[Mattice-commits] r56 - pkg/man

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

Author: andrew_hipp
Date: 2008-11-25 00:32:37 +0100 (Tue, 25 Nov 2008)
New Revision: 56

Modified:
   pkg/man/runBatchHansen.Rd
Log:
small additions to runBatchHansen.Rd

Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	2008-11-24 23:26:58 UTC (rev 55)
+++ pkg/man/runBatchHansen.Rd	2008-11-24 23:32:37 UTC (rev 56)
@@ -10,31 +10,36 @@
 runBatchHansen(ouchTrees, characterStates, cladeMembersList, nodeNames = NULL, maxNodes = NULL, regimeTitles = NULL, brown = F, rescale = 1, ...)}
 \arguments{
   \item{ouchTrees}{
-
+	A list of \code{ouchtree} style trees, or a single tree
   }
   \item{characterStates}{
-
+	A vector of character states to analyze. As written, the function accepts a named vector, with names corresponding to 
+	tip names in the trees, a vector of length equal to the number of terminal branches, or a vector of length equal
+	to the number of nodes in the trees. 
   }
   \item{cladeMembersList}{
-
+	A list of tip-name vectors, each defining a node of interest in the tree. Because these vectors are checked for monophyly on each tree, each
+	node must by defined by all tips descendent from that node.
     }
   \item{nodeNames}{
-
+	A vector of names for the nodes being analyzed. Not implemented. Optional.
     }
   \item{maxNodes}{
+  	The maximum number of nodes at which the regime is allowed to change. Optional.
     }
   \item{regimeTitles}{
-
+	Names for regimes; only enter if you know how many regimes you will be getting and have reason to name them. Optional.
     }
   \item{brown}{
-
+	Enter \code{T} or \code{F} according to whether you want to run the Brownian motion model.
     }
   \item{rescale}
-
+	Enter a value > 0 to rescale all trees to length = \code{rescale}.
     }
   \item{...}
     Arguments passed along to \code{hansen}. As written now, you have to include a beginning value for \code{sigma}
     and \code{alpha} for the optimizer to begin with. Other arguments are described in documentation for \code{hansen}.
+    To begin, it is easiest to set \code{sigma} = 1, \code{alpha} = 1.
     }
 }
 \details{
@@ -45,7 +50,8 @@
   }
 \author{Andrew Hipp ahipp at mortonarb.org}
 \seealso{
-   \code{batchHansen} running analysis on a single tree, \code{summary.hansenBatch} for summarizing data.
+   \code{batchHansen} for running analysis on a single tree under an explicit regime,
+   \code{summary.hansenBatch} for summarizing data.
 }
 \examples{
 XXX