[Mattice-commits] r105 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-22 19:04:32 +0100 (Mon, 22 Dec 2008)
New Revision: 105

Removed:
   pkg/man/mrcaOUCH.Rd
   pkg/man/nodeDescendents.Rd
Modified:
   pkg/man/isMonophyletic.Rd
Log:
mrcaOUCH and nodeDescendents now documented in isMonophyletic.Rd

Modified: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd	2008-12-22 17:23:48 UTC (rev 104)
+++ pkg/man/isMonophyletic.Rd	2008-12-22 18:04:32 UTC (rev 105)
@@ -1,8 +1,12 @@
 \name{isMonophyletic}
 \alias{isMonophyletic}
+\alias{mrcaOUCH}
+\alias{nodeDescendents}
 \title{Test whether a set of taxa is monophyletic on an ouch-style tree.}
 \usage{
   isMonophyletic(tree, taxa)
+  nodeDescendents(tree, startNode)
+  mrcaOUCH(cladeVector, tree)
 }
 \arguments{
   \item{tree}{
@@ -11,11 +15,22 @@
   \item{taxa}{
     A vector of taxon names.
     }
+  \item{startNode}{
+    The node of interest; nomenclature follows \code{tree at nodes}.
+    }
+  \item{cladeVector}{
+    A vector of tip labels.
+    }
 }
 \value{
-    Boolean, \code{TRUE} if taxa form a monophyletic group, \code{FALSE} if not.
+    \item{isMonophyletic}{
+    Boolean, TRUE if taxa form a monophyletic group, FALSE if not.
     }
+    \item{mrcaOUCH}{
+    A single node label; one of the items in \code{tree at nodes}.
+    }
+    \item{nodeDescendents}{
+    A vector of tip labels.
+    }
+  }
 \author{Andrew Hipp ahipp at mortonarb.org}
-\seealso{
-   \code{\link{nodeDescendents}}; \code{\link{mrcaOUCH}}
-}

Deleted: pkg/man/mrcaOUCH.Rd
===================================================================
--- pkg/man/mrcaOUCH.Rd	2008-12-22 17:23:48 UTC (rev 104)
+++ pkg/man/mrcaOUCH.Rd	2008-12-22 18:04:32 UTC (rev 105)
@@ -1,29 +0,0 @@
-\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}}
-}

Deleted: pkg/man/nodeDescendents.Rd
===================================================================
--- pkg/man/nodeDescendents.Rd	2008-12-22 17:23:48 UTC (rev 104)
+++ pkg/man/nodeDescendents.Rd	2008-12-22 18:04:32 UTC (rev 105)
@@ -1,25 +0,0 @@
-\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}}
-}