[Caic-commits] r67 - pkg/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Oct 2 14:33:56 CEST 2008 

Author: petzoldt
Date: 2008-10-02 14:33:56 +0200 (Thu, 02 Oct 2008)
New Revision: 67

Modified:
   pkg/man/caic-deprecated.Rd
   pkg/man/caic-package.Rd
   pkg/man/clade.matrix.Rd
   pkg/man/clade.members.Rd
   pkg/man/force.binary.tree.Rd
   pkg/man/pglm.Rd
   pkg/man/predict.caic.Rd
   pkg/man/vcv.array.Rd
   pkg/man/vcv.phylo.array.Rd
Log:
minor formal documentation fixes

Modified: pkg/man/caic-deprecated.Rd
===================================================================
--- pkg/man/caic-deprecated.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/caic-deprecated.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -9,11 +9,16 @@
 \title{Deprecated functions in the caic package}
 \description{These functions are deprecated and are now simply redirections to the replacement functions}
 \usage{
-profile.lambda(x, dat, V)
-profile.kappa(x, V)
-max.lik.lambda(x, V, dat)
-max.lik.kappa(x, V)
-all.clades(phy, tips=FALSE, tip.labels=FALSE)
+\method{profile}{lambda}(x, dat, V)
+\method{profile}{kappa}(x, V)
+\method{max.lik}{lambda}(x, V, dat)
+\method{max.lik}{kappa}(x, V)
+\method{all}{clades}(phy, tips=FALSE, tip.labels=FALSE)
+%profile.lambda(x, dat, V)
+%profile.kappa(x, V)
+%max.lik.lambda(x, V, dat)
+%max.lik.kappa(x, V)
+%all.clades(phy, tips=FALSE, tip.labels=FALSE)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

Modified: pkg/man/caic-package.Rd
===================================================================
--- pkg/man/caic-package.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/caic-package.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -1,11 +1,11 @@
-\name{caicPack-package}
-\alias{caicPack-package}
-\alias{caicPack}
+\name{caic-package}
+\alias{caic-package}
+%\alias{caicPack}
 \docType{package}
 \title{
 A package to carry out comparative analysis using independent contrasts.
 }
-\description{
+\description{The \pkg{CAIC} package implements methods CAIC and MacroCAIC for comparative analysis of independent contrasts and to derive correlates of species richness.
 }
 \details{
 \tabular{ll}{

Modified: pkg/man/clade.matrix.Rd
===================================================================
--- pkg/man/clade.matrix.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/clade.matrix.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -22,7 +22,7 @@
 }
 \author{David Orme}
 
-\seealso{}%%\code{\link{pd.calc}}, \code{\link{pd.bootstrap}}, \code{\link{clade.stats}}}
+%\seealso{}%%\code{\link{pd.calc}}, \code{\link{pd.bootstrap}}, \code{\link{clade.stats}}}
 \examples{
 data(SmallTree)
 clade.matrix(diTree)

Modified: pkg/man/clade.members.Rd
===================================================================
--- pkg/man/clade.members.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/clade.members.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -26,7 +26,7 @@
 \author{David Orme}
 
 
-\seealso{} %% \code{\link{clade.stats}} }
+%\seealso{} %% \code{\link{clade.stats}} }
 \examples{
 data(SmallTree)
 clade.members(22, diTree, tip.labels=TRUE)

Modified: pkg/man/force.binary.tree.Rd
===================================================================
--- pkg/man/force.binary.tree.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/force.binary.tree.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -15,8 +15,8 @@
   most purposes.}
   \item{node.suffix}{The node labels of the phylogeny are amended to indicate which are resolved polytomies - this suffix is used to identify originally polytomous nodes and the shared polychotomy from which they have been split.}
 }
-\details{
-}
+%\details{
+%}
 
 \value{
 An object of class \code{"phylo"} with no polytomies.

Modified: pkg/man/pglm.Rd
===================================================================
--- pkg/man/pglm.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/pglm.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -83,9 +83,9 @@
  \item{LamOptimised}{A logical indicating whether the fitted lambda has been optimised using \code{pglmEstLambda()}}
  \item{namey}{The name of the y variable.}
 }
-\references{ ~put references to the literature/web site here ~ }
+%\references{ ~put references to the literature/web site here ~ }
 \author{Rob Freckleton; David Orme}
-\note{}
+%\note{}
 \seealso{\code{\link{profile.lambda}} }
 \examples{
 

Modified: pkg/man/predict.caic.Rd
===================================================================
--- pkg/man/predict.caic.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/predict.caic.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -12,9 +12,9 @@
   \item{object}{A caic object}
   \item{\dots}{Arguments to be passed to 'predict.lm'.}
 }
-\details{
-  ~~ If necessary, more details than the description above ~~
-}
+%\details{
+%  ~~ If necessary, more details than the description above ~~
+%}
 \value{
   ~Describe the value returned
   If it is a LIST, use
@@ -24,11 +24,9 @@
 }
 \author{David Orme}
 \seealso{ \code{\link{predict.lm}}}
-\examples{
+%\examples{
+%}
 
-
-}
-
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{methods}

Modified: pkg/man/vcv.array.Rd
===================================================================
--- pkg/man/vcv.array.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/vcv.array.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -26,7 +26,7 @@
 When dim = 3, a 3 dimensional array of class 'vcv.array' with dimensions of the number of taxa in the phylogeny for the rows and columns and either the maximum number of branches on the root to tip path or the number of internal nodes as the depth, depending on the setting of \code{compact}. The rows and columns are named using the tip labels from the phylogeny and the depth only named with node numbers if \code{compact} is TRUE. 
 }
 \author{David Orme}
-\seealso{ \code{\link{vcv.phylo}}, \code{\link{lik.kappa}},}
+\seealso{ \code{\link[ape]{vcv.phylo}}, \code{\link{lik.kappa}},}
 \examples{
 tree <- rcoal(8)
 tree.VCV <- vcv.phylo(tree)

Modified: pkg/man/vcv.phylo.array.Rd
===================================================================
--- pkg/man/vcv.phylo.array.Rd	2008-10-02 11:27:18 UTC (rev 66)
+++ pkg/man/vcv.phylo.array.Rd	2008-10-02 12:33:56 UTC (rev 67)
@@ -15,7 +15,7 @@
 A 3 dimensional array of class 'vcv.phylo.array' with dimensions of the number of taxa in the phylogeny for the rows and columns and the maximum number of branches on root to tip path as the depth. The rows and columns are named using the tip labels from the phylogeny and the depth is not named. A pair of row and column coordinates will extract a vector of all branch lengths shared by a pair of taxa, padded with NA in order to accomodate the longest such vector. The apply function can be easily used to collapse the array down to a standard VCV matrix, as in the example.
 }
 \author{David Orme}
-\seealso{ \code{\link{vcv.phylo}}, \code{\link{lik.kappa}},}
+\seealso{ \code{\link[ape]{vcv.phylo}}, \code{\link{lik.kappa}},}
 \examples{
 tree <- rcoal(8)
 tree.VCV <- vcv.phylo(tree)

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