[Mattice-commits] r48 - pkg/man

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

Author: andrew_hipp
Date: 2008-11-20 22:47:43 +0100 (Thu, 20 Nov 2008)
New Revision: 48

Added:
   pkg/man/runBatchHansen.Rd
Modified:
   pkg/man/ouSim.Rd
Log:
added preliminary documentation for runBatchHansen; expanded ouSim.Rd

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2008-11-20 20:19:03 UTC (rev 47)
+++ pkg/man/ouSim.Rd	2008-11-20 21:47:43 UTC (rev 48)
@@ -51,6 +51,9 @@
     to run the simulation; and return results that are scaled correctly for the tree (I believe at this point that the 
     sigma and alpha parameters don't return results that match the distributions you get using \code{simulate} on a \code{hansentree}
     or \code{browntree} object, which you should.
+    
+    To do: split ouSim into two functions, one handling an \code{ape} format tree and the other handling an \code{ouchtree}
+    object, with the option in the latter case of catching a \code{hansentree} or \code{browntree} as discussed above.
 }
 \value{
   A list of class 'ouSim' that describes the phenotype at the beginning and end of each branch segment, as well as the model.

Added: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	                        (rev 0)
+++ pkg/man/runBatchHansen.Rd	2008-11-20 21:47:43 UTC (rev 48)
@@ -0,0 +1,53 @@
+\name{runBatchHansen}
+\alias{runBatchHansen}
+\title{Analyze Ornstein-Uhlenbeck models over a set of trees, with changes in regime corresponding to permutations
+       of the nodes fed to it.}
+\description{
+  \code{runBatchHansen} simulates the evolution of a single character on an \code{ape}-style user tree under arbitrarily
+  complex Ornstein-Uhlenbeck models.
+}
+\usage{
+runBatchHansen(ouchTrees, characterStates, cladeMembersList, nodeNames = NULL, maxNodes = NULL, regimeTitles = NULL, brown = F, rescale = 1, ...)}
+\arguments{
+  \item{ouchTrees}{
+
+  }
+  \item{characterStates}{
+
+  }
+  \item{cladeMembersList}{
+
+    }
+  \item{nodeNames}{
+
+    }
+  \item{maxNodes}{
+    }
+  \item{regimeTitles}{
+
+    }
+  \item{brown}{
+
+    }
+  \item{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}.
+    }
+}
+\details{
+    This function is the primary function for estimating the 
+}
+\value{
+  XXX
+  }
+\author{Andrew Hipp ahipp at mortonarb.org}
+\seealso{
+   \code{batchHansen} running analysis on a single tree, \code{summary.hansenBatch} for summarizing data.
+}
+\examples{
+XXX
+}
+\keyword{models}