[Mattice-commits] r266 - in pkg: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 3 08:57:38 CET 2014
Author: andrew_hipp
Date: 2014-03-03 08:57:37 +0100 (Mon, 03 Mar 2014)
New Revision: 266
Modified:
pkg/DESCRIPTION
pkg/man/carex.Rd
pkg/man/multiModel.Rd
pkg/man/ouSim.Rd
pkg/man/regimeMaker.Rd
pkg/man/regimeMatrix.Rd
pkg/man/runBatchHansen.Rd
Log:
updating Rd files for compliance
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/DESCRIPTION 2014-03-03 07:57:37 UTC (rev 266)
@@ -9,6 +9,6 @@
Maintainer: Andrew Hipp <ahipp at mortonarb.org>
Description: Tools for an information-theoretic approach to estimating
the probability of continuous character transitions on phylogenetic trees
-License: GPL
+License: GPL-3
URL: http://r-forge.r-project.org/projects/mattice/
-Revision: 3
\ No newline at end of file
+Revision: 4
\ No newline at end of file
Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/carex.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -51,11 +51,14 @@
# tree comes in in phylo format, but we need an ouchtree object
trees <- lapply(carex$ovales.bayesTrees[1:2], ape2ouch)
contree <- ape2ouch(carex$ovales.tree)
- # for expedience, only tests for changes at up to 2 of the first 4 nodes on 2 trees visited in the MCMC phylogenetic analysis
+ # for expedience, only tests for changes at up to 2 of the first 4 nodes
+ # on 2 trees visited in the MCMC phylogenetic analysis:
trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
- summary(trialBayesTrees) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
+ summary(trialBayesTrees) # summarizes results using summary.hansenBatch
+ # and displays the results using print.hansenSummary
# same analysis as above, but on a single tree
- trialBayesConsensus <- runBatchHansen(contree, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
+ trialBayesConsensus <- runBatchHansen(contree, carex$ovales.data,
+ carex$ovales.nodes[1:4], maxNodes = 2)
# compares five different models of character change at node 2
multiModel(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[[2]])
# simulates the evolution of the chromosome number under the model-averaged values
Modified: pkg/man/multiModel.Rd
===================================================================
--- pkg/man/multiModel.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/multiModel.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -8,7 +8,8 @@
discussion below).
}
\usage{
-multiModel(phy, dat, node, models = c("whole.brown", "whole.ou1", "whole.ou2", "part.brown", "part.ou"))
+multiModel(phy, dat, node,
+ models = c("whole.brown", "whole.ou1", "whole.ou2", "part.brown", "part.ou"))
}
\arguments{
\item{phy}{ An \pkg{ape}-style tree }
@@ -45,16 +46,17 @@
library(maticce)
data(carex)
attach(carex)
- mm2 <- multiModel(carex$ovales.tree, ovales.data, ovales.nodes[[2]]) # compares five different models of character change at node 2
+ # compare five different models of character change at node 2:
+ mm2 <- multiModel(carex$ovales.tree, ovales.data, ovales.nodes[[2]])
mm2
layout(matrix(1:4,2,2))
- pie(mm2$IC$AICwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main = "AIC weights")
- pie(mm2$IC$AICcwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main = "AICc weights")
- pie(mm2$IC$BICwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main = "BIC weights")
+ pie(mm2$IC$AICwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main="AIC weights")
+ pie(mm2$IC$AICcwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main="AICc weights")
+ pie(mm2$IC$BICwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main="BIC weights")
noChangeAICwi <- sum(mm2$IC$AICwi[1:2])
changeAICwi <- sum(mm2$IC$AICwi[3:5])
- barplot(c(noChangeAICwi, changeAICwi), ylim = c(0,1), names.arg = c('no transition', 'transition'),
- main = 'Transition vs. no-transition')
+ barplot(c(noChangeAICwi, changeAICwi), ylim = c(0,1),
+ names.arg = c('no transition', 'transition'), main = 'Transition vs. no-transition')
}
\author{Andrew L. Hipp \email{ahipp at mortonarb.org}}
\note{
Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/ouSim.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -13,8 +13,11 @@
}
\usage{
ouSim(object, ...)
- \method{ouSim}{phylo}(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, sqrt.alpha = 0, variance = 1, theta = rootState, model = "OU", branchMeans = NULL, steps = 1000, ...)
- \method{ouSim}{ouchtree}(object, rootState = 0, sqrt.alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
+ \method{ouSim}{phylo}(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL,
+ sqrt.alpha = 0, variance = 1, theta = rootState, model = "OU",
+ branchMeans = NULL, steps = 1000, ...)
+ \method{ouSim}{ouchtree}(object, rootState = 0, sqrt.alpha = 0, variance = 1,
+ theta = rootState, steps = 1000, ...)
\method{ouSim}{browntree}(object, ...)
\method{ouSim}{hansentree}(object, ...)
\method{ouSim}{hansenBatch}(object, ...)
Modified: pkg/man/regimeMaker.Rd
===================================================================
--- pkg/man/regimeMaker.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/regimeMaker.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -54,7 +54,8 @@
data(carex)
# tree comes in in phylo format, but we need an ouchtree object
trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch)
- # if we are interested in comparing the single-change models that allow changes only at nodes 1, 2, 4, 5, and 8, as well as the no-change model, we could do:
+ # if we are interested in comparing the single-change models that allow changes only at nodes
+ # 1, 2, 4, 5, and 8, as well as the no-change model, we could do:
mat <- regimeMatrix(n = 8, maxNodes = 1)[c(1,2,4,5,8,9), ] # the 9th row is the no-change model
#... then we make regimes based on that regime matrix...
regs <- regimeMaker(trees, mat, carex$ovales.nodes)
Modified: pkg/man/regimeMatrix.Rd
===================================================================
--- pkg/man/regimeMatrix.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/regimeMatrix.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -41,9 +41,10 @@
\code{\link{regimeMaker}}, \code{\link{paintBranches}}
}
\examples{
- # evaluating a set of models allowing all possible permutations of changes at 15 nodes will be quite time-consuming:
+ # allowing all possible permutations of changes at 15 nodes will be quite time-consuming:
print(paste("Number of models =", dim(regimeMatrix(15,15))[1]))
- # paring that down to all possible permutations of changes at 15 nodes, up to a maximum of 5 changes, is much more manageable:
+ # paring that down to all possible permutations of changes at 15 nodes,
+ # up to a maximum of 5 changes, is much more manageable:
print(paste("Number of models =", dim(regimeMatrix(15,5))[1]))
}
\keyword{models}
\ No newline at end of file
Modified: pkg/man/runBatchHansen.Rd
===================================================================
--- pkg/man/runBatchHansen.Rd 2014-03-03 07:39:26 UTC (rev 265)
+++ pkg/man/runBatchHansen.Rd 2014-03-03 07:57:37 UTC (rev 266)
@@ -5,7 +5,9 @@
\code{runBatchHansen} estimates the support for character change on taxon-defined nodes, integrating over uncertainty in the phylogeny and the model of trait evolution.
}
\usage{
-runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList), regimeTitles = NULL, brown = FALSE, ...)
+runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL,
+ di = NULL, nodeNames = NULL, maxNodes = length(cladeMembersList),
+ regimeTitles = NULL, brown = FALSE, ...)
}
\arguments{
\item{ouchTrees}{
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