simulate_rate_decay: Simulate the expected amount of trait evolution under...

Description Usage Arguments Value

View source: R/simulate_rate_decay.R

Description

Simulate the expected amount of trait evolution under lineage-age dependent decay of rates

Usage

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simulate_rate_decay(
  change_rate,
  start_rate = NULL,
  time_elapsed,
  plot = TRUE,
  npoints = 10,
  nsims = 1000
)

Arguments

change_rate

Numeric. The factor of exponential decay of rates in function of the age of the lineage.

start_rate

NULL or Numeric or matrix. If NULL, the function returns the fator of rate decay in function of the age of the lineage. If numeric or matrix, it represents the rate of trait evolution at the start of the simulation (lineage age of 0.0 My). If a single numeric number, the function assumes a Brownian Motion process. If a matrix, the model assumes it is a transition matrix (Q) for a discrete trait Markovian process.

time_elapsed

Numeric. The age of the lineage at the end of the simulation. Simulation will happen from 0.0 to 'time_elapsed' My.

plot

Logical. If TRUE a plot is made.

npoints

Integer. Number of time points to sample along the age of the lineage.

nsims

Integer. Number of simulation replicates used to estimate the number of expected transition events when 'start_rate' is a Q matrix. Transition events are estimated using forward simulations with the starting state randomly sampled from Q (with equal probability).

Value

a matrix with the information for the age and the expected amount of trait evolution at each 'npoints' time point.


Caetanods/buddPhy documentation built on Oct. 12, 2021, 12:14 p.m.