[Phylobase-commits] r866 - pkg/man

[noreply at r-forge.r-project.org]

Author: francois
Date: 2014-03-14 21:30:07 +0100 (Fri, 14 Mar 2014)
New Revision: 866

Modified:
   pkg/man/as-methods.Rd
   pkg/man/phylobubbles.Rd
   pkg/man/phylomat-class.Rd
   pkg/man/tip.data.plot.Rd
Log:
fixing formatting to pass R check without NOTEs

Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2014-03-14 20:20:38 UTC (rev 865)
+++ pkg/man/as-methods.Rd	2014-03-14 20:30:07 UTC (rev 866)
@@ -111,7 +111,8 @@
 
 
 \examples{
-tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
+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)
 ## 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/phylobubbles.Rd
===================================================================
--- pkg/man/phylobubbles.Rd	2014-03-14 20:20:38 UTC (rev 865)
+++ pkg/man/phylobubbles.Rd	2014-03-14 20:30:07 UTC (rev 866)
@@ -4,10 +4,11 @@
 \title{Bubble plots for phylo4d objects }
 \description{
 Plots either circles or squares corresponding to the magnitude of each cell of a \code{phylo4d} object.}
-\usage{
-phylobubbles(type, place.tip.label, show.node.label, rot, edge.color, node.color, tip.color, edge.width, newpage, ..., XXYY, square = FALSE, grid = TRUE)
-}
 
+\usage{ phylobubbles(type, place.tip.label, show.node.label, rot,
+edge.color, node.color, tip.color, edge.width, newpage, ..., XXYY,
+square = FALSE, grid = TRUE) }
+
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{type}{the type of plot }

Modified: pkg/man/phylomat-class.Rd
===================================================================
--- pkg/man/phylomat-class.Rd	2014-03-14 20:20:38 UTC (rev 865)
+++ pkg/man/phylomat-class.Rd	2014-03-14 20:30:07 UTC (rev 866)
@@ -30,7 +30,8 @@
 }
 \author{Ben Bolker}
 \examples{
-   tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
+   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)
   o2 <- as(tree.owls,"phylo4")
   ov <- as(o2,"phylo4vcov")
   o3 <- as(ov,"phylo4")

Modified: pkg/man/tip.data.plot.Rd
===================================================================
--- pkg/man/tip.data.plot.Rd	2014-03-14 20:20:38 UTC (rev 865)
+++ pkg/man/tip.data.plot.Rd	2014-03-14 20:30:07 UTC (rev 866)
@@ -3,9 +3,13 @@
 \alias{tip.data.plot}
 \title{Plotting trees and associated data}
 \description{Plotting phylogenetic trees and associated data}
-\usage{
-tip.data.plot(xxyy, type = c("phylogram", "cladogram", "fan"), show.tip.label = TRUE, show.node.label = FALSE, rot = 0, tip.plot.fun = grid.points, edge.color = "black", node.color = "black", tip.color = "black", edge.width = 1, ...)
-}
+
+\usage{ tip.data.plot(xxyy, type = c("phylogram", "cladogram", "fan"),
+show.tip.label = TRUE, show.node.label = FALSE, rot = 0, tip.plot.fun =
+grid.points, edge.color = "black", node.color = "black", tip.color =
+"black", edge.width = 1, ...)  }
+
+
 \arguments{
   \item{xxyy}{A list created by the  \code{\link{phyloXXYY}} function}
   \item{type}{ A character string indicating the shape of plotted tree }