[Mattice-commits] r180 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 25 16:24:38 CET 2009
Author: andrew_hipp
Date: 2009-02-25 16:24:38 +0100 (Wed, 25 Feb 2009)
New Revision: 180
Modified:
pkg/man/carex.Rd
pkg/man/informationCriterion.Rd
pkg/man/multiModel.Rd
pkg/man/ouSim.Rd
pkg/man/runBatchHansen.Rd
Log:
cleaning up documentation files
Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd 2009-02-25 15:23:59 UTC (rev 179)
+++ pkg/man/carex.Rd 2009-02-25 15:24:38 UTC (rev 180)
@@ -43,15 +43,14 @@
\examples{
library(maticce)
data(carex)
- attach(carex)
- ovales.tree <- ape2ouch(ovales.tree) # tree comes in in phylo format, but we need an ouchtree object
- trial <- runBatchHansen(ovales.tree, ovales.data, ovales.nodes[1:3], maxNodes = 2) # for expedience, only tests for changes at up to 2 of the first 4 nodes
+ ovales.tree <- ape2ouch(carex$ovales.tree) # tree comes in in phylo format, but we need an ouchtree object
+ trial <- runBatchHansen(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) # for expedience, only tests for changes at up to 2 of the first 4 nodes
summary(trial) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
- multiModel(carex$ovales.tree, ovales.data, ovales.nodes[[2]]) # compares five different models of character change at node 2
- trialSim <- ouSim(trial, ovales.tree) # simulates the evolution of the chromosome number under the model-averaged values
+ multiModel(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[[2]]) # compares five different models of character change at node 2
+ trialSim <- ouSim(trial, carex$ovales.tree) # simulates the evolution of the chromosome number under the model-averaged values
plot(trialSim) # plots the character simulation, with all branches black
- plot(trialSim, colors = paintBranches(ovales.nodes[1:4], ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
- plot(trialSim, colors = paintBranches(list(ovales.nodes[[2]]), ovales.tree)) # plots the character simulation, with branch colors changing only at node 2
+ plot(trialSim, colors = paintBranches(carex$ovales.nodes[1:4], carex$ovales.tree)) # plots the character simulation, with branch colors changing at all 8 nodes
+ plot(trialSim, colors = paintBranches(list(carex$ovales.nodes[[2]]), carex$ovales.tree)) # plots the character simulation, with branch colors changing only at node 2
}
\author{Andrew L. Hipp <ahipp at mortonarb.org>}
\keyword{datasets}
\ No newline at end of file
Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd 2009-02-25 15:23:59 UTC (rev 179)
+++ pkg/man/informationCriterion.Rd 2009-02-25 15:24:38 UTC (rev 180)
@@ -6,8 +6,8 @@
\description{Returns AIC, AICc, and BIC values and weights for a set of models.}
\usage{
informationCriterion(u = NULL, lnL = NULL, K, n = 1, names = NULL)
- informationCriterion.hansenBatch(hansenBatch)
- print.informationCriterion(x, ...)
+ \method{informationCriterion}{hansenBatch}(hansenBatch)
+ \method{print}{informationCriterion}(x, ...)
}
\details{
At the minimum, a vector of either the model log-likelihoods (\code{lnL}) or deviances (\code{u} = -2 * lnL) and a vector
Modified: pkg/man/multiModel.Rd
===================================================================
--- pkg/man/multiModel.Rd 2009-02-25 15:23:59 UTC (rev 179)
+++ pkg/man/multiModel.Rd 2009-02-25 15:24:38 UTC (rev 180)
@@ -18,9 +18,11 @@
\dQuote{part} indicates a model in which the tree is subdivided and treated as two entities }
}
\details{
- This function is useful after you have identified nodes at which significant character transitions are likely to have occurred.
- Its use is to identify whether shifts at a given node are
- whether the OU parameters are really necessary. five models tested are
+ This function is useful after you have identified nodes at which significant character transitions are likely to
+ have occurred. Its use is to identify whether shifts at a given node are compatible with a single Ornstein-Uhlenbeck
+ (O-U) model with a change in equilibrium value at the node; a two-tree model, with each tree evolving under a
+ separate Brownian motion or O-U model; or a no-change model, either Brownian motion or no-change O-U model.
