[Phylobase-commits] r140 - in pkg: . R inst/doc man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 6 11:03:04 CET 2008
Author: jombart
Date: 2008-03-06 11:03:04 +0100 (Thu, 06 Mar 2008)
New Revision: 140
Modified:
pkg/R/identify.R
pkg/R/phylo4.R
pkg/R/treestruc.R
pkg/R/treewalk.R
pkg/TODO
pkg/inst/doc/phylobase.Rnw
pkg/man/hasSingles.Rd
pkg/man/nNodes-methods.Rd
pkg/tests/misctests.R
Log:
Moved some CamelCases to camelCases.
Changes concern: RootEdge, EdgeLength, NodeLabels, EdgeLabels.
Modified: pkg/R/identify.R
===================================================================
--- pkg/R/identify.R 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/R/identify.R 2008-03-06 10:03:04 UTC (rev 140)
@@ -11,7 +11,7 @@
tips <- labels(x)
if (!hasNodeLabels(x)) {
nodes <- (N.tip+1):(N.tip+N.node)
- } else nodes <- NodeLabels(x)
+ } else nodes <- nodeLabels(x)
labs<-c(rep("",N.tip), nodes)
click <- identify(last$xx, last$yy, labels=labs, n=n)
## if (click > N.tip) {
Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/R/phylo4.R 2008-03-06 10:03:04 UTC (rev 140)
@@ -84,10 +84,10 @@
x at edge
})
-setGeneric("RootEdge", function(x,order,...) {
- standardGeneric("RootEdge")
+setGeneric("rootEdge", function(x,order,...) {
+ standardGeneric("rootEdge")
})
-setMethod("RootEdge","phylo4", function(x,order,...) {
+setMethod("rootEdge","phylo4", function(x,order,...) {
x at root.edge
})
@@ -131,10 +131,10 @@
length(x at edge.length)>0
})
-setGeneric("EdgeLength", function(x) {
- standardGeneric("EdgeLength")
+setGeneric("edgeLength", function(x) {
+ standardGeneric("edgeLength")
})
-setMethod("EdgeLength","phylo4", function(x) {
+setMethod("edgeLength","phylo4", function(x) {
if (!hasEdgeLength(x)) NULL else x at edge.length
})
@@ -174,37 +174,37 @@
object
})
-setGeneric("NodeLabels", function(x) {
- standardGeneric("NodeLabels")
+setGeneric("nodeLabels", function(x) {
+ standardGeneric("nodeLabels")
})
-setMethod("NodeLabels","phylo4", function(x) {
+setMethod("nodeLabels","phylo4", function(x) {
x at node.label
})
-setGeneric("NodeLabels<-",
+setGeneric("nodeLabels<-",
function(object,...,value) {
- standardGeneric("NodeLabels<-")
+ standardGeneric("nodeLabels<-")
})
-setMethod("NodeLabels<-","phylo4", function(object,...,value) {
+setMethod("nodeLabels<-","phylo4", function(object,...,value) {
object at node.label <- value
object
})
-setGeneric("EdgeLabels", function(x) {
- standardGeneric("EdgeLabels")
+setGeneric("edgeLabels", function(x) {
+ standardGeneric("edgeLabels")
})
-setMethod("EdgeLabels","phylo4", function(x) {
+setMethod("edgeLabels","phylo4", function(x) {
x at edge.label
})
-setGeneric("EdgeLabels<-",
+setGeneric("edgeLabels<-",
function(object,...,value) {
- standardGeneric("EdgeLabels<-")
+ standardGeneric("edgeLabels<-")
})
-setMethod("EdgeLabels<-","phylo4", function(object,...,value) {
+setMethod("edgeLabels<-","phylo4", function(object,...,value) {
object at edge.label <- value
object
})
@@ -297,9 +297,9 @@
# if (length(ancestor)>0) ancestor <- c(NA, ancestor)
ancestor <- E[idx,1]
# branch.length <- c(x at root.edge, x at edge.length) # root.edge is not an edge length
- branch.length <- EdgeLength(x)[idx]
+ branch.length <- edgeLength(x)[idx]
# if (length(branch.length) == 1) branch.length <- rep("", n.tip+n.int)
- if(is.null(EdgeLength(x))) branch.length <- rep(NA, length(node))
+ if(is.null(edgeLength(x))) branch.length <- rep(NA, length(node))
## node and tip labels ##
## beware: they cannot be NULL
## there are always tip labels (or check_phylo4 complains)
@@ -392,9 +392,9 @@
nod <- unique(E[,1])
idx <- match(nod,E[,1])
res$degree <- res$degree[idx]
- names(res$degree) <- NodeLabels(x)
+ names(res$degree) <- nodeLabels(x)
