[Mattice-commits] r204 - pkg/man

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

Author: andrew_hipp
Date: 2009-08-27 16:26:42 +0200 (Thu, 27 Aug 2009)
New Revision: 204

Modified:
   pkg/man/carex.Rd
   pkg/man/ouSim.Rd
   pkg/man/summary.hansenBatch.Rd
Log:
Correcting three small formatting errors in documentation files

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2009-08-26 03:23:17 UTC (rev 203)
+++ pkg/man/carex.Rd	2009-08-27 14:26:42 UTC (rev 204)
@@ -9,6 +9,7 @@
 \usage{data(carex)}
 \format{
   A list with four items:
+  \itemize{
     \item{\code{ovales.tree}}{
      An ultrametric tree in \code{phylo} format with 53 tips
      }
@@ -22,6 +23,7 @@
      A list of 100 ultrametric trees in \code{phylo} format, subsampled from the MCMC analysis underlying 
      \code{carex$ovales.bayesTrees}.
      }
+  }
 }
 \details{
   Phylogeny (\code{ovales.tree}) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2009-08-26 03:23:17 UTC (rev 203)
+++ pkg/man/ouSim.Rd	2009-08-27 14:26:42 UTC (rev 204)
@@ -22,6 +22,7 @@
 }
 \details{
   A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
+  \itemize{
   \item{\code{phylo}}{
     With an \pkg{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
     
@@ -56,6 +57,7 @@
     this simulation method is really a heuristic device, not appropriate for estimating parameter distributions. For
     analysis purposes, you should utilize the \code{simulate} and \code{bootstrap} methods in \pkg{ouch}.
   }
+  }
 }
 \arguments{
   \item{object}{

Modified: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd	2009-08-26 03:23:17 UTC (rev 203)
+++ pkg/man/summary.hansenBatch.Rd	2009-08-27 14:26:42 UTC (rev 204)
@@ -35,6 +35,7 @@
   }
   \item{nodeWeightsMatrix}{
     A list of length two with two matrices: 
+    \itemize{
     \item{unnormalized}{
       The cumulative information criterion weight for each node, averaged only over trees that possess that node
       }
@@ -42,6 +43,7 @@
       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
     }