[Mattice-commits] r98 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 22 17:21:12 CET 2008
Author: andrew_hipp
Date: 2008-12-22 17:21:12 +0100 (Mon, 22 Dec 2008)
New Revision: 98
Modified:
pkg/man/isMonophyletic.Rd
pkg/man/mrcaOUCH.Rd
pkg/man/nodeDescendents.Rd
pkg/man/ouSim.Rd
pkg/man/paintBranches.Rd
pkg/man/plot.ouSim.Rd
pkg/man/print.hansenSummary.Rd
pkg/man/regimeVectors.Rd
pkg/man/runBatchHansen.Rd
pkg/man/summary.hansenBatch.Rd
Log:
bracket formatting error fixed in documentation files
Modified: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/isMonophyletic.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -5,10 +5,10 @@
isMonophyletic(tree, taxa)
}
\arguments{
- \item{tree} {
+ \item{tree}{
An \code{ouchtree} object.
}
- \item{taxa} {
+ \item{taxa}{
A vector of taxon names.
}
}
@@ -17,5 +17,5 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{nodeDescendents}} \code{\link{mrcaOUCH}}
+ \code{\link{nodeDescendents}}; \code{\link{mrcaOUCH}}
}
Modified: pkg/man/mrcaOUCH.Rd
===================================================================
--- pkg/man/mrcaOUCH.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/mrcaOUCH.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -13,10 +13,10 @@
mrcaOUCH(cladeVector, tree)
}
\arguments{
- \item{cladeVector} {
+ \item{cladeVector}{
A vector of tip labels.
}
- \item{tree} {
+ \item{tree}{
An \code{ouchtree} object.
}
}
@@ -25,5 +25,5 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{isMonophyletic}} \code{\link{nodeDescendents}}
+ \code{\link{isMonophyletic}}; \code{\link{nodeDescendents}}
}
Modified: pkg/man/nodeDescendents.Rd
===================================================================
--- pkg/man/nodeDescendents.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/nodeDescendents.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -9,10 +9,10 @@
nodeDescendents(tree, startNode)
}
\arguments{
- \item{tree} {
+ \item{tree}{
An \code{ouchtree} object.
}
- \item{startNode} {
+ \item{startNode}{
The node of interest; nomenclature follows \code{tree at nodes}.
}
}
@@ -21,5 +21,5 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{isMonophyletic}} \code{\link{mrcaOUCH}}
+ \code{\link{isMonophyletic}}; \code{\link{mrcaOUCH}}
}
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/ouSim.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -14,26 +14,26 @@
}
\details{
A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
- \item{phylo} {
+ \item{phylo}{
With an \code{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
}
- \item{ouchtree} {
+ \item{ouchtree}{
With an \code{ouch}-style (S4) tree, again, all parameters of the model are specified by branch.
Somewhat less flexibility than \code{ouSim.phylo} but all the pain. Typically just called by the next two methods.
}
- \item{browntree} {
+ \item{browntree}{
All Brownian motion model parameters and tree are extracted from the \code{browntree} object.
}
- \item{hansentree} {
+ \item{hansentree}{
All Ornstein-Uhlenbeck model parameters and tree are extracted from the \code{hansentree} object.
Only the first regime is utilized.
}
- \item{hansenBatch} {
+ \item{hansenBatch}{
Model-averaged parameters from the \code{hansenBatch} object are used for analysis.
One of the trees used for analysis must be provided, and a corrsponding tree number must be provided so that
branches are indexed correctly.
}
- \item{hansenSummary} {
+ \item{hansenSummary}{
Behaves exactly like a \code{hansenBatch} object.
}
\code{ouSim.phylo} is a very basic simulation engine, but also the most flexible. As written, the user has to specify the
@@ -42,27 +42,27 @@
analysis purposes, you should utilize the \code{simulate} and \code{bootstrap} methods in \code{ouch}.
