.R
pkg/R/identify.R
pkg/R/methods-phylo4.R
pkg/R/methods-phylo4d.R
pkg/R/treewalk.R
pkg/inst/doc/phylobase.Rnw
pkg/inst/doc/phylobase.pdf
pkg/man/check.phylo4d.Rd
Log:
attempt to make arguments consistent: c('tip', 'internal', 'allnode')
Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/checkdata.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -76,7 +76,7 @@
}
## make sure that tip and node labels are unique
- lb <- labels(object, "all")
+ lb <- labels(object, "allnode")
lb <- lb[nchar(lb) > 0]
lb <- na.omit(lb)
if(any(table(lb) > 1))
@@ -174,7 +174,7 @@
}
else {
## Some tips are non-unique
- tipsTable <- table(labels(object))
+ tipsTable <- table(tipLabels(object))
if(any(nU <- tipsTable > 1)) {
nonUnique <- paste(names(tipsTable[nU]), collapse=", ")
nonUniqueMsg <- paste("Tip \'", nonUnique, "\' not unique", sep = "")
Modified: pkg/R/class-phylo4d.R
===================================================================
--- pkg/R/class-phylo4d.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/class-phylo4d.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -69,7 +69,7 @@
}
if(!is.null(node.data)) {
emptyTipData <- array(, dim = c(nTips(x), ncol(node.data)),
- dimnames = list(labels(x), colnames(node.data)))
+ dimnames = list(tipLabels(x), colnames(node.data)))
tmpNodeData <- rbind(emptyTipData, node.data)
## TODO? - add test
tmpNodeData <- tmpNodeData[match(rownames(all.data), rownames(tmpNodeData)) ,, drop = FALSE]
@@ -89,7 +89,7 @@
}
else {
emptyTipData <- array(, dim = c(nTips(x), ncol(node.data)),
- dimnames = list(labels(x), colnames(node.data)))
+ dimnames = list(tipLabels(x), colnames(node.data)))
emptyNodeData <- array(, dim = c(nNodes(x), ncol(tip.data)),
dimnames = list(nodeLabels(x), colnames(tip.data)))
tmpTipData <- rbind(tip.data, emptyNodeData)
Modified: pkg/R/identify.R
===================================================================
--- pkg/R/identify.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/identify.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -1,12 +1,12 @@
## setGeneric("identify")
-##
+##
## setMethod("identify","phylo4",
## function(x,n=1,...) {
## plot(x, ...)
## last <- .last_plot.phylo # information return from plot.phylo
## N.tip <- nTips(x)
## N.node <- nNodes(x)
-## tips <- labels(x)
+## tips <- tipLabels(x)
## if (!hasNodeLabels(x)) {
## nodes <- (N.tip+1):(N.tip+N.node)
## } else nodes <- nodeLabels(x)
Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/methods-phylo4.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -113,11 +113,11 @@
})
setMethod("labels", "phylo4", function(object, which = c("tip",
- "node", "allnode"), ...) {
+ "internal", "allnode"), ...) {
which <- match.arg(which)
switch(which,
tip = object at tip.label[order(nodeId(object,"tip"))],
- node = {
+ internal = {
if (hasNodeLabels(object)) {
object at node.label[order(nodeId(object))]
}
@@ -145,7 +145,7 @@
setReplaceMethod("labels",
signature(object="phylo4", value="character"),
- function(object, which = c("tip", "node", "allnode"), ..., value) {
+ function(object, which = c("tip", "internal", "allnode"), ..., value) {
which <- match.arg(which)
tipOrder <- order(nodeId(object, "tip"))
intOrder <- order(nodeId(object, "internal"))
@@ -162,8 +162,8 @@
object
}
},
- ## If 'node'
- node = {
+ ## If 'internal'
+ internal = {
if(length(value) != nNodes(object))
stop("Number of node labels does not match number of internal nodes.")
else {
@@ -201,26 +201,26 @@
setMethod("nodeLabels", "phylo4", function(object) {
#x at node.label
- labels(object, which="node")
+ labels(object, which="internal")
})
setMethod("tipLabels", "phylo4", function(object) {
labels(object, which="tip")
})
-setMethod("nodeId", "phylo4", function(x,which=c("internal","tip","all")) {
+setMethod("nodeId", "phylo4", function(x,which=c("internal","tip","allnode")) {
which <- match.arg(which)
nid <- switch(which,
internal=x at edge[x at edge[,2]>nTips(x),2],
tip = x at edge[x at edge[,2]<=nTips(x),2],
- all = x at edge[,2])
+ allnode = x at edge[,2])
#sort(nid)
return(nid)
})
setReplaceMethod("nodeLabels", signature(object="phylo4", value="character"),
function(object, ..., value) {
- labels(object, which="node", ...) <- value
+ labels(object, which="internal", ...) <- value
return(object)
})
Modified: pkg/R/methods-phylo4d.R
===================================================================
--- pkg/R/methods-phylo4d.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/methods-phylo4d.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -3,10 +3,10 @@
setMethod("show", "phylo4d", function(object) printphylo4(object))
setMethod("tdata", "phylo4d", function(x, which = c("tip",
- "node", "allnode"), label.type=c("row.names","column"), ...) {
+ "internal", "allnode"), label.type=c("row.names","column"), ...) {
which <- match.arg(which)
