[Phylobase-commits] r877 - pkg/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Mar 17 14:15:10 CET 2014 

Author: francois
Date: 2014-03-17 14:15:09 +0100 (Mon, 17 Mar 2014)
New Revision: 877

Modified:
   pkg/man/as-methods.Rd
   pkg/man/extract.tree.Rd
   pkg/man/hasSingles.Rd
   pkg/man/multiPhylo-class.Rd
   pkg/man/phylo4-display.Rd
   pkg/man/phylo4d-class.Rd
   pkg/man/phylo4d.Rd
   pkg/man/phylomat-class.Rd
   pkg/man/printphylo4.Rd
   pkg/man/reorder-methods.Rd
   pkg/man/treewalk.Rd
Log:
cleanup/added pointers to ape in examples

Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/as-methods.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -112,7 +112,7 @@
 
 \examples{
 trString <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
-tree.owls <- read.tree(text=trString)
+tree.owls <- ape::read.tree(text=trString)
 ## round trip conversion
 tree_in_phylo <- tree.owls                  # tree is a phylo object
 (tree_in_phylo4 <- as(tree.owls,"phylo4"))  # phylo converted to phylo4

Modified: pkg/man/extract.tree.Rd
===================================================================
--- pkg/man/extract.tree.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/extract.tree.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -16,7 +16,7 @@
 \author{ Ben Bolker }
 \seealso{\code{\link{phylo4}}, \code{\link{phylo4d}}, \code{\link{coerce-methods}} for translation functions. }
 \examples{
-tree.phylo <- read.tree(text = "((a,b),c);")
+tree.phylo <- ape::read.tree(text = "((a,b),c);")
 tree <- as(tree.phylo, "phylo4")
 plot(tree)
 tip.data <- data.frame(size = c(1, 2, 3), row.names = c("a", "b", "c"))

Modified: pkg/man/hasSingles.Rd
===================================================================
--- pkg/man/hasSingles.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/hasSingles.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -34,8 +34,7 @@
   other cases to represent events occurring along a branch.)
 }
 \examples{
-library(ape)
-tree.owls.bis <- read.tree(text = "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);")
+tree.owls.bis <- ape::read.tree(text = "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);")
 owls4 <- as(tree.owls.bis, "phylo4")
 hasPoly(owls4)
 hasSingle(owls4)

Modified: pkg/man/multiPhylo-class.Rd
===================================================================
--- pkg/man/multiPhylo-class.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/multiPhylo-class.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -59,7 +59,7 @@
 % \examples{
 % ### An extract from Sibley and Ahlquist (1990)
 % cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "\n")
-% tree.owls <- read.tree("ex.tre", keep.multi = TRUE)
+% tree.owls <- ape::read.tree("ex.tre", keep.multi = TRUE)
 % tree.owls
 % (as(tree.owls, "multiPhylo4"))
 % }

Modified: pkg/man/phylo4-display.Rd
===================================================================
--- pkg/man/phylo4-display.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/phylo4-display.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -74,7 +74,7 @@
 \examples{
 
   tOwls <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
-  tree.owls <- read.tree(text=tOwls)
+  tree.owls <- ape::read.tree(text=tOwls)
   P1 <- as(tree.owls, "phylo4")
   P1
   summary(P1)

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/phylo4d-class.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -42,8 +42,7 @@
 
 \author{Ben Bolker, Thibaut Jombart}   
 \examples{
-  library(ape)
-  example(read.tree)
+  example(read.tree, "ape")
   obj <- phylo4d(as(tree.owls.bis,"phylo4"), data.frame(wing=1:3))
   obj
   names(obj)

Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/phylo4d.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -126,7 +126,7 @@
 }
 \examples{
 treeOwls <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
-tree.owls.bis <- read.tree(text=treeOwls)
+tree.owls.bis <- ape::read.tree(text=treeOwls)
 try(phylo4d(as(tree.owls.bis,"phylo4"),data.frame(wing=1:3)), silent=TRUE)
 obj <- phylo4d(as(tree.owls.bis,"phylo4"),data.frame(wing=1:3), match.data=FALSE)
 obj
@@ -178,10 +178,9 @@
 (exGeo7 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE))
 (exGeo8 <- phylo4d(trGeo, tip.data=tDt, match.data=FALSE))
 
-require(ape) ## for rcoal
 ## generate a tree and some data
 set.seed(1)
-p3 <- rcoal(5)
+p3 <- ape::rcoal(5)
 dat <- data.frame(a = rnorm(5), b = rnorm(5), row.names = p3$tip.label)
 dat.defaultnames <- dat
 row.names(dat.defaultnames) <- NULL

Modified: pkg/man/phylomat-class.Rd
===================================================================
--- pkg/man/phylomat-class.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/phylomat-class.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -31,7 +31,7 @@
 \author{Ben Bolker}
 \examples{
    trString <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
-   tree.owls <- read.tree(text=trString)
+   tree.owls <- ape::read.tree(text=trString)
   o2 <- as(tree.owls,"phylo4")
   ov <- as(o2,"phylo4vcov")
   o3 <- as(ov,"phylo4")

Modified: pkg/man/printphylo4.Rd
===================================================================
--- pkg/man/printphylo4.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/printphylo4.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -38,7 +38,7 @@
 \note{This is the default show() method for phylo4, phylo4d. It prints the user-supplied information for building a phylo4 object. For a full description of the phylo4 S4 object and slots, see \code{\link{phylo4}}. }
 \examples{
 
-tree.phylo <- read.tree(text="((a,b),c);")
+tree.phylo <- ape::read.tree(text="((a,b),c);")
 tree <- as(tree.phylo, "phylo4")
 ##plot(tree,show.node=TRUE) ## plotting broken with empty node labels: FIXME
 tip.data <- data.frame(size=c(1,2,3), row.names=c("a", "b", "c"))

Modified: pkg/man/reorder-methods.Rd
===================================================================
--- pkg/man/reorder-methods.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/reorder-methods.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -61,7 +61,7 @@
  \code{\link{children}} \code{\link{descendants}}
 }
 \examples{
-phy <- phylo4(rtree(5))
+phy <- phylo4(ape::rtree(5))
 edges(reorder(phy, "preorder"))
 edges(reorder(phy, "postorder"))
 }

Modified: pkg/man/treewalk.Rd
===================================================================
--- pkg/man/treewalk.Rd	2014-03-17 13:14:12 UTC (rev 876)
+++ pkg/man/treewalk.Rd	2014-03-17 13:15:09 UTC (rev 877)
@@ -102,9 +102,6 @@
   shortestPath(geospiza, "fortis", "fuliginosa")
   shortestPath(geospiza, "F", "L")
 
-  ## FIXME
-  ## if(require(ape)){ edgelabels() }
-
   ## branch length from a tip to the root
   sumEdgeLength(geospiza, ancestors(geospiza, "fortis", type="ALL"))

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