}
\arguments{
- \item{object} {
+ \item{object}{
In a call to the generic function, an object of class ouchtree, browntree, hansentree, hansenBatch, or hansenSummary.
}
- \item{phy} {
+ \item{phy}{
An \code{ape}-style tree, class \code{phylo}.
}
- \item{rootState} {
+ \item{rootState}{
The character state at the root of the tree. In a {browntree} object, this value is provided. In a {hansentree} or
{batchHansen} object, the value at the root is not provided, but it is taken to be the equilibrium or optimum
(\code{theta}) at the root of the tree.
}
- \item{shiftBranches} {
+ \item{shiftBranches}{
For a \code{phylo} tree only. 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} {
+ \item{shiftStates}{
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{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
@@ -70,26 +70,26 @@
This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate},
\code{hansenBatch} or \code{hansenSummary} (model-averaged).
}
- \item{variance} {
+ \item{variance}{
The variance on the stochastic portion of the Ornstein-Uhlenbeck model.
This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate},
\code{hansenBatch} or \code{hansenSummary} (model-averaged).
}
- \item{theta} {
+ \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.
This parameter is taken from the analysis results for \code{browntree} (\code{alpha} = 0), \code{hansentree} (point estimate},
\code{hansenBatch} or \code{hansenSummary} (model-averaged).
}
- \item{model} {
+ \item{model}{
For a \code{phylo} tree only. Specify "OU" for Ornstein-Uhlenbeck and Brownian motion models, "meanVar" for a model
in which the variance is constant across the tree, but mean varies by branch, and distribution in each generation
depends on only these parameters (ancestry is not considered, only current mean and variance).
}
- \item{branchMeans} {
+ \item{branchMeans}{
For a \code{phylo} tree only. The mean for each branch, utilized only in the "meanVar" model.
}
- \item{steps} {
+ \item{steps}{
The number of slices into which the tree is divided for simulation.
}
}
@@ -98,8 +98,7 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{plot.ouSim}} for visualizing simulation;
- \code{\link{carex}} for examples
+ \code{\link{plot.ouSim}} for visualizing simulation; \code{\link{carex}} for examples
}
\references{
Hansen, T.F. (1997)
Modified: pkg/man/paintBranches.Rd
===================================================================
--- pkg/man/paintBranches.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/paintBranches.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -19,7 +19,7 @@
nodes you use to call runBatchHansen. This parameter may include the root but does
not need to.
}
- \item{regimeTitles} {
+ \item{regimeTitles}{
Titles for the regimes.
}
}
Modified: pkg/man/plot.ouSim.Rd
===================================================================
--- pkg/man/plot.ouSim.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/plot.ouSim.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -8,20 +8,20 @@
plot.ouSim(ouSim, nodeColor = "blue", nodeDotSize = 1.4, colors = NULL, ...)
}
\arguments{
- \item{ouSim} {
+ \item{ouSim}{
An \code{ouSim} object.
}
- \item{nodeColor} {
+ \item{nodeColor}{
A single color for the dot indicating nodes, or a vector of colors corrsponding to node numbers.
}
- \item{nodeDotSize} {
+ \item{nodeDotSize}{
Size of the dot at the nodes.
}
- \item{colors} {
+ \item{colors}{
A vector correponding to branches. If not provided, color is extracted from the regime in a \code{hansentree} object.
This vector can be the same format as a regime, so you can color branches with a call to \code{\link{paintBranches}}.
}
- \item{...} {
+ \item{...}{
Additional arguments passed along to \code{lines} (e.g., \code{lwd} for line width, \code{lty} for line type).
}
}
@@ -30,6 +30,5 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{ouSim}} for simulations;
- \code{\link{carex}} for examples
+ \code{\link{ouSim}} for simulations; \code{\link{carex}} for examples
}
Modified: pkg/man/print.hansenSummary.Rd
===================================================================
--- pkg/man/print.hansenSummary.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/print.hansenSummary.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -17,6 +17,6 @@
in the name of the summary object.
