[Mattice-commits] r171 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 24 04:35:55 CET 2009
Author: andrew_hipp
Date: 2009-02-24 04:35:55 +0100 (Tue, 24 Feb 2009)
New Revision: 171
Modified:
pkg/R/batchHansen.R
pkg/man/carex.Rd
pkg/man/informationCriterion.Rd
pkg/man/isMonophyletic.Rd
pkg/man/ouSim.Rd
pkg/man/paintBranches.Rd
pkg/man/plot.ouSim.Rd
pkg/man/regimeVectors.Rd
pkg/man/runBatchHansen.Rd
pkg/man/summary.hansenBatch.Rd
Log:
cleaning up documentation
Modified: pkg/R/batchHansen.R
===================================================================
--- pkg/R/batchHansen.R 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/R/batchHansen.R 2009-02-24 03:35:55 UTC (rev 171)
@@ -17,7 +17,7 @@
# "cladeMembersList" = list of vectors containing names of the members of each clade (except for the root of the tree)
# "brown" = whether to analyse the data under a Brownian motion model
# "..." = additional arguments to pass along to hansen
-function(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = F, ...) {
+function(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = FALSE, ...) {
## do all the objects in ouchTrees inherit ouchtree?
if(is(ouchTrees,'ouchtree')) ouchTrees <- list(ouchTrees)
treeCheck <- unlist(lapply(ouchTrees, function(x) is(x,'ouchtree')))
Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/carex.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -9,13 +9,13 @@
\usage{data(carex)}
\format{
A list with three items:
- \item{ovales.tree}{
+ \item{\code{ovales.tree}}{
An ultrametric tree in \code{phylo} format with 53 tips
}
- \item{ovales.data}{
+ \item{\code{ovales.data}}{
A named numeric vector of log-transformed mean chromosome counts for all 53 taxa
}
- \item{ovales.nodes}{
+ \item{\code{ovales.nodes}}{
A list of eight taxon vectors defining the eight nodes studied.
}
}
@@ -33,11 +33,11 @@
\references{
Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006)
Phylogeny and classification of Carex section Ovales (Cyperaceae).
- International Journal of Plant Sciences 167:1029-1048.
+ \emph{International Journal of Plant Sciences} 167:1029-1048.
Hipp, A.L. (2007)
Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae).
- Evolution 61:2175-2194.
+ \emph{Evolution} 61:2175-2194.
}
\examples{
Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/informationCriterion.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -72,9 +72,9 @@
}
}
-\author{Andrew Hipp ahipp at mortonarb.org}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\references{
Burnham, K. P., and D. R. Anderson (2002)
- Model selection and multimodel inference: a practical information-theoretic approach.
+ \emph{Model selection and multimodel inference: a practical information-theoretic approach.}
Springer, New York.
}
\ No newline at end of file
Modified: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/isMonophyletic.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -36,4 +36,4 @@
A vector of tip labels.
}
}
-\author{Andrew Hipp ahipp at mortonarb.org}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\ No newline at end of file
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/ouSim.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -22,29 +22,29 @@
}
\details{
A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
- \item{phylo}{
+ \item{\code{phylo}}{
With an \pkg{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
}
- \item{ouchtree}{
+ \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{browntree}{
+ \item{\code{browntree}}{
All Brownian motion model parameters and tree are extracted from the \code{browntree} object.
}
- \item{hansentree}{
+ \item{\code{hansentree}}{
All Ornstein-Uhlenbeck model parameters and tree are extracted from the \code{hansentree} object.
Only the first regime is utilized.
}
- \item{hansenBatch}{
+ \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{hansenSummary}{
+ \item{\code{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
+ \code{\code{ouSim.phylo}} is 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}.
@@ -111,16 +111,16 @@
\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}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\seealso{
\code{\link{plot.ouSim}} for visualizing simulation; \code{\link{carex}} for examples
}
\references{
Hansen, T.F. (1997)
Stabilizing selection and the comparative analysis of adaptation.
- Evolution 51:1341-1351.
+ \emph{Evolution} 51:1341-1351.
Butler, M. and A.A. King. (2004)
Phylogenetic comparative analysis: a modeling approach for adaptive evolution.
- American Naturalist 164:683-695.
+ \emph{American Naturalist} 164:683-695.
}
Modified: pkg/man/paintBranches.Rd
===================================================================
--- pkg/man/paintBranches.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/paintBranches.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -32,6 +32,7 @@
A regime in which shifts in optimum are coded as occuring at all nodes specified in \code{regimeShiftNodes}.
The regime is formated to input directly into \code{hansen}
}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\seealso{
\code{\link{regimeVectors}}, \code{\link{isMonophyletic}}
}
Modified: pkg/man/plot.ouSim.Rd
===================================================================
--- pkg/man/plot.ouSim.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/plot.ouSim.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -28,7 +28,7 @@
\value{
None. Called for its side-effect (plotting).
}
-\author{Andrew Hipp ahipp at mortonarb.org}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\seealso{
\code{\link{ouSim}} for simulations; \code{\link{carex}} for examples
}
Modified: pkg/man/regimeVectors.Rd
===================================================================
--- pkg/man/regimeVectors.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/regimeVectors.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -24,10 +24,17 @@
}
\value{
A list with three items:
-\item{regList} A list (by tree) of lists of regimes that can be input directly into \code{hansen}.
-\item{nodeMatrix} A matrix indicating which nodes are presentin each tree.
-\item{regMatrix} A list (by tree) of matrices indicating which nodes are present in each model.
+\item{regList}{
+ A list (by tree) of lists of regimes that can be input directly into \code{hansen}.
+ }
+\item{nodeMatrix}{
+ A matrix indicating which nodes are presentin each tree.
+ }
+\item{regMatrix}{
+ A list (by tree) of matrices indicating which nodes are present in each model.
+ }
}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\seealso{
-\code{\link{paintBranches}}
+ \code{\link{paintBranches}}
}
\ No newline at end of file
Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/runBatchHansen.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -6,7 +6,7 @@
complex Ornstein-Uhlenbeck models.
}
\usage{
-runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = F, ...)
+runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = FALSE, ...)
}
\arguments{
\item{ouchTrees}{
@@ -93,4 +93,4 @@
\author{Andrew Hipp <ahipp at mortonarb.org>}
\seealso{
\code{\link{summary.hansenBatch}} for summarizing data; \code{\link{carex}} for an example
-}
+}
\ No newline at end of file
Modified: pkg/man/summary.hansenBatch.Rd
===================================================================
--- pkg/man/summary.hansenBatch.Rd 2009-02-24 03:10:49 UTC (rev 170)
+++ pkg/man/summary.hansenBatch.Rd 2009-02-24 03:35:55 UTC (rev 171)
@@ -53,7 +53,7 @@
(the character equilibrium or optimum value) for each branch on each tree
}
}
-\author{Andrew Hipp <ahipp at mortonarb.org>}
+\author{Andrew Hipp \email{ahipp at mortonarb.org}}
\seealso{
\code{\link{carex}} for an example
}
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