[Mattice-commits] r260 - pkg/man

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

Author: andrew_hipp
Date: 2013-01-02 14:04:22 +0100 (Wed, 02 Jan 2013)
New Revision: 260

Modified:
   pkg/man/carex.Rd
   pkg/man/ouSim.Rd
Log:
updating documentation and example timing to meet package requirements

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2012-11-20 20:57:12 UTC (rev 259)
+++ pkg/man/carex.Rd	2013-01-02 13:04:22 UTC (rev 260)
@@ -49,9 +49,9 @@
 \examples{
   data(carex)
   # tree comes in in phylo format, but we need an ouchtree object
-  trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch) 
+  trees <- lapply(carex$ovales.bayesTrees[1:2], ape2ouch) 
   contree <- ape2ouch(carex$ovales.tree)
-  # for expedience, only tests for changes at up to 2 of the first 4 nodes on 10 trees visited in the MCMC phylogenetic analysis
+  # for expedience, only tests for changes at up to 2 of the first 4 nodes on 2 trees visited in the MCMC phylogenetic analysis
   trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) 
   summary(trialBayesTrees) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
   # same analysis as above, but on a single tree

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2012-11-20 20:57:12 UTC (rev 259)
+++ pkg/man/ouSim.Rd	2013-01-02 13:04:22 UTC (rev 260)
@@ -13,8 +13,8 @@
 }
 \usage{
   ouSim(object, ...)
-  \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}{phylo}(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, sqrt.alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...)
+  \method{ouSim}{ouchtree}(object, rootState = 0, sqrt.alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
   \method{ouSim}{browntree}(object, ...)
   \method{ouSim}{hansentree}(object, ...)
   \method{ouSim}{hansenBatch}(object, ...)
@@ -77,12 +77,12 @@
     For a \code{phylo} tree only. An optional vector of length = \code{length(shiftStates)} indicating 
     the ancestral states for the branches at which the state shifts.
     }
-  \item{alpha}{
+  \item{sqrt.alpha}{
     The rate of evolution toward an equilibrium or optimum. This term is refered to as the rate of evolution by Hansen (1997)
     and the strength of selection by Butler and King (2004). It is a multiplier by the difference between the character state and the
     character state optimum. Alpha can be submitted as a single value applied to all branches or as a vector corresponding to branches
-    in the \code{phylo} object. At \code{alpha = 0}, the simulation approximates a Brownian motion process.
-    This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate), 
+    in the \code{phylo} object. At \code{sqrt.alpha = 0}, the simulation approximates a Brownian motion process.
+    This parameter is taken from the analysis results for \code{browntree} (\code{sqrt.alpha} = 0), \code{hansentree} (point estimate), 
     \code{hansenBatch} or \code{hansenSummary} (model-averaged).
     }
   \item{variance}{