}
\author{Andrew Hipp <ahipp at mortonarb.org>}
-\examples{
-## See \code{\link{carex}} for example
+\seealso{
+\code{\link{carex}} for example
}
Modified: pkg/man/regimeVectors.Rd
===================================================================
--- pkg/man/regimeVectors.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/regimeVectors.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -9,13 +9,13 @@
regimeVectors(ouchTrees, cladeMembersList, maxNodes = NULL)
}
\arguments{
-\item{ouchTrees} {
+\item{ouchTrees}{
A list of S4 ouchtree objects
}
-\item{cladeMembersList} {
+\item{cladeMembersList}{
A list of taxa defining nodes.
}
-\item{maxNodes} {
+\item{maxNodes}{
The maximum number of nodes at which a regime may change.
}
}
Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/runBatchHansen.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -58,40 +58,39 @@
}
\value{
A list of class \code{hansenBatch} with the following items:
- \item{hansens} {
+ \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).
}
- \item{thetas} {
+ \item{thetas}{
A list of vectors with a \code{theta} corresponding to each regime on the tree.
}
- \item{regList} {
+ \item{regList}{
A list indexed by tree of lists indexed by model, with the regime corresponding to each model on each tree.
}
- \item{regMatrix} {
+ \item{regMatrix}{
The nodes by regimes matrix returned by \code{regimeMatrix} at the outset of analysis.
}
- \item{nodeMatrix} {
+ \item{nodeMatrix}{
A nodes by tree matrix, indicating for each tree which nodes are present.
}
- \item{brown} {
+ \item{brown}{
A boolean vector of length one indicating whether the brownian motion model was fitted.
}
- \item{N} {
+ \item{N}{
The sample size (number of terminals on the trees).
}
- \item{analysisDate} {
+ \item{analysisDate}{
Data of analysis.
}
- \item{call} {
+ \item{call}{
Verbatim call to \code{runBatchHansen}.
}
}
\author{Andrew Hipp <ahipp at mortonarb.org>}
\seealso{
- \code{\link{summary.hansenBatch}} for summarizing data;
- \code{\link{carex}} for an example
+ \code{\link{summary.hansenBatch}} for summarizing data; \code{\link{carex}} for an example
}
Modified: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd 2008-12-19 03:37:47 UTC (rev 97)
+++ pkg/man/summary.hansenBatch.Rd 2008-12-22 16:21:12 UTC (rev 98)
@@ -19,31 +19,30 @@
}
\value{
A list of class \code{hansenSummary} with the following items:
- \item{modelsMatrix} {
+ \item{modelsMatrix}{
A list of matrices, indexed by tree, providing the information criterion weights for each model.
}
- \item{nodeWeightsMatrix} {
+ \item{nodeWeightsMatrix}{
A list of length two with two matrices:
- \item{unnormalized} {
+ \item{unnormalized}{
The cumulative information criterion weight for each node, averaged only over trees that possess that node
}
- \item{allNodes} {
+ \item{allNodes}{
The cumulative information criterion weight for each node, averaged over all trees.
}
}
- \item{modelAvgAlpha} {
+ \item{modelAvgAlpha}{
The model-averaged estimate of \code{alpha}, the rate of evolution toward the equilibrium / optimum
}
- \item{modelAvgSigmaSq} {
+ \item{modelAvgSigmaSq}{
The model-averaged estimate of \code{sigma.squared}, the variance or rate of stochastic evolution.
}
- \item{thetaMatrix} {
+ \item{thetaMatrix}{
A matrix with trees as the rows, branch number as the columns, containing the model-averaged value of \code{theta}
(the character equilibrium or optimum value) for each branch on each tree
}
}
\author{Andrew Hipp <ahipp at mortonarb.org>}
\seealso{
- \code{\link{print.hansenSummary}} for a readable screen output summarizing most of the above
- \code{\link{carex}} for an example
+ \code{\link{print.hansenSummary}} for a readable screen output summarizing most of the above; \code{\link{carex}} for an example
}
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