res$polytomy <- res$polytomy[idx]
- names(res$polytomy) <- NodeLabels(x)
+ names(res$polytomy) <- nodeLabels(x)
}
## model info
@@ -476,7 +476,7 @@
## cat(" Tree plus data object of type:", class(x), "\n")
## cat(" Species Names :", labels(x), "\n")
## if (hasEdgeLength(x)){
-## cat(" Has Branch Lengths (first 10):", EdgeLength(x)[1:min(length(EdgeLength(x)),10)], "\n")
+## cat(" Has Branch Lengths (first 10):", edgeLength(x)[1:min(length(edgeLength(x)),10)], "\n")
## }
## cat(" Rooted :", isRooted(x), "\n\n\n")
##
@@ -557,7 +557,7 @@
nrow(x at node.data)>0
})
-setMethod("NodeLabels<-","phylo4d", function(object,...,value) {
+setMethod("nodeLabels<-","phylo4d", function(object,...,value) {
object at node.label <- value
rownames(object at node.data) <- value
object
Modified: pkg/R/treestruc.R
===================================================================
--- pkg/R/treestruc.R 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/R/treestruc.R 2008-03-06 10:03:04 UTC (rev 140)
@@ -2,7 +2,7 @@
## not bothering to check for zero branch lengths:
## consensus is that this isn't very important,
## and that it's simple enough to do
-## any(EdgeLength(x)==0) if necessary
+## any(edgeLength(x)==0) if necessary
hasPoly <- function(object) {
if(!check_phylo4(object)) stop("to be used with a phylo4 object")
degree <- tabulate(edges(object)[, 1])
Modified: pkg/R/treewalk.R
===================================================================
--- pkg/R/treewalk.R 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/R/treewalk.R 2008-03-06 10:03:04 UTC (rev 140)
@@ -2,7 +2,7 @@
## matching node labels with node numbers ...
## e.g.
## 14 tips, 13 int nodes
-## N04 = NodeLabels[4]
+## N04 = nodeLabels[4]
## <-> node 18
## x = n-nTips(phy)
## so: n = x+nTips(phy)
@@ -18,7 +18,7 @@
vals <- ifelse(!is.na(tipmatch),
tipmatch,
if (!hasNodeLabels(phy)) { NA } else {
- nt+match(node,NodeLabels(phy))
+ nt+match(node,nodeLabels(phy))
})
names(vals) <- node
return(vals)
@@ -30,7 +30,7 @@
ifelse(node<=nt+nNodes(phy),
if (!hasNodeLabels(phy)) { NA }
else {
- NodeLabels(phy)[pmax(0,node-nt)]
+ nodeLabels(phy)[pmax(0,node-nt)]
},NA))
## pmax above to avoid error from negative indices
names(node) <- vals
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/TODO 2008-03-06 10:03:04 UTC (rev 140)
@@ -70,7 +70,7 @@
### Some things to think about (re)naming:
* tree walking: `getDescend`, `getAncest`, `allDescend`, `allAncest` -- sons and fathers, daughters and mothers, tips/leaves, ?
* should `check_data` be `check_phylo4d` for consistency with `check_phylo4` (or should `check_phylo4` be `check_tree`?)
-* EdgeLength/BranchLength?
+* edgeLength/BranchLength?
* root, Root, rootNode, RootNode?
* `subset(phy,node.subtree= )` == `subset(phy,subtree= )` ?
Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/inst/doc/phylobase.Rnw 2008-03-06 10:03:04 UTC (rev 140)
@@ -115,12 +115,12 @@
Print internal node labels (R automatically assigns values):
<<>>=
-NodeLabels(g1)
+nodeLabels(g1)
@
Print edge labels (also automatically assigned):
<<>>=
-EdgeLabels(g1)
+edgeLabels(g1)
@
Is it rooted?
Modified: pkg/man/hasSingles.Rd
===================================================================
--- pkg/man/hasSingles.Rd 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/man/hasSingles.Rd 2008-03-06 10:03:04 UTC (rev 140)
@@ -24,7 +24,7 @@
We haven't bothered to check for zero branch lengths:
the consensus is that it doesn't come up much,
and that it's simple enough to
- test \code{any(EdgeLength(x)==0)} in these cases.
+ test \code{any(edgeLength(x)==0)} in these cases.
(Single-descendant nodes are used e.g. in OUCH, or in
other cases to represent events occurring along a branch.)
