[Mattice-commits] r169 - pkg/man

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

Author: andrew_hipp
Date: 2009-02-24 04:09:40 +0100 (Tue, 24 Feb 2009)
New Revision: 169

Modified:
   pkg/man/informationCriterion.Rd
   pkg/man/ouSim.Rd
   pkg/man/plot.ouSim.Rd
   pkg/man/runBatchHansen.Rd
   pkg/man/summary.hansenBatch.Rd
Log:
fixing documentation files


Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd	2009-02-24 02:11:07 UTC (rev 168)
+++ pkg/man/informationCriterion.Rd	2009-02-24 03:09:40 UTC (rev 169)
@@ -32,10 +32,10 @@
      Optional vector of model names, indexed by model.
      }
    \item{hansenBatch}{
-     Output from \{runBatchHansen}.
+     Output from \code{runBatchHansen}.
      }
    \item{x}{
-     Output from \{informationCriterion}.
+     Output from \code{informationCriterion}.
      }
    \item{...}{
      Additional arguments to be passed along to \code{print}

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2009-02-24 02:11:07 UTC (rev 168)
+++ pkg/man/ouSim.Rd	2009-02-24 03:09:40 UTC (rev 169)
@@ -13,12 +13,12 @@
 }
 \usage{
   ouSim(object, ...)
-  ouSim.phylo(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...)
-  ouSim.ouchtree(object, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
-  ouSim.browntree(object, ...)
-  ouSim.hansentree(object, ...)
-  ouSim.hansenBatch(object, ...)
-  ouSim.hansenSummary(object, tree, treeNum = 1, rootState = NULL, ...) 
+  \method{ouSim}{phylo}(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...)
+  \method{ouSim}{ouchtree}(object, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
+  \method{ouSim}{browntree}(object, ...)
+  \method{ouSim}{hansentree}(object, ...)
+  \method{ouSim}{hansenBatch}(object, ...)
+  \method{ouSim}{hansenSummary}(object, tree, treeNum = 1, rootState = NULL, ...) 
 }
 \details{
   A call to \code{ouSim} detects the class of \code{object} and behaves as follows:

Modified: pkg/man/plot.ouSim.Rd
===================================================================
--- pkg/man/plot.ouSim.Rd	2009-02-24 02:11:07 UTC (rev 168)
+++ pkg/man/plot.ouSim.Rd	2009-02-24 03:09:40 UTC (rev 169)
@@ -5,7 +5,7 @@
   \code{plot.ouSim} is a \code{plot} method for an \code{ouSim} object.
 }
 \usage{
-  plot.ouSim(x, nodeColor = "blue", nodeDotSize = 1.4, colors = NULL, ...)
+  \method{plot}{ouSim}(x, nodeColor = "blue", nodeDotSize = 1.4, colors = NULL, ...)
 }
 \arguments{
   \item{x}{
@@ -30,5 +30,5 @@
 }
 \author{Andrew Hipp ahipp at mortonarb.org}
 \seealso{
-   \code{\link{ouSim}} for simulations; \code{carex} for examples
+   \code{\link{ouSim}} for simulations; \code{\link{carex}} for examples
 }

Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	2009-02-24 02:11:07 UTC (rev 168)
+++ pkg/man/runBatchHansen.Rd	2009-02-24 03:09:40 UTC (rev 169)
@@ -92,5 +92,5 @@
 }
 \author{Andrew Hipp <ahipp at mortonarb.org>}
 \seealso{
-   \code{\link{summary.hansenBatch}} for summarizing data; \code{carex} for an example
+   \code{\link{summary.hansenBatch}} for summarizing data; \code{\link{carex}} for an example
 }

Modified: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd	2009-02-24 02:11:07 UTC (rev 168)
+++ pkg/man/summary.hansenBatch.Rd	2009-02-24 03:09:40 UTC (rev 169)
@@ -7,8 +7,8 @@
   \code{print.hansenSummary} is a print method for a \code{hansenSummary} object.
 }
 \usage{
-summary.hansenBatch(object, ...)
-print.hansenSummary(x, ...)
+  \method{summary}{hansenBatch}(object, ...)
+  \method{print}{hansenSummary}(x, ...)
 }
 \arguments{
   \item{object}{