sim_radiation: Main Niche Filling Simulation Function

Description Usage Arguments Value Parameter List K_parms a_parms macro_parms

View source: R/main_niche_fill_sim.R

Description

Function to setup and run the niche filling simulation

Usage

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sim_radiation(parms, save_tree = TRUE, progress = TRUE, trait_hist = TRUE,
  trait_hist_prop = 0.01)

Arguments

parms

A named list containing three named list elements:

  • "K_parms": Named list of parameters relating to the carrying capacity landscape function

  • "a_parms": Named list of parameters relating to the competition function

  • "macro_parms": Named list of parameters relating to the macroevolutionary simulation

See Parameter List section for details on what parameters are in which lists.

save_tree

A logical determining whether the simulation should save intermediate states of the phylogeny during the simulation run

progress

Print progress bar if TRUE.

trait_hist

A logical determining whether the simulation should save all trait evolution histories. Set to FALSE if you are only interested in the end state of the simulation in order to save memory.

trait_hist_prop

If trait_hist is TRUE, what proportion of data should be kept? For example setting this parameter to 0.5 would tell the simulation to store 50% of the generations in the full simulation. I recommend setting this low to save storage space, and because it is often possible to get a very good animation with only a small proportion of the full simulation (default is 0.01 and this is usually plenty).

Value

A niche_fill_sim object containing the final simulation object, a set of intermediate phylogenies, and the parameters used to run the simulation

Parameter List

There are three named lists in the parms parameter, relating to the carrying capacity, the competition, and the macroevolutionary model. The parameters found in each one are as follows:

K_parms

a_parms

macro_parms


rdinnager/nichefillr documentation built on March 19, 2018, 7:02 a.m.