motmot: Models of Trait Macroevolution on Trees

motmot provides functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions are based around tests of variation in the rates of trait evolution.

AuthorGavin Thomas, Rob Freckleton
Date of publication2012-12-14 14:02:07
MaintainerGavin Thomas <gavin.thomas@sheffield.ac.uk>
LicenseGPL (>= 2)
Version1.1.2
http://gavinhthomas.wordpress.com/motmot/

View on R-Forge

Man pages

anolis.data: Anolis data

anolis.tree: Anolis phylogeny

as.rateData: Conversion among data and phylogeny objects

as.rateMatrix: Conversion among data and phylogeny objects

cladeIdentity: Identify branches (including tips) descended from a node...

fairProportions: Calculate fair proportions phylogenetic diversity metric

likRatePhylo: Log-likelihood rate estimation for traits and phylogenies

likTraitPhylo: Log-likelihood rate estimation for traits and phylogenies

make.anc: Create design matrix (internal function)

make.likRatePhylo: Internal function

ML.RatePhylo: Maximum likelihood rate estimation for traits and phylogenies

motmot-package: Models of trait macroevolution on trees

node.descendents: Identify nodes and tips descended from a node (internal...

optim.likRatePhylo: Maximum likelihood rate estimation for traits and phylogenies

phyloCovar: Calculation of Brownian (co)variance using independent...

phyloMean: Calculation of phylogenetically corrected mean.

phyloVar: Calculation of Brownian variance.

pic.motmot: Phylogenetically independent contrasts (internal)

plotPhylo.motmot: Tree plotting for rates

RatePhylo.allCI: Confidence intervals for rate parameters

RatePhylo.CI: Confidence intervals for rate parameters

traitMedusaSummary: Identify shifts in the rate of trait diversification

transformPhylo: Phylogenetic tree transformations

transformPhylo.ll: Log-likelhood for models of trait evoluion.

transformPhylo.ML: Maximum likelhood for models of trait evoluion.

transformPhylo.sim: Simulate trait data

transformRateMatrix: Conversion among data and phylogeny objects

Functions

anolis.data Man page
anolis.tree Man page
as.rateData Man page
as.rateMatrix Man page
cladeIdentity Man page
fairProportions Man page
likRatePhylo Man page
likTraitPhylo Man page
make.anc Man page
make.likRatePhylo Man page
ML.RatePhylo Man page
motmot Man page
motmot-package Man page
node.descendents Man page
optim.likRatePhylo Man page
phyloCovar Man page
phyloMean Man page
phyloVar Man page
pic.motmot Man page
plotPhylo.motmot Man page
RatePhylo.allCI Man page
RatePhylo.CI Man page
traitMedusaSummary Man page
transformPhylo Man page
transformPhylo.ll Man page
transformPhylo.ML Man page
transformPhylo.sim Man page
transformRateMatrix Man page

Files

motmot
motmot/data
motmot/data/anolis.tree.rda
motmot/data/anolis.data.rda
motmot/R
motmot/R/pic.motmot.R motmot/R/fairProportions.R motmot/R/transformPhylo.ll.R motmot/R/transformPhylo.sim.R motmot/R/optim.likRatePhylo.R motmot/R/ML.RatePhylo.R motmot/R/as.rateData.R motmot/R/plotPhylo.motmot.R motmot/R/phyloMean.R motmot/R/likRatePhylo.R motmot/R/as.rateMatrix.R motmot/R/transformPhylo.ML.R motmot/R/phyloVar.R motmot/R/node.descendents.R motmot/R/transformPhylo.R motmot/R/make.likRatePhylo.R motmot/R/phyloCovar.R motmot/R/transformRateMatrix.R motmot/R/RatePhylo.CI.R motmot/R/cladeIdentity.R motmot/R/traitMedusaSummary.R motmot/R/make.anc.R motmot/R/RatePhylo.allCI.R
motmot/R/allCladeMembers.r
motmot/R/likTraitPhylo.R
motmot/NAMESPACE
motmot/dataSources
motmot/dataSources/anolis.data.R
motmot/dataSources/anolis.tree.R
motmot/dataSources/anolis.tree.nex
motmot/dataSources/anolis.data.csv
motmot/DESCRIPTION
motmot/man
motmot/man/make.anc.Rd motmot/man/fairProportions.Rd motmot/man/as.rateMatrix.Rd motmot/man/likRatePhylo.Rd motmot/man/traitMedusaSummary.Rd motmot/man/optim.likRatePhylo.Rd motmot/man/RatePhylo.CI.Rd motmot/man/phyloVar.Rd motmot/man/transformPhylo.Rd motmot/man/RatePhylo.allCI.Rd motmot/man/ML.RatePhylo.Rd motmot/man/likTraitPhylo.Rd motmot/man/plotPhylo.motmot.Rd motmot/man/transformRateMatrix.Rd motmot/man/motmot-package.Rd motmot/man/anolis.tree.Rd motmot/man/anolis.data.Rd motmot/man/node.descendents.Rd motmot/man/transformPhylo.sim.Rd motmot/man/transformPhylo.ML.Rd motmot/man/phyloCovar.Rd motmot/man/as.rateData.Rd motmot/man/phyloMean.Rd motmot/man/pic.motmot.Rd motmot/man/transformPhylo.ll.Rd motmot/man/cladeIdentity.Rd motmot/man/make.likRatePhylo.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.