[Mattice-commits] r94 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-19 03:29:25 +0100 (Fri, 19 Dec 2008)
New Revision: 94

Added:
   pkg/man/isMonophyletic.Rd
   pkg/man/mrcaOUCH.Rd
   pkg/man/nodeDescendents.Rd
Modified:
   pkg/man/ouSim.Rd
   pkg/man/plot.ouSim.Rd
Log:
Added tree-traversal documentation; cleaned up ouSim and plot.ouSim documentation

Added: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd	                        (rev 0)
+++ pkg/man/isMonophyletic.Rd	2008-12-19 02:29:25 UTC (rev 94)
@@ -0,0 +1,22 @@
+\name{isMonophyletic}
+\alias{isMonophyletic}
+\title{Test whether a set of taxa is monophyletic on an ouch-style tree.}
+\usage{
+  isMonophyletic(tree, taxa)
+}
+\arguments{
+  \item{tree} {
+    An \code{ouchtree} object.
+    }
+  \item{taxa} {
+    A vector of taxon names.
+    }
+}
+\value{
+    Boolean, \code{TRUE} if taxa form a monophyletic group, \code{FALSE} if not.
+    }
+\author{Andrew Hipp ahipp at mortonarb.org}
+\seealso{
+   \code{\link{nodeDescendents}} \code{\link{mrcaOUCH}}
+}
+/keyword{tree}
\ No newline at end of file

Added: pkg/man/mrcaOUCH.Rd
===================================================================
--- pkg/man/mrcaOUCH.Rd	                        (rev 0)
+++ pkg/man/mrcaOUCH.Rd	2008-12-19 02:29:25 UTC (rev 94)
@@ -0,0 +1,30 @@
+\name{mrcaOUCH}
+\alias{mrcaOUCH}
+\title{Find the most recent common ancestor for a vector of taxa}
+\description {
+  Looks at the intersection of ancestor lines for all taxa in \code{cladeVector}, and returns the most recent as
+  the most recent common ancestor.
+}
+\details{
+  As written, a zero-length branch could cause the function to return something other than the m.r.c.a.; this will be
+  fixed in subsequent versions.
+}
+\usage {
+  mrcaOUCH(cladeVector, tree)
+}
+\arguments{
+  \item{cladeVector} {
+    A vector of tip labels.
+    }
+  \item{tree} {
+    An \code{ouchtree} object.
+    }
+}
+\value{
+  A single node label; one of the items in \code{tree at nodes}.
+}
+\author{Andrew Hipp ahipp at mortonarb.org}
+\seealso{
+   \code{\link{isMonophyletic}} \code{\link{nodeDescendents}}
+}
+/keyword{tree}
\ No newline at end of file

Added: pkg/man/nodeDescendents.Rd
===================================================================
--- pkg/man/nodeDescendents.Rd	                        (rev 0)
+++ pkg/man/nodeDescendents.Rd	2008-12-19 02:29:25 UTC (rev 94)
@@ -0,0 +1,26 @@
+\name{nodeDescendents}
+\alias{nodeDescendents}
+\title{Find all descendents of a node}
+\description {
+  Recursive function to find all the descendents of a node on an \code{ouchtree} object; returns only terminals, not
+  internal nodes descendent from \code{startNode}.
+}
+\usage {
+  nodeDescendents(tree, startNode) 
+}
+\arguments{
+  \item{tree} {
+    An \code{ouchtree} object.
+    }
+  \item{startNode} {
+    The node of interest; nomenclature follows \code{tree at nodes}.
+    }
+}
+\value{
+  A vector of tip labels.
+}
+\author{Andrew Hipp ahipp at mortonarb.org}
+\seealso{
+   \code{\link{isMonophyletic}} \code{\link{mrcaOUCH}}
+}
+/keyword{tree}
\ No newline at end of file

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2008-12-18 15:43:06 UTC (rev 93)
+++ pkg/man/ouSim.Rd	2008-12-19 02:29:25 UTC (rev 94)
@@ -110,4 +110,4 @@
   Phylogenetic comparative analysis: a modeling approach for adaptive evolution. 
   American Naturalist 164:683-695.
   }
-\keyword{models}
+\keyword{simulation}

Modified: pkg/man/plot.ouSim.Rd
===================================================================
--- pkg/man/plot.ouSim.Rd	2008-12-18 15:43:06 UTC (rev 93)
+++ pkg/man/plot.ouSim.Rd	2008-12-19 02:29:25 UTC (rev 94)
@@ -33,3 +33,4 @@
    \code{\link{ouSim}} for simulations
    \code{\link{carex}} for examples
 }
+\keyword{simulation}
\ No newline at end of file