run_optim_empirical_sims: Run optimisation on trees simulated from empirical...

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

Description

Run optimisation on trees simulated from empirical phylogenies

Usage

run_optim_empirical_sims(
  family_name,
  sim,
  optim,
  rangemc = 1:1000,
  outputfile = paste0(family_name, "_sim", sim, "_optim", optim, ".rds"),
  jobID = NA,
  return_results = FALSE,
  save_results = TRUE
)

Arguments

family_name	character, the name of the family from which the simulated trees were generated from. Must match a file in "DDvTD/data/empirical_trees/".
sim	character, name of the simulation model, either "DD" or "TD".
optim	character, name of the optimisation model, either "DD" or "TD".
rangemc	numeric vector, a set of tree indices ranging from 1 to 1000.
outputfile	character, the name of the file to save the output data frame in.
jobID	SLURM job ID passed when the function is called from a cluster script.
return_results	logical. Should the results be returned?
save_results	logical. Should the results be saved to outputfile?

Author(s)

Théo Pannetier

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