+ Details and discussion of biological interpretation of these models is in Hipp 2007.
}
\value{
A list with two items:
@@ -58,7 +60,7 @@
\note{
In \pkg{ouch} version 2.x, the \code{ouchtree} function rescales trees to depth = 1. The alpha and sigma parameters
are thus not directly comparable between subtrees, as they were in previous versions of \pkg{ouch}, and this function as currently implemented
- should not be used to test for shifts in evolutionary rate within a tree (cf. O'Meara et al. 2006). This test can be implemented
+ should not be used to test for shifts in evolutionary rate within a tree (cf. O'Meara et al. 2006). Such a test can be performed
in \pkg{geiger}, an \pkg{R} package, or \acronym{brownie}, which is available as a stand-alone application or a set of \acronym{MATLAB} modules.
}
\seealso{ \code{\link{carex}} for an example}
\ No newline at end of file
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2009-02-25 15:23:59 UTC (rev 179)
+++ pkg/man/ouSim.Rd 2009-02-25 15:24:38 UTC (rev 180)
@@ -24,27 +24,34 @@
A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
\item{\code{phylo}}{
With an \pkg{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
+
}
\item{\code{ouchtree}}{
With an \pkg{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{\code{browntree}}{
All Brownian motion model parameters and tree are extracted from the \code{browntree} object.
+
}
\item{\code{hansentree}}{
All Ornstein-Uhlenbeck model parameters and tree are extracted from the \code{hansentree} object.
Only the first regime is utilized.
+
}
\item{\code{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{\code{hansenSummary}}{
Behaves exactly like a \code{hansenBatch} object.
+
}
- \code{\code{ouSim.phylo}} is a very basic simulation engine, but also the most flexible. As written, the user has to specify the
+ \item{\code{ouSim.phylo}}{
+ A very basic simulation engine, but also the most flexible. As written, the user has to specify the
model using two vectors that correspond to the branches in an \code{ape}-format tree. It is important to note that
this simulation method is really a heuristic device, not appropriate for estimating parameter distributions. For
analysis purposes, you should utilize the \code{simulate} and \code{bootstrap} methods in \pkg{ouch}.
Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd 2009-02-25 15:23:59 UTC (rev 179)
+++ pkg/man/runBatchHansen.Rd 2009-02-25 15:24:38 UTC (rev 180)
@@ -1,12 +1,12 @@
\name{runBatchHansen}
-\alias{runBatchHansen}
+\alias{runBatchHansen}
\title{Analyze Ornstein-Uhlenbeck models over a set of trees}
\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, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = FALSE, ...)
+runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = FALSE, ...)
}
\arguments{
\item{ouchTrees}{
@@ -49,12 +49,6 @@
\details{
This function is the primary function for estimating the probability of a change in with changes in regime at the nodes
specified, with changes corresponding to permutations of the nodes fed to the function. See vignette for additional details.
-
- Note: summary estimates of the probability of change on a branch are only valid if
- (1) the maximum number of regimes permitted approximates the actual maximum;
- (2) nodes at which changes actually occurred were included among the nodes being tested; and
- (3) any matrix you may have utilized to conduct analysis was balanced,
- such that all nodes are present in the same number of models.
}
\value{
A list of class \code{hansenBatch} with the following items:
@@ -91,6 +85,13 @@
}
}
\author{Andrew Hipp <ahipp at mortonarb.org>}
+\note{
+ Summary estimates of the probability of change on a branch are only valid if
+ (1) the maximum number of regimes permitted approximates the actual maximum;
+ (2) nodes at which changes actually occurred were included among the nodes being tested; and
+ (3) any matrix you may have utilized to conduct analysis was balanced,
+ such that all nodes are present in the same number of models.
+}
\seealso{
\code{\link{summary.hansenBatch}} for summarizing data; \code{\link{carex}} for an example
}
\ No newline at end of file
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