[Phylobase-commits] r164 - pkg/man

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

Author: pdc
Date: 2008-03-16 01:16:25 +0100 (Sun, 16 Mar 2008)
New Revision: 164

Modified:
   pkg/man/NexusToDataFrame.Rd
   pkg/man/NexusToPhylo4.Rd
   pkg/man/extract.tree.Rd
   pkg/man/geospiza.Rd
   pkg/man/hasSingles.Rd
   pkg/man/identify-methods.Rd
   pkg/man/multiPhylo-class.Rd
   pkg/man/nNodes-methods.Rd
Log:
reformat examples, now hopefully a touch more readable

Modified: pkg/man/NexusToDataFrame.Rd
===================================================================
--- pkg/man/NexusToDataFrame.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/NexusToDataFrame.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -12,7 +12,7 @@
    }
  }
  \usage{
-NexusToDataFrame(fileToRead,allchar=FALSE, polymorphictomissing=TRUE, levelsall=TRUE)
+NexusToDataFrame(fileToRead, allchar = FALSE, polymorphictomissing = TRUE, levelsall = TRUE)
 }
 \arguments{
   \item{fileToRead}{a Nexus file}
@@ -22,7 +22,7 @@
   if one character is missing a state}
 }
 \value{
-  A data.frame suitable to use with \linkS4class{phylo4d}.
+  A dataframe suitable to use with \linkS4class{phylo4d}.
 }
 \seealso{the \linkS4class{phylo4d} class, the \linkS4class{phylo4} class}
 \author{Brian O'Meara, Derrick Zwickl}

Modified: pkg/man/NexusToPhylo4.Rd
===================================================================
--- pkg/man/NexusToPhylo4.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/NexusToPhylo4.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -12,7 +12,7 @@
    }
  }
  \usage{
-NexusToPhylo4(fileToRead,multi=FALSE)
+NexusToPhylo4(fileToRead, multi = FALSE)
 }
 \arguments{
   \item{fileToRead}{a Nexus file}

Modified: pkg/man/extract.tree.Rd
===================================================================
--- pkg/man/extract.tree.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/extract.tree.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -8,7 +8,7 @@
 extract.tree(from)
 }
 \arguments{
-  \item{from}{ a \code{phylo4d} object, containing a phylogenetic tree plus associated phenotypic data. Created from \code{phylo4d() function}. }
+  \item{from}{ a \code{phylo4d} object, containing a phylogenetic tree plus associated phenotypic data. Created by the \code{phylo4d()} function. }
 }
 \details{
   \code{extract.tree} extracts just the phylogeny from a tree+data object. The phylogeny contains the topology (how the nodes are linked together), the branch lengths (if any), and any tip and/or node labels. This may be useful for extracting a tree from a \code{phylo4d} object, and associating with another phenotypic dataset, or to convert the tree to another format. 
@@ -16,14 +16,13 @@
 \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 <- 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"))
+tip.data <- data.frame(size = c(1, 2, 3), row.names = c("a", "b", "c"))
 treedata <- phylo4d(tree, tip.data)
 plot(treedata)
 print(treedata)
-
 tree1 <- extract.tree(treedata)
 print(tree1)
 }

Modified: pkg/man/geospiza.Rd
===================================================================
--- pkg/man/geospiza.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/geospiza.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -26,6 +26,6 @@
 }
 \examples{
 data(geospiza)
-plot(geospiza,adj=.4,cex.lab=.7,cex.sym=.8)
+plot(geospiza, adj = 0.4, cex.lab = 0.7, cex.sym = 0.8)
 }
 \keyword{datasets}

Modified: pkg/man/hasSingles.Rd
===================================================================
--- pkg/man/hasSingles.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/hasSingles.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -24,14 +24,14 @@
   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.)
 }
 \examples{
 library(ape)
 example(read.tree)
-owls4 = as(tree.owls.bis,"phylo4")
+owls4 = as(tree.owls.bis, "phylo4")
 hasPoly(owls4)
 hasSingles(owls4)
 }

Modified: pkg/man/identify-methods.Rd
===================================================================
--- pkg/man/identify-methods.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/identify-methods.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -13,7 +13,7 @@
     (or extensions)}
 }}
 \usage{
-    \S4method{identify}{phylo4}(x,n=1,\dots)
+    \S4method{identify}{phylo4}(x, n=1, \dots)
 }
 \arguments{
   \item{x}{a phylo4 object}

Modified: pkg/man/multiPhylo-class.Rd
===================================================================
--- pkg/man/multiPhylo-class.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/multiPhylo-class.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -59,7 +59,7 @@
   library(ape)
   example(read.tree)
   p1 = tree.owls
-  P1 = as(tree.owls,"phylo4")
+  P1 = as(tree.owls, "phylo4")
   P1
   sumryP1 = summary(P1)
   sumryP1

Modified: pkg/man/nNodes-methods.Rd
===================================================================
--- pkg/man/nNodes-methods.Rd	2008-03-16 00:13:33 UTC (rev 163)
+++ pkg/man/nNodes-methods.Rd	2008-03-16 00:16:25 UTC (rev 164)
@@ -92,7 +92,7 @@
 }
 }
 \section{usage}{
-  \S4method{tdata}{phylo4d}(x,which="tip",\dots)
+  \S4method{tdata}{phylo4d}(x, which = "tip", \dots)
 }
 \arguments{
   \item{which}{Which data to extract: "tip" (tips only), "node"