[Caic-commits] r92 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 5 18:51:09 CEST 2009
Author: davidorme
Date: 2009-05-05 18:51:09 +0200 (Tue, 05 May 2009)
New Revision: 92
Modified:
pkg/man/SmallTree.Rd
pkg/man/brunch.Rd
pkg/man/crunch.Rd
pkg/man/fusco.test.Rd
pkg/man/macrocaic.Rd
pkg/man/phylo.d.Rd
pkg/man/piclm.Rd
pkg/man/profileLik.lambda.Rd
Log:
Minor changes to .Rd files to meet new parse_RD() specs
Modified: pkg/man/SmallTree.Rd
===================================================================
--- pkg/man/SmallTree.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/SmallTree.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -14,7 +14,7 @@
data(SmallTree)
}
\format{
-SmallTree contains two phylogenies stored in the ape package 'phylo' format. The first (\code{diTree}) is a 15 tip, fully bifurcating phylogeny. The second (\code{polyTree}) is based on \code{diTree} but has had three nodes collapsed to give three way polytomies. The are also two accompanying datasets (\code{SmallTreeDat} and \code{SmallTreeDatNA}), which contain data for each of the tips in the tree. They contain a column of tip names (tip), two continuous variables (weight and othervar), a column of the number of species in the tip group (nSpp) and two categorical variables (catX2 and catX3). \\code{SmallTreeDatNA} differs only in having two lines for which no data is available.
+SmallTree contains two phylogenies stored in the ape package 'phylo' format. The first (\code{diTree}) is a 15 tip, fully bifurcating phylogeny. The second (\code{polyTree}) is based on \code{diTree} but has had three nodes collapsed to give three way polytomies. The are also two accompanying datasets (\code{SmallTreeDat} and \code{SmallTreeDatNA}), which contain data for each of the tips in the tree. They contain a column of tip names (tip), two continuous variables (weight and othervar), a column of the number of species in the tip group (nSpp) and two categorical variables (catX2 and catX3). \code{SmallTreeDatNA} differs only in having two lines for which no data is available.
One reason these comparatively trivial toy examples have been preserved as a dataset is that they are also used to provide a reference dataset back to analyses performed in the original CAIC and MacroCAIC programs for Mac Classic.
}
Modified: pkg/man/brunch.Rd
===================================================================
--- pkg/man/brunch.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/brunch.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -37,14 +37,14 @@
\value{
A list of class 'caic' containing the following:
\item{contrast.data}{ A list of the following:
+ \describe{
\item{contr}{A list containing matrices of the contrasts in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{nodalVals}{A list containing matrices of the nodal values in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{contrVar}{A numeric vector of the calculated variances for each contrast.}
\item{nChild}{A vector showing the number of nodes descending from each internal node}
\item{nodeDepth}{A vector showing the maximum number of nodes between each internal node and the tips of the phylogeny (including both the node in question and the tip and hence always >=2) }
\item{validNodes}{A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.}
-
- }
+ }}
\item{phy}{A 'phylo' object describing the phylogeny used to calculate contrasts. This is the phylogeny in the original call reduced to those tips that are also named in the provided data but possibly including tips with missing data.}
\item{lm}{An 'lm' object containing a regression model through the origin for the calculated contrasts}
}
Modified: pkg/man/crunch.Rd
===================================================================
--- pkg/man/crunch.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/crunch.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -42,14 +42,14 @@
\value{
A list of class 'caic' containing the following:
\item{contrast.data}{ A list of the following:
+ \describe{
\item{contr}{A list containing matrices of the contrasts in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{nodalVals}{A list containing matrices of the nodal values in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{contrVar}{A numeric vector of the calculated variances for each contrast.}
\item{nChild}{A vector showing the number of nodes descending from each internal node}
\item{nodeDepth}{A vector showing the maximum number of nodes between each internal node and the tips of the phylogeny (including both the node in question and the tip and hence always >=2) }
\item{validNodes}{A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.}
-
- }
+ }}
\item{phy}{A 'phylo' object describing the phylogeny used to calculate contrasts. This is the phylogeny in the original call reduced to those tips that are also named in the provided data but possibly including tips with missing data.}
\item{lm}{An 'lm' object containing a regression model through the origin for the calculated contrasts}
}
Modified: pkg/man/fusco.test.Rd
===================================================================
--- pkg/man/fusco.test.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/fusco.test.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -35,8 +35,8 @@
