[Mattice-commits] r92 - in pkg: R man

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

Author: andrew_hipp
Date: 2008-12-17 23:54:46 +0100 (Wed, 17 Dec 2008)
New Revision: 92

Modified:
   pkg/R/batchHansen.R
   pkg/man/runBatchHansen.Rd
Log:
cleaning up runBatchHansen and its documentation

Modified: pkg/R/batchHansen.R
===================================================================
--- pkg/R/batchHansen.R	2008-12-17 22:45:13 UTC (rev 91)
+++ pkg/R/batchHansen.R	2008-12-17 22:54:46 UTC (rev 92)
@@ -82,8 +82,6 @@
     thetas[[i]] <- hb$thetas
     message(paste("Tree",i,"of",length(ouchTrees),"complete", "\n-----------------------------"))
   }
-    
-    ## right now no summary is returned; perhaps one is needed, summarizing over trees what is summarized for each tree in batchHansen
   outdata <- list(hansens = hansenBatch, thetas = thetas, regList = ar$regList, regMatrix = ar$regMatrix, nodeMatrix = ar$nodeMatrix, brown = brown, N = ouchTrees[[i]]@nterm, analysisDate = date(), call = match.call())
   class(outdata) <- 'hansenBatch'
   return(outdata)}

Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd	2008-12-17 22:45:13 UTC (rev 91)
+++ pkg/man/runBatchHansen.Rd	2008-12-17 22:54:46 UTC (rev 92)
@@ -59,20 +59,37 @@
 \value{
   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).
+    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())
+  \item{thetas} {
+    A list of vectors with a \code{theta} corresponding to each regime on the tree.
   }
+  \item{regList} {
+    A list indexed by tree of lists indexed by model, with the regime corresponding to each model on each tree. 
+  }
+  \item{regMatrix} {
+    The nodes by regimes matrix returned by \code{regimeMatrix} at the outset of analysis.
+  }
+  \item{nodeMatrix} {
+    A nodes by tree matrix, indicating for each tree which nodes are present.
+  }
+  \item{brown} {
+    A boolean vector of length one indicating whether the brownian motion model was fitted.
+  }
+  \item{N} {
+    The sample size (number of terminals on the trees).
+  }
+  \item{analysisDate} {
+    Data of analysis.
+  }
+  \item{call} {
+    Verbatim call to \code{runBatchHansen}.
+  }
+}
 \author{Andrew Hipp <ahipp at mortonarb.org>}
 \seealso{
    \code{\link{summary.hansenBatch}} for summarizing data