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.

Author
Gavin Thomas, Rob Freckleton
Date of publication
2012-12-14 14:02:07
Maintainer
Gavin Thomas <gavin.thomas@sheffield.ac.uk>
License
GPL (>= 2)
Version
1.1.2
URLs

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

Files in this package

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