motmot-package |
Models Of Trait Macroevolution On Trees |
addFossilToPhy |
add a fossil to an interior branch of a time-scaled phylogeny |
allopatric.data |
Finch allopatric data |
anolis.data |
Anolis phenotype data |
anolis.tree |
Anolis phylogeny |
as.rateData |
Conversion among data and phylogeny objects |
as.rateMatrix |
Conversion among data and phylogeny objects |
blomberg.k |
Blomberg's K Estimate Blomberg's K (Blomberg et al. 2003) |
calcCutOff |
Calculate multiple-test cut-off |
chr.disp.lrt |
Character displacement likelihood ratio test |
chr.disp.param |
Simulate character displacement data wrapper |
chr.disp.sim |
Simulate character displacement data |
contemporaryPhy |
prune tree and data to lineages present in a time bin in the past |
dropTipPartial |
Drop tips from a phylogenetic tree while preserving deleted nodes |
fairProportions |
Calculate fair proportions phylogenetic diversity metric |
finch.data |
Finch phenotype data |
finch.tree |
Finch tree |
likRatePhylo |
Log-likelihood rate estimation for traits and phylogenies |
likTraitPhylo |
Log-likelihood estimation for traits and phylogenies |
mammals |
Mammal data |
mcmc.plot |
plot the output from transformPhylo.MCMC |
ML.RatePhylo |
Maximum likelihood rate estimation for traits and phylogenies |
motmot |
Models Of Trait Macroevolution On Trees |
node.descendents |
Identify nodes and tips descended from a node |
nodeTimes |
Get times for nodes and tips |
optim.likRatePhylo |
Maximum likelihood rate estimation for traits and phylogenies |
phyloCovar |
Calculation of Brownian (co)variance using independent contrasts. |
phyloMean |
Calculation of phylogenetically corrected mean. |
phyloVar |
Calculation of Brownian variance. |
pic.pgls |
Fast PLGS estimation based on contrasts |
plot.timeSlice.ML |
Identify shifts in the rate of trait diversification through time |
plot.traitMedusa.model |
Tree plotting for rates |
RatePhylo.allCI |
Confidence intervals for rate parameters |
sampleShid |
Sample hidden speciation events along branches of a tree |
sortTraitData |
Sort data and remove missing entries for tree and trait data |
summary.traitMedusa |
Identify shifts in the rate of trait diversification |
traitData.plot |
plot a univariate continuous trait data on a phylogeny |
transformPhylo |
Phylogenetic tree transformations |
transformPhylo.ll |
Log-likelhood for models of trait evolution. |
transformPhylo.MCMC |
Bayesian MCMC for models of trait evolution |
transformPhylo.ML |
Maximum likelihood for models of trait evoluion |
transformPhylo.sim |
Phylogenetic tree transformations |
transformRateMatrix |
Conversion among data and phylogeny objects |