## FIXME: should have no labels in this case?
- if (!hasNodeLabels(x) && which=="node" && missing(label.type)) { }
+ if (!hasNodeLabels(x) && which=="internal" && missing(label.type)) { }
label.type <- match.arg(label.type)
if (which == "tip") {
if (all(dim(x at tip.data)==0)) {
@@ -32,7 +32,7 @@
return(tdata)
}
- if (which == "node") {
+ if (which == "internal") {
if (all(dim(x at node.data)==0)) {
return(x at node.data)
}
@@ -67,7 +67,7 @@
nodedata <- data.frame(label=nodeLabels(x))
}
else {
- nodedata <- tdata(x, "node", label.type="column")
+ nodedata <- tdata(x, "internal", label.type="column")
}
if (all(dim(x at tip.data)==0)) {
tipdata <- data.frame(label=x at tip.label)
@@ -100,7 +100,7 @@
})
setReplaceMethod("tdata", "phylo4d", function(object, which = c("tip",
- "node", "allnode"), ..., value) {
+ "internal", "allnode"), ..., value) {
which <- match.arg(which)
if (which == "allnode") {
namesmatch <- all(colnames(object at tip.data) == colnames(object at node.data))
@@ -115,7 +115,7 @@
stop("For now, only data.frame or matrix can be provided")
switch(which,
tip = object at tip.data <- value,
- node = object at node.data <- value,
+ internal = object at node.data <- value,
allnode = stop("for now, must set tip and node data separately"))
if(check_data(object, ...)) object <- attach_data(object, ...)
object
@@ -128,7 +128,7 @@
x <- object
summary(as(x, "phylo4"))
tips <- tdata(object, "tip")
- nodes <- tdata(object, "node")
+ nodes <- tdata(object, "internal")
cat("\nComparative data:\n")
if (nrow(tips) > 0) {
cat("\nTips: data.frame with", nTips(object), "taxa and",
Modified: pkg/R/treewalk.R
===================================================================
--- pkg/R/treewalk.R 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/R/treewalk.R 2008-12-30 18:42:00 UTC (rev 411)
@@ -16,7 +16,7 @@
if (is.character(node)) {
## old getNodeByLabel()
nt <- nTips(phy)
- tipmatch <- match(node,labels(phy,"all"))
+ tipmatch <- match(node,labels(phy,"allnode"))
vals <- ifelse(!is.na(tipmatch),
tipmatch,
ifelse(nolabs,NA,nt+match(node,nodeLabels(phy))))
@@ -26,7 +26,7 @@
## old getLabelByNode
nt <- nTips(phy)
vals <- ifelse(node<=nt, ## tips
- labels(phy,"all")[node],
+ labels(phy,"allnode")[node],
ifelse(node<=nt+nNodes(phy),
ifelse(nolabs,NA,
nodeLabels(phy)[pmax(0,node-nt)]),
@@ -70,7 +70,7 @@
node <- getNode(phy,node)
if (is.na(node)) stop("node ",node," not found in tree")
n <- nTips(phy)
- if (node <= n) return(labels(phy,"all")[node])
+ if (node <= n) return(labels(phy,"allnode")[node])
l <- numeric()
d <- children(phy, node)
for (j in d) {
Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/inst/doc/phylobase.Rnw 2008-12-30 18:42:00 UTC (rev 411)
@@ -147,7 +147,7 @@
Print node numbers:
<<nodenumbergeodata>>=
-nodeId(g1, which = 'all')
+nodeId(g1, which = 'allnode')
@
Print edge labels (also empty in this case):
@@ -232,7 +232,7 @@
summary(g2)
@
-Or use \code{tdata()} to extract the data (i.e., \code{tdata(g2)}). By default, \code{tdata()} will retrieve tip data, but you can also get internal node data only (\code{tdata(tree,"node")}) or --- if the tip and node data have the same format --- all the data combined (\code{tdata(tree,"allnode")}).
+Or use \code{tdata()} to extract the data (i.e., \code{tdata(g2)}). By default, \code{tdata()} will retrieve tip data, but you can also get internal node data only (\code{tdata(tree,"internal")}) or --- if the tip and node data have the same format --- all the data combined (\code{tdata(tree,"allnode")}).
Plotting calls \code{plot.phylog} from the \code{ade4} package.
@@ -444,7 +444,7 @@
\subsection{phylo4d}
The \code{phylo4d} class extends \code{phylo4} with data. Tip data, and (internal) node data are stored separately, but can be retrieved together or separately with \code{tdata(x,"tip")},
-\code{tdata(x,"node")} or \code{tdata(x,"all")}.
+\code{tdata(x,"internal")} or \code{tdata(x,"all")}.
There is no separate slot for edge data, but these
can be stored as node data associated with the
descendant node.
Modified: pkg/inst/doc/phylobase.pdf
===================================================================
--- pkg/inst/doc/phylobase.pdf 2008-12-28 15:39:20 UTC (rev 410)
+++ pkg/inst/doc/phylobase.pdf 2008-12-30 18:42:00 UTC (rev 411)
@@ -10,7 +10,7 @@
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 411
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