run_sim: Simulate a set of phylogenetic trees under a time-dependent...

In TheoPannetier/DDvTDtools: Compare diversity-dependent (DD) and time-dependent (TD) diversification models

Description

Sets parameter values and calls DDD::dd_sim() or DDD::td_sim() to simulate a set of phylogenetic trees.

Usage

run_sim(
  sim,
  para,
  nb_trees = 1000,
  seed = 42,
  outputfile = paste0("./data/sim/sim", sim, "-", para, ".RData"),
  save_results = TRUE,
  return_results = FALSE
)

Arguments

sim	character, name of the simulation model, either "DD" or "TD".
para	numeric, a four-digits number coding for a set of four parameter values. Refer to arg_para() doc for details, and call arg_para() to see possible inputs.
nb_trees	numeric. How many trees should be generated?
seed	numeric, the number to seed the random number generator.
outputfile	path and name for output file, by default generated automatically from sim and para.
save_results	logical. Should save the results to outpufile (default) or not.
return_results	logical. Should results be returned? Default to TRUE.

Value

A list containing nb_trees simulated trees. Each element is itself a list of four elements, as the the output of DDD::dd_sim(). Refer to the relevant documentation in DDD for more details.

Author(s)

Cesar Martinez and Theo Pannetier

TheoPannetier/DDvTDtools documentation built on Oct. 22, 2020, 2:31 p.m.