transitions_through_time: Summarize trait dynamics through time

In mongiardino/extendedSurface: Fit Complex Multi-OU Models by Extending SURFACE and Providing an Interface with OUwie

Description

This function provides a way of summarizing the temporal dynamics of traits by registering the times when there are transitions between character states. First, a number of replicates of stochastic character mappings are created (see make.simmap for more details), and the phylogeny is traversed in order to register the moments in time when there are transitions between states. For every time a transition occurs, the function will follow all descendants and also register the point in time where that instance of a given state goes extinct (either by all descendants transitioning to a different state or by all tips going extinct).

Usage

transitions_through_time(tree, char, repl = 100, model = "ER", plot = T)

Arguments

tree	Phylogenetic tree in 'phylo' format.
char	Named vector including character states for all tips. Names need to correspond to tips in the phylogeny.
repl	Number of replicates of stochastic character mapping (default = 100)
model	A character specifying the model of evolution used to reconstruct the evolutionary history of the character. Options include 'ER' (default), 'SYM' and 'ARD', see ace.
plot	A logical indicating whether to plot the results. Default is TRUE.

Details

The funtion only requires a tree and a character, and allows the user to modify the number of replicates, the model used for character mapping, as well as whether to return a plot summarizing the results. More control on what and how to plot these results is attained by providing the output to the function plot_ttt.

Value

A data.frame including the times of birth and death of each instance of a character across replicates. This object can be passed to plot_ttt to obtain different visualizations.

Author(s)

Nicolás Mongiardino Koch

References

Mongiardino Koch N. 2021. Exploring adaptive landscapes across deep time: A case study using echinoid body size. Evolution, https://doi.org/10.1111/evo.14219.

See Also

For details on stochastic character mapping visit make.simmap. Plots can be explored with plot_ttt

mongiardino/extendedSurface documentation built on July 6, 2021, 7:13 p.m.