\item{markov.simulate}{Use simulated Markov trees to generate confidence intervals on median I and quartile deviation.}
\item{reps}{Number of replicates to use in simulation or randomization.}
\item{conf.int}{Width of confidence intervals required.}
- \nTips{The number of tips in the tree to be simulated.}
- \nSpecies{The number of species distributed across those tips.}
+ \item{nTips}{The number of tips in the tree to be simulated.}
+ \item{nSpecies}{The number of species distributed across those tips.}
\item{object}{An object of class 'fusco'.}
\item{x}{A object of class 'fusco'.}
\item{correction}{Apply the correction described in Appendix A of Fusco and Cronk (1995) to the histogram of nodal imbalance.}
Modified: pkg/man/macrocaic.Rd
===================================================================
--- pkg/man/macrocaic.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/macrocaic.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -27,14 +27,14 @@
\value{
A list of class 'caic' containing the following:
\item{contrast.data}{ A list of the following:
+ \describe{
\item{contr}{A list containing matrices of the contrasts in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{nodalVals}{A list containing matrices of the nodal values in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{contrVar}{A numeric vector of the calculated variances for each contrast.}
\item{nChild}{A vector showing the number of nodes descending from each internal node}
\item{nodeDepth}{A vector showing the maximum number of nodes between each internal node and the tips of the phylogeny (including both the node in question and the tip and hence always >=2) }
\item{validNodes}{A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.}
-
- }
+ }}
\item{phy}{A 'phylo' object describing the phylogeny used to calculate contrasts. This is the phylogeny in the original call reduced to those tips that are also named in the provided data but possibly including tips with missing data.}
\item{lm}{An 'lm' object containing a regression model through the origin for the calculated contrasts}
Modified: pkg/man/phylo.d.Rd
===================================================================
--- pkg/man/phylo.d.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/phylo.d.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -24,6 +24,7 @@
\item{verbose}{If TRUE, the function reports progress and other output likely to be important to users}
\item{x}{An object of class 'phylo.d'}
\item{object}{An object of class 'phylo.d'}
+ \item{\ldots}{Further arguments to print and summary methods}
}
\details{
@@ -44,7 +45,6 @@
\item{dsName}{The name of the dataframe used}
\item{nPermut}{The number of permutations used}
}
-}
\references{ S. A. Fritz & A. Purvis (2009) In prep. }
\author{Susanne Fritz (SFritz at bio.ku.dk)}
\examples{
Modified: pkg/man/piclm.Rd
===================================================================
--- pkg/man/piclm.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/piclm.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -33,14 +33,14 @@
\value{
A list of class 'caic' containing the following:
\item{contrast.data}{ A list of the following:
+ \describe{
\item{contr}{A list containing matrices of the contrasts in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{nodalVals}{A list containing matrices of the nodal values in the response variable (contr\$response) and explanatory variables (contr\$explanatory).}
\item{contrVar}{A numeric vector of the calculated variances for each contrast.}
\item{nChild}{A vector showing the number of nodes descending from each internal node}
\item{nodeDepth}{A vector showing the maximum number of nodes between each internal node and the tips of the phylogeny (including both the node in question and the tip and hence always >=2) }
\item{validNodes}{A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.}
-
- }
+ }}
\item{phy}{A 'phylo' object describing the phylogeny used to calculate contrasts. This is the phylogeny in the original call reduced to those tips that are also named in the provided data but possibly including tips with missing data.}
\item{lm}{An 'lm' object containing a regression model through the origin for the calculated contrasts}
}
Modified: pkg/man/profileLik.lambda.Rd
===================================================================
--- pkg/man/profileLik.lambda.Rd 2009-04-22 13:01:36 UTC (rev 91)
+++ pkg/man/profileLik.lambda.Rd 2009-05-05 16:51:09 UTC (rev 92)
@@ -54,9 +54,9 @@
}
\value{
Both \code{lik.lambda} and \code{lik.kappa} return a list:
- \item{ll} Calculated log likelihood for the supplied lambda or kappa.
- \item{mu} Estimated phylogenitically weighted mean.
- \item{s2} Estimated variance of the mean.
+ \item{ll}Calculated log likelihood for the supplied lambda or kappa.
+ \item{mu}Estimated phylogenitically weighted mean.
+ \item{s2}Estimated variance of the mean.
The \code{profile} functions invisibly return a data frame of the \code{at} values and their associated log likelihoods.
The \code{maxLik} functions return \code{optimize} output: namely, a list with components maximum and objective which give the location of the maximum likelihood and the value of the lambda or kappa at that point.
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