[Mattice-commits] r97 - in pkg: . DATA man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 19 04:37:47 CET 2008
Author: andrew_hipp
Date: 2008-12-19 04:37:47 +0100 (Fri, 19 Dec 2008)
New Revision: 97
Added:
pkg/DATA/carex2.Rdata
Modified:
pkg/DESCRIPTION
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/regimeVectors.Rd
pkg/man/runBatchHansen.Rd
pkg/man/summary.hansenBatch.Rd
Log:
cleaning up documentation files
Added: pkg/DATA/carex2.Rdata
===================================================================
(Binary files differ)
Property changes on: pkg/DATA/carex2.Rdata
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/DESCRIPTION 2008-12-19 03:37:47 UTC (rev 97)
@@ -4,7 +4,7 @@
Version: 0.4
Date: 2008-12-18
Depends: ouch
-Suggests: ape, phylobase
+Suggests: ape
Enhances: ouch
Author: Andrew Hipp <ahipp at mortonarb.org>, with contributions from Marcial Escudero.
Maintainer: Andrew Hipp <ahipp at mortonarb.org>
Modified: pkg/man/isMonophyletic.Rd
===================================================================
--- pkg/man/isMonophyletic.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/isMonophyletic.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -19,4 +19,3 @@
\seealso{
\code{\link{nodeDescendents}} \code{\link{mrcaOUCH}}
}
-/keyword{tree}
\ No newline at end of file
Modified: pkg/man/mrcaOUCH.Rd
===================================================================
--- pkg/man/mrcaOUCH.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/mrcaOUCH.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -27,4 +27,3 @@
\seealso{
\code{\link{isMonophyletic}} \code{\link{nodeDescendents}}
}
-/keyword{tree}
\ No newline at end of file
Modified: pkg/man/nodeDescendents.Rd
===================================================================
--- pkg/man/nodeDescendents.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/nodeDescendents.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -23,4 +23,3 @@
\seealso{
\code{\link{isMonophyletic}} \code{\link{mrcaOUCH}}
}
-/keyword{tree}
\ No newline at end of file
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/ouSim.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -36,7 +36,7 @@
\item{hansenSummary} {
Behaves exactly like a \code{hansenBatch} object.
}
- ouSim.phylo is a very basic simulation engine, but also the most flexible. As written, the user has to specify the
+ \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 heuristic device, not appropriate for estimating parameter distributions. For
analysis purposes, you should utilize the \code{simulate} and \code{bootstrap} methods in \code{ouch}.
@@ -98,7 +98,7 @@
}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{plot.ouSim}} for visualizing simulation
+ \code{\link{plot.ouSim}} for visualizing simulation;
\code{\link{carex}} for examples
}
\references{
@@ -109,5 +109,4 @@
Butler, M. and A.A. King. (2004)
Phylogenetic comparative analysis: a modeling approach for adaptive evolution.
American Naturalist 164:683-695.
- }
-\keyword{simulation}
+}
Modified: pkg/man/paintBranches.Rd
===================================================================
--- pkg/man/paintBranches.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/paintBranches.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -2,38 +2,36 @@
\alias{paintBranches}
\title{Paint branches for Ornstein-Uhlenbeck analysis}
\description{
-Paints branches with regimes changing at nodes specified. Called by
-\code{regimeVectors}.
- }
+ Paints branches with regimes changing at nodes specified. Called by
+ \code{regimeVectors}.
+}
\usage{
-paintBranches(tree, regimeShiftNodes, regimeTitles)
- }
+ paintBranches(tree, regimeShiftNodes, regimeTitles)
+}
\arguments{
-\item{tree}{An S4 ouchtree object, generated using
-\code{ape2ouch}
-or
-\code{ouchtree}. Old-style ouch trees (data frames) will not work but can be translated using
-\code{ouchtree}.
+ \item{tree}{
+ An S4 ouchtree object, generated using \code{ape2ouch} or \code{ouchtree}.
+ Old-style ouch trees (data frames) will not work but can be translated using \code{ouchtree}.
+ }
+ \item{regimeShiftNodes}{
+ Either a vector of nodes (by number) at which the selective regime changes,
+ or a list of taxa defining nodes. This allows you to use paintBranches with the same
+ nodes you use to call runBatchHansen. This parameter may include the root but does
+ not need to.
+ }
+ \item{regimeTitles} {
+ Titles for the regimes.
+ }
}
-\item{regimeShiftNodes}{Either a vector of nodes (by number) at which the selective regime changes,
- or a list of taxa defining nodes. This allows you to use paintBranches with the same
- nodes you use to call runBatchHansen. This parameter may include the root but does
- not need to.}
-\item{regimeTitles}{Titles for the regimes.}
-}
\details{
-\code{regimeTitles} is a vector of titles for the regimes that begin at the root and at the nodes indicated in "regimeShiftNodes",
-# in order of description in "regimeShiftNodes", except that the root is listed first in "regimeTitles"
-# but may not be included at all in "regimeShiftNodes."
+ \code{regimeTitles} is a vector of titles for the regimes that begin at the root and at the nodes indicated in
+ \code{regimeShiftNodes} in order of description in "regimeShiftNodes", except that the root is listed first in
+ \code{regimeTitles} but may not be included at all in \code{regimeShiftNodes}.
}
\value{
-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}
+ 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}
}
-
-\examples{
-}
-
\seealso{
\code{\link{regimeVectors}}, \code{\link{isMonophyletic}}, \code{\link{nodeDescendents}}, \code{\link{mrcaOUCH}}
}
Modified: pkg/man/plot.ouSim.Rd
===================================================================
--- pkg/man/plot.ouSim.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/plot.ouSim.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -26,11 +26,10 @@
}
}
\value{
- None. Called for its side-effect (plotting).
- }
+ None. Called for its side-effect (plotting).
+}
\author{Andrew Hipp ahipp at mortonarb.org}
\seealso{
- \code{\link{ouSim}} for simulations
+ \code{\link{ouSim}} for simulations;
\code{\link{carex}} for examples
}
-\keyword{simulation}
\ No newline at end of file
Modified: pkg/man/regimeVectors.Rd
===================================================================
--- pkg/man/regimeVectors.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/regimeVectors.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -28,9 +28,6 @@
\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.
}
-\examples{
-}
-
\seealso{
\code{\link{paintBranches}}
}
\ No newline at end of file
Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd 2008-12-19 02:52:01 UTC (rev 96)
+++ pkg/man/runBatchHansen.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -92,6 +92,6 @@
}
\author{Andrew Hipp <ahipp at mortonarb.org>}
\seealso{
- \code{\link{summary.hansenBatch}} for summarizing data
+ \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 02:52:01 UTC (rev 96)
+++ pkg/man/summary.hansenBatch.Rd 2008-12-19 03:37:47 UTC (rev 97)
@@ -47,6 +47,3 @@
\code{\link{print.hansenSummary}} for a readable screen output summarizing most of the above
\code{\link{carex}} for an example
}
-\examples{
-## See \code{\link{carex}} for example
-}
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