[Mattice-commits] r153 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 14 06:02:11 CET 2009
Author: andrew_hipp
Date: 2009-01-14 06:02:11 +0100 (Wed, 14 Jan 2009)
New Revision: 153
Modified:
pkg/R/informationCriterion.R
pkg/R/ouSim.ouchtree.R
pkg/R/ouSim.phylo.R
pkg/man/informationCriterion.Rd
pkg/man/ouSim.Rd
Log:
trying to fix all remaining R check errors and warnings
Modified: pkg/R/informationCriterion.R
===================================================================
--- pkg/R/informationCriterion.R 2009-01-14 04:46:34 UTC (rev 152)
+++ pkg/R/informationCriterion.R 2009-01-14 05:02:11 UTC (rev 153)
@@ -37,6 +37,6 @@
items <- c('u', 'K', 'AIC', 'AICc', 'BIC', 'AICwi', 'AICcwi', 'BICwi')
out <- matrix(NA, nrow = length(ic$names), ncol = length(items), dimnames = list(ic$names, items))
for(i in items) out[, i] <- ic[[i]]
- print(out)
+ print(out, ...)
return(NULL)
}
\ No newline at end of file
Modified: pkg/R/ouSim.ouchtree.R
===================================================================
--- pkg/R/ouSim.ouchtree.R 2009-01-14 04:46:34 UTC (rev 152)
+++ pkg/R/ouSim.ouchtree.R 2009-01-14 05:02:11 UTC (rev 153)
@@ -1,4 +1,4 @@
-ouSim.ouchtree <- function(tree, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000) {
+ouSim.ouchtree <- function(object, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000, ...) {
## function to plot a simulated dataset under brownian motion or Ornstein-Uhlenbeck (OU) model
## Arguments:
## tree is an ouch-style (S4) tree
Modified: pkg/R/ouSim.phylo.R
===================================================================
--- pkg/R/ouSim.phylo.R 2009-01-14 04:46:34 UTC (rev 152)
+++ pkg/R/ouSim.phylo.R 2009-01-14 05:02:11 UTC (rev 153)
@@ -1,4 +1,4 @@
-ouSim.phylo <- function(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000) {
+ouSim.phylo <- function(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...) {
## function to plot a simulated dataset under brownian motion or Ornstein-Uhlenbeck (OU) model
## Arguments:
## phy is an ape-style tree
Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd 2009-01-14 04:46:34 UTC (rev 152)
+++ pkg/man/informationCriterion.Rd 2009-01-14 05:02:11 UTC (rev 153)
@@ -5,7 +5,7 @@
\title{Information criterion and weights for a set of models}
\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(u = NULL, lnL = NULL, K, n = 1, names = NULL)
informationCriterion.hansenBatch(hansenBatch)
print.informationCriterion(x, ...)
}
@@ -33,8 +33,13 @@
}
\item{hansenBatch}{
Output from \{runBatchHansen}.
+ }
\item{x}{
Output from \{informationCriterion}.
+ }
+ \item{...}{
+ Additional arguments to be passed along to \code{print}
+ }
}
\value{
A list with the following vectors, all indexed by model number:
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2009-01-14 04:46:34 UTC (rev 152)
+++ pkg/man/ouSim.Rd 2009-01-14 05:02:11 UTC (rev 153)
@@ -9,20 +9,20 @@
\title{Discrete-time simulation of Ornstein-Uhlenbeck models on a user tree.}
\description{
\code{ouSim} simulates the evolution of a single character for visualization purposes; for parametric bootstrapping,
- utilize the \code{simulate} methods in \code{ouch}.
+ utilize the \code{simulate} methods in \pkg{ouch}.
}
\usage{
ouSim(object, ...)
- ouSim.phylo(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000)
- ouSim.ouchtree(object, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000)
+ ouSim.phylo(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...)
+ ouSim.ouchtree(object, rootState = 0, alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
ouSim.browntree(object, ...)
ouSim.hansentree(object, ...)
ouSim.hansenBatch(object, ...)
- ouSim.hansenSummary(analysis, tree, treeNum = 1, rootState = NULL, ...)
+ ouSim.hansenSummary(object, tree, treeNum = 1, rootState = NULL, ...)
}
\details{
A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
- \item{object}{
+ \item{phylo}{
With an \pkg{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
}
\item{ouchtree}{
@@ -46,16 +46,13 @@
}
\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}.
- }
+ 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}.
+}
\arguments{
\item{object}{
- In a call to the generic function, an object of class ouchtree, browntree, hansentree, hansenBatch, or hansenSummary.
+ In a call to the generic function, an object of class phylo, ouchtree, browntree, hansentree, hansenBatch, or hansenSummary.
}
- \item{phy}{
- An \code{ape}-style tree, class \code{phylo}.
- }
\item{rootState}{
The character state at the root of the tree. In a {browntree} object, this value is provided. In a {hansentree} or
{batchHansen} object, the value at the root is not provided, but it is taken to be the equilibrium or optimum
@@ -95,11 +92,21 @@
depends on only these parameters (ancestry is not considered, only current mean and variance).
}
\item{branchMeans}{
- For a \code{phylo} tree only. The mean for each branch, utilized only in the "meanVar" model.
+ For a \code{phylo} tree only. The mean for each branch, utilized only in the \dQuote{meanVar} model.
}
\item{steps}{
The number of slices into which the tree is divided for simulation.
}
+ \item{tree}{
+ The \code{ouch}-style tree to simulate on.
+ }
+ \item{treeNum}{
+ In a \code{hansenBatch} or \code{hansenSummary} object, the number of the tree from which analysis
+ parameters should be drawn; should match the tree provided with \code{tree}.
+ }
+ \item{...}{
+ Additional arguments to be passed along to \code{ouSim}.
+ }
}
\value{
A list of class 'ouSim' that describes the phenotype at the beginning and end of each branch segment, as well as the model.
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