maticce: Mapping Transitions in Continuous Character Evolution

Tools for an information-theoretic approach to estimating the probability of continuous character transitions on phylogenetic trees

Author
Andrew Hipp <ahipp@mortonarb.org>, with contributions from Marcial Escudero
Date of publication
2014-03-03 08:29:55
Maintainer
Andrew Hipp <ahipp@mortonarb.org>
License
GPL-3
Version
1.0-4
URLs

View on R-Forge

Man pages

carex
Carex section Ovales tree, chromosome data, and nodes
informationCriterion
Information criterion and weights for a set of models
isMonophyletic
Test whether a set of taxa is monophyletic on an ouch-style...
multiModel
Test multiple models of character transition at a single node
ouSim
Discrete-time simulation of Ornstein-Uhlenbeck models on a...
paintBranches
Paint branches for Ornstein-Uhlenbeck analysis
plot.ouSim
Visualizing discrete-time simulation of Ornstein-Uhlenbeck...
regimeMaker
Paint ouch-style regimes over a set of trees based on a...
regimeMatrix
Create a matrix that defines models for batch analysis
regimeVectors
Paint all possible regimes
runBatchHansen
Analyze Ornstein-Uhlenbeck models over a set of trees
summary.hansenBatch
Summarize output from runBatchHansen

Files in this package

maticce/DESCRIPTION
maticce/NAMESPACE
maticce/R
maticce/R/batchHansen.R
maticce/R/informationCriterion.R
maticce/R/multiModel.R
maticce/R/ouSim.hansenBatch.R
maticce/R/ouSim.ouchtree.R
maticce/R/ouSim.phylo.R
maticce/R/ouSimHead.R
maticce/R/plot.ouSim.R
maticce/R/regimes.R
maticce/R/summarizingAnalyses.R
maticce/R/treeTraversal.R
maticce/TODO
maticce/build
maticce/build/vignette.rds
maticce/data
maticce/data/carex.rda
maticce/inst
maticce/inst/VERSIONS
maticce/inst/doc
maticce/inst/doc/maticce.R
maticce/inst/doc/maticce.Rnw
maticce/inst/doc/maticce.pdf
maticce/man
maticce/man/carex.Rd
maticce/man/informationCriterion.Rd
maticce/man/isMonophyletic.Rd
maticce/man/multiModel.Rd
maticce/man/ouSim.Rd
maticce/man/paintBranches.Rd
maticce/man/plot.ouSim.Rd
maticce/man/regimeMaker.Rd
maticce/man/regimeMatrix.Rd
maticce/man/regimeVectors.Rd
maticce/man/runBatchHansen.Rd
maticce/man/summary.hansenBatch.Rd
maticce/misc
maticce/misc/OLDregimes.R
maticce/misc/batchHansenVignette.Rnw
maticce/misc/carex.R
maticce/misc/carex.rda
maticce/misc/chromo.txt
maticce/misc/multiModels-dataFormat.csv
maticce/misc/nodes.R
maticce/misc/oldRegimeMatrix.R
maticce/misc/originalApeToOuch_NU.R
maticce/misc/originalBatchHansenFit.R
maticce/misc/ouSim.ouchtree-2jun09WorkingSnap-versionFromTextfileSVN.R
maticce/misc/ouSim.ouchtree-2jun09WorkingSnap.R
maticce/misc/preorderOU-29may09.snapshot
maticce/misc/taxonSets.R
maticce/misc/timingRegimeMatrix.txt
maticce/vignettes
maticce/vignettes/maticce.Rnw