Tip-based metrics of trait evolution

Usage

calc_tip_based_trait_evo(
  tree,
  trait,
  nsim = 1,
  method = c("transition_rates", "last_transition_time", "stasis_time")
)

Arguments

tree: A phylogenetic tree as an object of class "phylo"
trait: A named vector containing the tip states for a discretely valued character. The names must match the tip labels of the tree.
nsim: Number of simulations to stochastic character mapping.
method: Tip-based metric, partial match to "transition_rates", "last_transition_time" and "stasis_time".

Value

A list (length equal to nsim) with tip-based metrics estimated per species.

Details

This function calculates three metrics that represent the macroevolutionary dynamic of traits for each species in a phylogenetic tree. They are Transition rates, last transition time and stasis time, all originally proposed in Luza et al (2021). Transition rates indicate how many times the ancestral character has changed over time. Stasis time indicates the maximum branch length (time interval) which the current tip-character was maintained across the whole phylogeny. Finally, last transition time is the sum of branch lengths from the tip to the previous node with a reconstructed character equal to the current tip-character. Originally the function uses a stochastic character mapping on discrete trait data, but other types of trait reconstruction can be used.

Author

André Luza and Vanderlei Debastiani

Examples

 
if (FALSE) {
data(rodent.phylo) # phylogenetic tree
data(trait) # categorical traits on species diet
trans_rates <- calc_tip_based_trait_evo(tree=match_data$phy,trait =trait ,
    nsim = 50,method = c("transition_rates", "last_transition_time", "stasis_time")
    )
}