[Mattice-commits] r91 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-17 23:45:13 +0100 (Wed, 17 Dec 2008)
New Revision: 91

Added:
   pkg/man/print.hansenSummary.Rd
   pkg/man/summary.hansenBatch.Rd
Modified:
   pkg/man/carex.Rd
   pkg/man/runBatchHansen.Rd
Log:
summary.hansenBatch documentation

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2008-12-17 15:45:46 UTC (rev 90)
+++ pkg/man/carex.Rd	2008-12-17 22:45:13 UTC (rev 91)
@@ -44,10 +44,10 @@
 
 \examples{
   data(carex)
-  carex$tree <- ape2ouch(carex$tree) # tree comes in in \code{phylo} format, but we need an \code{ouchtree} object
+  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)
+  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

Added: pkg/man/print.hansenSummary.Rd
===================================================================
--- pkg/man/print.hansenSummary.Rd	                        (rev 0)
+++ pkg/man/print.hansenSummary.Rd	2008-12-17 22:45:13 UTC (rev 91)
@@ -0,0 +1,22 @@
+\name{print.hansenSummary}
+\alias{print.hansenSummary}
+\title{Print method for a hansenSummary object}
+\description{
+  \code{print.hansenSummary} is a print method for a \code{hansenSummary} object.
+}
+\usage{
+print(hansenSummary)
+}
+\arguments{
+  \item{hansenSummary}{
+  Output from \code{summary.hansenBatch}.
+  }
+}
+\details{
+    This function provides an easy-to-read synopsis of the analysis summary. Called automatically when you simply type
+    in the name of the summary object.
+}
+\author{Andrew Hipp <ahipp at mortonarb.org>}
+\examples{
+## See \code{\link{carex}} for example
+}

Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	2008-12-17 15:45:46 UTC (rev 90)
+++ pkg/man/runBatchHansen.Rd	2008-12-17 22:45:13 UTC (rev 91)
@@ -75,8 +75,7 @@
   }
 \author{Andrew Hipp <ahipp at mortonarb.org>}
 \seealso{
-   \code{\link{batchHansen}} for running analysis on a single tree under an explicit regime,
-   \code{\link{summary.hansenBatch}} for summarizing data.
+   \code{\link{summary.hansenBatch}} for summarizing data
    \code{\link{carex}} for an example
 }
 \examples{

Added: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd	                        (rev 0)
+++ pkg/man/summary.hansenBatch.Rd	2008-12-17 22:45:13 UTC (rev 91)
@@ -0,0 +1,52 @@
+\name{summary.hansenBatch}
+\alias{summary.hansenBatch}
+\title{Summarize output from runBatchHansen}
+\description{
+  \code{summary.hansenBatch} is a summary method for a \code{hansenBatch} object.
+}
+\usage{
+summary(hansenBatch)
+}
+\arguments{
+  \item{hansenBatch}{
+  Output from \code{runBatchHansen}.
+  }
+}
+\details{
+    This function averages parameters over models and over trees, and provides the cumulative information-criterion weight
+    for models containing each node as an estimate of the support for the hypothesis that there was a character shift
+    at that node.
+}
+\value{
+  A list of class \code{hansenSummary} with the following items:
+  \item{modelsMatrix} {
+    A list of matrices, indexed by tree, providing the information criterion weights for each model.
+  }
+  \item{nodeWeightsMatrix} {
+    A list of length two with two matrices: 
+    \item{unnormalized} {
+      The cumulative information criterion weight for each node, averaged only over trees that possess that node
+      }
+    \item{allNodes} {
+      The cumulative information criterion weight for each node, averaged over all trees.
+      }
+    }
+  \item{modelAvgAlpha} {
+    The model-averaged estimate of \code{alpha}, the rate of evolution toward the equilibrium / optimum
+    }
+  \item{modelAvgSigmaSq} {
+    The model-averaged estimate of \code{sigma.squared}, the variance or rate of stochastic evolution.
+    }
+  \item{thetaMatrix} {
+    A matrix with trees as the rows, branch number as the columns, containing the model-averaged value of \code{theta} 
+    (the character equilibrium or optimum value) for each branch on each tree
+    }
+  }
+\author{Andrew Hipp <ahipp at mortonarb.org>}
+\seealso{
+   \code{\link{print.hansenSummary}} for a readable screen output summarizing most of the above
+   \code{\link{carex}} for an example
+}
+\examples{
+## See \code{\link{carex}} for example
+}