[Mattice-commits] r126 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-30 16:09:19 +0100 (Tue, 30 Dec 2008)
New Revision: 126

Modified:
   pkg/man/informationCriterion.Rd
   pkg/man/isMonophyletic.Rd
   pkg/man/ouSim.Rd
   pkg/man/summary.hansenBatch.Rd
Log:
fixing bracket problems; adding needed arguments to print and summary methods

Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd	2008-12-30 15:08:47 UTC (rev 125)
+++ pkg/man/informationCriterion.Rd	2008-12-30 15:09:19 UTC (rev 126)
@@ -3,15 +3,15 @@
 \alias{informationCriterion.hansenBatch}
 \alias{print.informationCriterion}
 \title{Information criterion and weights for a set of models}
-\description {
+\description{
   Returns AIC, AICc, and BIC values and weights for a set of models.
 }
-\usage {
+\usage{
   informationCriterion(u = NULL, lnL = NULL, K, n = 0, names = NULL)
   informationCriterion.hansenBatch(hansenBatch)
-  print.informationCriterion(ic)
+  print.informationCriterion(ic, ...)
 }
-\details {
+\details{
   At the minimum, a vector of either the model log-likelihoods (\code{lnL}) or deviances (\code{u} = -2 * lnL) and a vector
   of number of free parameters for each model (\code{K}) must be provided for the function to work. If the sample size
   (\code{n}) is not provided, the function calculates AICc and BIC assuming \code{n} = 1. Information criterion statistics

Modified: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd	2008-12-30 15:08:47 UTC (rev 125)
+++ pkg/man/isMonophyletic.Rd	2008-12-30 15:09:19 UTC (rev 126)
@@ -3,6 +3,9 @@
 \alias{mrcaOUCH}
 \alias{nodeDescendents}
 \title{Test whether a set of taxa is monophyletic on an ouch-style tree.}
+\description{
+  A somewhat clunky monophyly-checker for an \code{ouchtree} object
+}
 \usage{
   isMonophyletic(tree, taxa)
   nodeDescendents(tree, startNode)

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2008-12-30 15:08:47 UTC (rev 125)
+++ pkg/man/ouSim.Rd	2008-12-30 15:09:19 UTC (rev 126)
@@ -71,18 +71,18 @@
     and the strength of selection by Butler and King (2004). It is a multiplier by the difference between the character state and the
     character state optimum. Alpha can be submitted as a single value applied to all branches or as a vector corresponding to branches
     in the \code{phylo} object. At \code{alpha = 0}, the simulation approximates a Brownian motion process.
-    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate}, 
+    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate), 
     \code{hansenBatch} or \code{hansenSummary} (model-averaged).
     }
   \item{variance}{
     The variance on the stochastic portion of the Ornstein-Uhlenbeck model.
-    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate}, 
+    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate), 
     \code{hansenBatch} or \code{hansenSummary} (model-averaged).
     }
   \item{theta}{
     The character state optimum. \code{theta} can be submitted as a single value or, like \code{alpha}, 
     as a vector corresponding to branches of the tree.
-    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate}, 
+    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate), 
     \code{hansenBatch} or \code{hansenSummary} (model-averaged).
     }
   \item{model}{
@@ -102,7 +102,7 @@
   }
 \author{Andrew Hipp ahipp at mortonarb.org}
 \seealso{
-   \code{\link{plot.ouSim}} for visualizing simulation; \code{carex} for examples
+   \code{plot.ouSim} for visualizing simulation; \code{carex} for examples
 }
 \references{
   Hansen, T.F. (1997)

Modified: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd	2008-12-30 15:08:47 UTC (rev 125)
+++ pkg/man/summary.hansenBatch.Rd	2008-12-30 15:09:19 UTC (rev 126)
@@ -7,8 +7,8 @@
   \code{print.hansenSummary} is a print method for a \code{hansenSummary} object.
 }
 \usage{
-summary(hansenBatch)
-print(hansenSummary)
+summary(hansenBatch, ...)
+print(hansenSummary, ...)
 }
 \arguments{
   \item{hansenBatch}{