[Ecopd-commits] r72 - branches/single-tree/man

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

Author: regetz
Date: 2009-11-17 05:19:10 +0100 (Tue, 17 Nov 2009)
New Revision: 72

Added:
   branches/single-tree/man/phylo4com.Rd
Removed:
   branches/single-tree/man/ecophylo.Rd
Log:
renamed documentation file for phylo4com constructor


Deleted: branches/single-tree/man/ecophylo.Rd
===================================================================
--- branches/single-tree/man/ecophylo.Rd	2009-11-17 04:18:08 UTC (rev 71)
+++ branches/single-tree/man/ecophylo.Rd	2009-11-17 04:19:10 UTC (rev 72)
@@ -1,46 +0,0 @@
-\name{ecophylo}
-\alias{phylo4com}
-\title{Create list of community phylogenies}
-\description{
-  Function to combine species abundance data with phylogenetic
-  information for a set of communities.
-}
-\usage{
-  phylo4com(communityID, species, abundance, tree,
-    missing=c("warn", "OK", "fail"))
-}
-\arguments{
-  \item{communityID}{Vector of community identifiers.}
-  \item{species}{Vector of species names; must correspond to tip labels
-    of the supplied tree.}
-  \item{abundance}{Numeric vector of abundances of each species in each
-    community.}
-  \item{tree}{A \code{phylo4} object (or one that inherits from it).}
-  \item{missing}{(not currently implemented) What to do if some
-    requested node IDs or names are not in the tree: warn, do nothing,
-    or stop with an error.}
-}
-\details{
-  TODO
-
-  If the species vector contains values that do not appear in the tree,
-  they are ignored with a warning. If a community has fewer than one
-  species matched in the tree, an error will result. In both cases, the
-  behavior is simply a result of how the phylobase \code{subset} method
-  works; see the help page for this method for more information.
-}
-\value{
-  A list of \code{phylo4d} objects, one per unique value in the
-  \code{communityID} vector. List element names are taken from the
-  \code{communityID} vector.
-}
-\author{Jim Regetz (regetz at nceas.ucsb.edu)}
-\seealso{
-  \code{\link[phylobase]{subset}} in the phylobase package
-}
-\examples{
-  ##TODO -- contruction example
-  # Example of a phylo4com result
-  data(weeds)
-  print(weeds)
-}

Copied: branches/single-tree/man/phylo4com.Rd (from rev 54, branches/single-tree/man/ecophylo.Rd)
===================================================================
--- branches/single-tree/man/phylo4com.Rd	                        (rev 0)
+++ branches/single-tree/man/phylo4com.Rd	2009-11-17 04:19:10 UTC (rev 72)
@@ -0,0 +1,46 @@
+\name{ecophylo}
+\alias{phylo4com}
+\title{Create list of community phylogenies}
+\description{
+  Function to combine species abundance data with phylogenetic
+  information for a set of communities.
+}
+\usage{
+  phylo4com(communityID, species, abundance, tree,
+    missing=c("warn", "OK", "fail"))
+}
+\arguments{
+  \item{communityID}{Vector of community identifiers.}
+  \item{species}{Vector of species names; must correspond to tip labels
+    of the supplied tree.}
+  \item{abundance}{Numeric vector of abundances of each species in each
+    community.}
+  \item{tree}{A \code{phylo4} object (or one that inherits from it).}
+  \item{missing}{(not currently implemented) What to do if some
+    requested node IDs or names are not in the tree: warn, do nothing,
+    or stop with an error.}
+}
+\details{
+  TODO
+
+  If the species vector contains values that do not appear in the tree,
+  they are ignored with a warning. If a community has fewer than one
+  species matched in the tree, an error will result. In both cases, the
+  behavior is simply a result of how the phylobase \code{subset} method
+  works; see the help page for this method for more information.
+}
+\value{
+  A list of \code{phylo4d} objects, one per unique value in the
+  \code{communityID} vector. List element names are taken from the
+  \code{communityID} vector.
+}
+\author{Jim Regetz (regetz at nceas.ucsb.edu)}
+\seealso{
+  \code{\link[phylobase]{subset}} in the phylobase package
+}
+\examples{
+  ##TODO -- contruction example
+  # Example of a phylo4com result
+  data(weeds)
+  print(weeds)
+}