[Mattice-commits] r90 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-17 16:45:46 +0100 (Wed, 17 Dec 2008)
New Revision: 90

Modified:
   pkg/man/runBatchHansen.Rd
Log:
cleaning up documentation

Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	2008-12-17 15:30:23 UTC (rev 89)
+++ pkg/man/runBatchHansen.Rd	2008-12-17 15:45:46 UTC (rev 90)
@@ -6,7 +6,8 @@
   complex Ornstein-Uhlenbeck models.
 }
 \usage{
-runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = NULL, regimeTitles = NULL, brown = F, rescale = 1, ...)}
+runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = F, ...)
+}
 \arguments{
   \item{ouchTrees}{
 	A list of \code{ouchtree} style trees, or a single tree
@@ -14,24 +15,25 @@
   \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. 
+	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.
+	node must by defined by all tips descendent from that node
     }
   \item{filePrefix}{
   	A file prefix for saving hansen objects. If left at default (\code{NULL}), no hansen objects will be saved. Typically 
-  	this is fine, but if you want to extract parameters from the hansen objects, or do any bootstrapping, you'll need these.
+  	this is fine, but if you want to extract parameters from individual hansen objects, or do any bootstrapping, 
+  	it is helpful to save the individual analyses.
     }
   \item{di}{
 	A directory in which to save hansen objects. Not required, but strongly recommended if you are saving hansen objects.  
     }
   \item{nodeNames}{
-	A vector of names for the nodes being analyzed. Not implemented. Optional.
+	A vector of names for the nodes being analyzed. Not implemented.
     }
   \item{maxNodes}{
-  	The maximum number of nodes at which the regime is allowed to change. Optional.
+  	The maximum number of nodes at which the regime is allowed to change. Defaults to the number of nodes specified.
     }
   \item{regimeTitles}{
 	Names for regimes; only enter if you know how many regimes you will be getting and have reason to name them. Optional.
@@ -39,13 +41,9 @@
   \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.
+    Arguments passed along to \code{hansen}. As written now, \code{sigma} and \code{alpha} are set at 1
+    for the optimizer to begin with. Other arguments are described in documentation for \code{hansen}.
     }
 }
 \details{
@@ -59,14 +57,28 @@
         such that all nodes are present in the same number of models.
 }
 \value{
-  XXX
+  A list of class \code{hansenBatch} with the following items:
+  \item{hansens} {
+  A matrix with rows equal to the number of models analyzed, and four columns: \code{loglik} = log-likelihood of the model;
+  \code{dof} = number of free parameters in the model; \code{sigma.squared} = estimate of the variance parameter;
+  \code{theta / alpha} = estimate of either the root character state (for the brownian motion model) or the \code{alpha}
+  parameter (for Ornstein-Uhlenbeck models).
   }
+  thetas = thetas
+  regList = ar$regList
+  regMatrix = ar$regMatrix
+  nodeMatrix = ar$nodeMatrix
+  brown = brown
+  N = ouchTrees[[i]]@nterm
+  analysisDate = date()
+  call = match.call())
+  }
 \author{Andrew Hipp <ahipp at mortonarb.org>}
 \seealso{
-   \code{batchHansen} for running analysis on a single tree under an explicit regime,
-   \code{summary.hansenBatch} for summarizing data.
+   \code{\link{batchHansen}} for running analysis on a single tree under an explicit regime,
+   \code{\link{summary.hansenBatch}} for summarizing data.
+   \code{\link{carex}} for an example
 }
 \examples{
-XXX
+## See \code{\link{carex}} for example
 }
-\keyword{models}