[Mattice-commits] r46 - pkg/man

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

Author: amesclir
Date: 2008-11-20 21:08:18 +0100 (Thu, 20 Nov 2008)
New Revision: 46

Modified:
   pkg/man/ouSim.Rd
Log:
Updated documentation for ouSim.Rd, indicating what kind of simulations it allows

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2008-11-20 12:40:08 UTC (rev 45)
+++ pkg/man/ouSim.Rd	2008-11-20 20:08:18 UTC (rev 46)
@@ -1,59 +1,59 @@
-\name{ouSim}
-\alias{ouSim}
-\title{Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree.}
-\description{
-  \code{ouSim} simulates the evolution of a single character on an \code{ape}-style user tree under arbitrarily
-  complex Ornstein-Uhlenbeck models.
-}
-\usage{
-(phy, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000)
-}
-\arguments{
-  \item{phy}{
-    An object of class \code{phylo}.
-  }
-  \item{rootState}{
-    The character state at the root of the tree
-  }
-  \item{shiftBranches}{
-    An optional vector indicating any branches at which an OU model has a determined shift in ancestral state. 
-    Same order as \code{shiftStates}. This argument and \code{shiftStates} are only needed if you want to specify a model with
-    a disjunction in phenotype, similar to restarting evolution at a new point.
-    }
-  \item{shiftStates}{
-    An optional vector of length = \code{length(shiftStates)} indicating the ancestrat states for the branches at which the state shifts.
-    }
-  \item{alpha}{
-    The strength of attraction 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.
-    }
-  \item{variance}{
-    The variance on the stochastic portion of the Ornstein-Uhlenbeck model.
-    }
-  \item{theta}{
-    The character state optimum. \code{theta} can be submitted as a single value or, like \code{alpha}, as a vector corresponding to
-    branches of the tree.
-    }
-  \item{branchMeans}
-    The mean for each branch, utilized only in the Platt model. 
-    }
-  \item{steps}
-    The number of slices into which the tree is divided for simulation.
-    }
-}
-\details{
-    XXX
-}
-\value{
-  A list of class 'ouSim' that describes the phenotype at the beginning and end of each branch segment, as well as the model.
-  }
-\author{Andrew Hipp ahipp at mortonarb.org}
-\seealso{
-   \code{plot.ouSim} for visualizing simulation
-}
-\examples{
-XXX
-}
-\keyword{models}
+\name{ouSim}
+\alias{ouSim}
+\title{Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree.}
+\description{
+  \code{ouSim} simulates the evolution of a single character on an \code{ape}-style user tree under arbitrarily
+  complex Ornstein-Uhlenbeck models.
+}
+\usage{
+(phy, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000)
+}
+\arguments{
+  \item{phy}{
+    An object of class \code{phylo}.
+  }
+  \item{rootState}{
+    The character state at the root of the tree
+  }
+  \item{shiftBranches}{
+    An optional vector indicating any branches at which an OU model has a determined shift in ancestral state. 
+    Same order as \code{shiftStates}. This argument and \code{shiftStates} are only needed if you want to specify a model with
+    a disjunction in phenotype, similar to restarting evolution at a new point.
+    }
+  \item{shiftStates}{
+    An optional vector of length = \code{length(shiftStates)} indicating the ancestrat states for the branches at which the state shifts.
+    }
+  \item{alpha}{
+    The strength of attraction 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.
+    }
+  \item{variance}{
+    The variance on the stochastic portion of the Ornstein-Uhlenbeck model.
+    }
+  \item{theta}{
+    The character state optimum. \code{theta} can be submitted as a single value or, like \code{alpha}, as a vector corresponding to
+    branches of the tree.
+    }
+  \item{branchMeans}
+    The mean for each branch, utilized only in the Platt model. 
+    }
+  \item{steps}
+    The number of slices into which the tree is divided for simulation.
+    }
+}
+\details{
+    ouSim as currently written is a very basic simulation engine, but also very flexible.
+}
+\value{
+  A list of class 'ouSim' that describes the phenotype at the beginning and end of each branch segment, as well as the model.
+  }
+\author{Andrew Hipp ahipp at mortonarb.org}
+\seealso{
+   \code{plot.ouSim} for visualizing simulation
+}
+\examples{
+XXX
+}
+\keyword{models}