[Ecopd-commits] r74 - branches/single-tree/man

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

Author: regetz
Date: 2009-11-17 06:14:23 +0100 (Tue, 17 Nov 2009)
New Revision: 74

Added:
   branches/single-tree/man/phylo4com-class.Rd
Log:
added skeleton documentation for phylo4com class


Added: branches/single-tree/man/phylo4com-class.Rd
===================================================================
--- branches/single-tree/man/phylo4com-class.Rd	                        (rev 0)
+++ branches/single-tree/man/phylo4com-class.Rd	2009-11-17 05:14:23 UTC (rev 74)
@@ -0,0 +1,33 @@
+\name{phylo4com-class}
+\docType{class}
+\alias{phylo4com-class}
+
+\title{phylo4com class}
+\description{S4 class for community phylogenies.}
+\section{Objects from the Class}{
+  Objects can be created from trees and community-specific abundance
+  data using various forms of the \code{phylo4d} constructor, or using
+  \code{new("phylo4com", \dots)} for empty objects.
+}
+\section{Slots}{
+  \describe{
+    \item{\code{edge}:}{Matrix of edges}
+    \item{\code{edge.label}:}{Character vector of edge (branch) labels}
+    \item{\code{edge.length}:}{Numeric vector of edge (branch) lengths}
+    \item{\code{label}:}{Character vector of tip (and optionally
+      internal node) labels}
+    \item{\code{data}:}{data frame for traits of tips and internal nodes}
+    \item{\code{subtrees}:}{list of subset trees corresponding to
+      individual communities}
+    \item{\code{order}:}{character: tree ordering}
+    \item{\code{annote}:}{annotation data for tree (currently
+      unstructured/unused by methods)}
+    \item{\code{metadata}:}{metadata for node/tip data (currently
+      used to store some community information)}
+  }
+}
+\author{Jim Regetz}
+\examples{
+  showClass("phylo4com")
+}
+\keyword{classes}


Property changes on: branches/single-tree/man/phylo4com-class.Rd
___________________________________________________________________
Name: svn:eol-style
   + native