}
Modified: pkg/man/nNodes-methods.Rd
===================================================================
--- pkg/man/nNodes-methods.Rd 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/man/nNodes-methods.Rd 2008-03-06 10:03:04 UTC (rev 140)
@@ -20,15 +20,15 @@
\alias{hasEdgeLength}
\alias{hasEdgeLength-methods}
\alias{hasEdgeLength,phylo4-method}
-\alias{EdgeLength}
-\alias{EdgeLength-methods}
-\alias{EdgeLength,phylo4-method}
+\alias{edgeLength}
+\alias{edgeLength-methods}
+\alias{edgeLength,phylo4-method}
\alias{isRooted}
\alias{isRooted-methods}
\alias{isRooted,phylo4-method}
-\alias{RootEdge}
-\alias{RootEdge-methods}
-\alias{RootEdge,phylo4-method}
+\alias{rootEdge}
+\alias{rootEdge-methods}
+\alias{rootEdge,phylo4-method}
\alias{rootNode}
\alias{rootNode-methods}
\alias{rootNode,phylo4-method}
@@ -40,20 +40,20 @@
\alias{hasNodeData}
\alias{hasNodeData-methods}
\alias{hasNodeData,phylo4d-method}
-\alias{NodeLabels}
-\alias{NodeLabels-methods}
-\alias{NodeLabels,phylo4-method}
-\alias{NodeLabels<-}
-\alias{NodeLabels<-,phylo4-method}
-\alias{NodeLabels<-,phylo4d-method}
+\alias{nodeLabels}
+\alias{nodeLabels-methods}
+\alias{nodeLabels,phylo4-method}
+\alias{nodeLabels<-}
+\alias{nodeLabels<-,phylo4-method}
+\alias{nodeLabels<-,phylo4d-method}
\alias{hasEdgeLabels}
\alias{hasEdgeLabels-methods}
\alias{hasEdgeLabels,phylo4-method}
-\alias{EdgeLabels}
-\alias{EdgeLabels<-}
-\alias{EdgeLabels-methods}
-\alias{EdgeLabels,phylo4-method}
-\alias{EdgeLabels<-,phylo4-method}
+\alias{edgeLabels}
+\alias{edgeLabels<-}
+\alias{edgeLabels-methods}
+\alias{edgeLabels,phylo4-method}
+\alias{edgeLabels<-,phylo4-method}
\alias{tdata}
\alias{tdata-methods}
@@ -71,23 +71,23 @@
tree has (internal) node labels}
\item{hasNodeData}{\code{signature(object = "phylo4d")}: whether
tree has (internal) node data}
- \item{NodeLabels}{\code{signature(object = "phylo4")}: internal
+ \item{nodeLabels}{\code{signature(object = "phylo4")}: internal
node labels}
\item{nEdges}{\code{signature(object = "phylo4")}: number of edges}
\item{edges}{\code{signature(object = "phylo4")}: edge matrix}
\item{hasEdgeLength}{\code{signature(object = "phylo4")}: whether
tree has edge (branch) lengths}
- \item{EdgeLength}{\code{signature(object = "phylo4")}: edge (branch)
+ \item{edgeLength}{\code{signature(object = "phylo4")}: edge (branch)
lengths (or NULL if none)}
\item{hasEdgeLabels}{\code{signature(object = "phylo4")}: whether
tree has (internal) edge labels}
- \item{EdgeLabels}{\code{signature(object = "phylo4")}: internal
+ \item{edgeLabels}{\code{signature(object = "phylo4")}: internal
edge labels}
\item{isRooted}{\code{signature(object = "phylo4")}: whether tree is
rooted (i.e. has explicit root edge defined \emph{or} root node has
<= 2 descendants)}
- \item{RootEdge}{\code{signature(object = "phylo4")}: root edge}
+ \item{rootEdge}{\code{signature(object = "phylo4")}: root edge}
\item{tdata}{\code{signature(object = "phylo4d")}: trait data}
}
}
Modified: pkg/tests/misctests.R
===================================================================
--- pkg/tests/misctests.R 2008-03-06 03:10:33 UTC (rev 139)
+++ pkg/tests/misctests.R 2008-03-06 10:03:04 UTC (rev 140)
@@ -48,10 +48,10 @@
plot(q2)
plot(q2,treetype="cladogram")
-## plot(p2,type="dotchart",labels.nodes=NodeLabels(p2))
+## plot(p2,type="dotchart",labels.nodes=nodeLabels(p2))
## trace("plot", browser, signature = c("phylo4d","missing"))
labels(q1) <- paste("q",1:5,sep="")
-NodeLabels(q1) <- paste("n",1:4,sep="")
+nodeLabels(q1) <- paste("n",1:4,sep="")
p3 <- phylo4d(r1,tip.data=tipdat,node.data=data.frame(b=6:9))
summary(p3)
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