[Mattice-commits] r128 - in pkg: man misc

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

Author: andrew_hipp
Date: 2008-12-30 16:14:26 +0100 (Tue, 30 Dec 2008)
New Revision: 128

Added:
   pkg/man/carex.Rd
Removed:
   pkg/misc/carex.Rd
Log:
moved carex.Rd back into pkg/man and updated object names

Added: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	                        (rev 0)
+++ pkg/man/carex.Rd	2008-12-30 15:14:26 UTC (rev 128)
@@ -0,0 +1,62 @@
+\name{carex}
+\alias{carex}
+\docType{data}
+\title{Carex section Ovales tree, chromosome data, and nodes}
+\description{
+  This is the Carex dataset used in Hipp (2007). It is a list with three items: a tree of 53 taxa for which chromosome
+  counts are known; a vector of log-transformed mean chromosome counts for all taxa; and a list of eight taxon vectors.
+}
+\usage{data(carex)}
+\format{
+  A list with three items:
+  \describe{
+    \item{ovales.tree}{
+     An ultrametric tree in \code{phylo} format with 53 tips
+     }
+    \item{ovales.data}{
+     A named numeric vector of log-transformed mean chromosome counts for all 53 taxa
+     }
+    \item{ovales.nodes}{
+     A list of eight taxon vectors defining the eight nodes studied.
+     }
+  }
+}
+\details{
+  \item{phylogeny}{
+  Phylogeny (\code{ovales.tree}) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using penalized likelihood
+  in \pkg{ape}, and then the tree was pruned down to only those taxa for which chromosome counts were available.
+  }
+  \item{chromosome counts}{
+  Chromosome counts (\code{ovales.data}) were averaged by population, and the means log-transformed for analysis.
+  }
+  \item{ovales.nodes}{
+  Eight nodes were selected for analysis based on clade support and number of taxa in the clade.
+  }
+}
+\source{
+  Hipp, A.L. (2007) 
+  Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). 
+  Evolution 61:2175-2194.
+}
+\references{
+  Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006) 
+  Phylogeny and classification of Carex section Ovales (Cyperaceae). 
+  International Journal of Plant Sciences 167:1029-1048.
+  
+  Hipp, A.L. (2007) 
+  Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). 
+  Evolution 61:2175-2194.
+}
+
+\examples{
+  data(carex)
+  attach(carex)
+  ovales.tree <- ape2ouch(ovales.tree) # tree comes in in \code{phylo} format, but we need an ouchtree object
+  trial <- runBatchHansen(ovales.tree, ovales.data, ovales.nodes, maxNodes = 3) # for expedience, only allows regime changes at up to 3 nodes
+  summary(trial) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
+  trialSim <- ouSim(trial, ovales.tree) # simulates the evolution of the chromosome number under the model-averaged values
+  plot(trialSim) # plots the character simulation, with all branches black
+  plot(trialSim, colors = paintBranches(ovales.nodes, ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
+  plot(trialSim, colors = paintBranches(list(ovales.nodes[[2]]), ovales.tree)) # plots the character simulation, with branch colors changing only at node 2
+}
+\author{Andrew L. Hipp <ahipp at mortonarb.org>}

Deleted: pkg/misc/carex.Rd
===================================================================
--- pkg/misc/carex.Rd	2008-12-30 15:09:36 UTC (rev 127)
+++ pkg/misc/carex.Rd	2008-12-30 15:14:26 UTC (rev 128)
@@ -1,62 +0,0 @@
-\name{carex}
-\alias{carex}
-\docType{data}
-\title{Carex section Ovales tree, chromosome data, and nodes}
-\description{
-  This is the Carex dataset used in Hipp (2007). It is a list with three items: a tree of 53 taxa for which chromosome
-  counts are known; a vector of log-transformed mean chromosome counts for all taxa; and a list of eight taxon vectors.
-}
-\usage{data(carex)}
-\format{
-  A list with three items:
-  \describe{
-    \item{tree}{
-     An ultrametric tree in \code{phylo} format with 53 tips
-     }
-    \item{dat}{
-     A named numeric vector of log-transformed mean chromosome counts for all 53 taxa
-     }
-    \item{nodes}{
-     A list of eight taxon vectors defining the eight nodes studied.
-     }
-  }
-}
-\details{
-  \item{phylogeny}{
-  Phylogeny (\code{tree}) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using penalized likelihood
-  in \pkg{ape}, and then the tree was pruned down to only those taxa for which chromosome counts were available.
-  }
-  \item{chromosome counts}{
-  Chromosome counts (\code{dat}) were averaged by population, and the means log-transformed for analysis.
-  }
-  \item{nodes}{
-  Eight nodes were selected for analysis based on clade support and number of taxa in the clade.
-  }
-}
-\source{
-  Hipp, A.L. (2007) 
-  Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). 
-  Evolution 61:2175-2194.
-}
-\references{
-  Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006) 
-  Phylogeny and classification of Carex section Ovales (Cyperaceae). 
-  International Journal of Plant Sciences 167:1029-1048.
-  
-  Hipp, A.L. (2007) 
-  Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). 
-  Evolution 61:2175-2194.
-}
-
-\examples{
-  data(carex)
-  carex$tree <- ape2ouch(carex$tree) # tree comes in in \code{phylo} format, but we need an ouchtree object
-  attach(carex)
-  trial <- runBatchHansen(tree, dat, nodes, maxNodes = 3) # for expedience, only allows regime changes at up to 3 nodes
-  summary(trial) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
-  trialSim <- ouSim(trial, tree) # simulates the evolution of the chromosome number under the model-averaged values
-  plot(trialSim) # plots the character simulation, with all branches black
-  plot(trialSim, colors = paintBranches(nodes, tree)) # plots the character simulation, with branch colors changing at all 8 nodes
-  plot(trialSim, colors = paintBranches(list(nodes[[2]]), tree)) # plots the character simulation, with branch colors changing only at node 2
-}
-\author{Andrew L. Hipp <ahipp at mortonarb.org>}