calc_tip_based_trait_evo: Tip-based metrics of trait evolution

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

Tip-based metrics of trait evolution

Description

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".

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.

Value

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

Author(s)

André Luza and Vanderlei Debastiani

Examples

 
## Not run: 
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")
    )

## End(Not run)

GabrielNakamura/Rrodotus documentation built on Aug. 31, 2023, 2:13 p.m.