allCladeMembers (internal function)
Extimate ancestral state (internal function)
Maximum likelihood rate estimation for traits and phylogenies
Confidence intervals for rate parameters
Create design matrix (internal function)
Internal function
Get times for nodes and tips
Maximum likelihood rate estimation for traits and phylogenies
Anolis phenotype data
Name check (internal function)
Identify nodes and tips descended from a node (internal function).
Tree plotting for rates
Plots trees with colours based on rates of trait evolution. Also provides simple coloured plotting for trait values using the "ace" function in the ape library.
remove species occuring before time in the past (internal function)
Identify shifts in the rate of trait diversification
Anolis phylogeny
Conversion among data and phylogeny objects
Conversion among data and phylogeny objects
Identify branches (including tips) descended from a node (internal function).
prune tree and data to lineages present in a time bin in the past
Maximum likelihood for models of trait evoluion
Phylogenetic tree transformations
Log-likelihood rate estimation for traits and phylogenies
Log-likelihood rate estimation for traits and phylogenies
Calculation of Brownian (co)variance using independent contrasts.
Calculation of phylogenetically corrected mean.
Sort data and remove missing entries for tree and trait data
Identify shifts in the rate of trait diversification through time
Bayesian MCMC for models of trait evolution
Confidence intervals for rate parameters
add a fossil to an interior branch of a time-scaled phylogeny
Drop tips from a phylogenetic tree while preserving deleted nodes
Calculate fair proportions phylogenetic diversity metric
Sample hidden speciation events along branches of a tree (internal function)
Slice tree (internal function)
Log-likelhood for models of trait evolution.
Phylogenetic tree transformations
Calculation of Brownian variance.
Phylogenetically independent contrasts (internal)
timeTravelPhy (internal function)
plot a univariate continuous trait data on a phylogeny
Conversion among data and phylogeny objects