metasim.disturbance: A metacommunity simulation for ecologists

In sokole/MCSim: Metacommunity simulations for ecologists

A metacommunity simulation for ecologists

Description

Wrapper function for MCSim::metasim, sends landscape list and interval duration list, along with other metasim parameters that will be fixed across all simulations

Usage

metasim.disturbance(scenario.name, landscape.list, time.interval.durations)

Arguments

scenario.name	text string naming the scenario
landscape.list	list of landscapes to run in series
time.interval.durations	vector of integers representing the number of timesteps to use for each landscape in the landscape_list, MUST be same length as landscape_list
J.t0.initial	Initial species abundance matrix for timestep "t0"
scenario_name	DEPRECATED: use scenario.name
landscape_list	DEPRECATED: use landscape.list
time_interval_durations	DEPRECATED: use time.interval.durations
J.t0_initial	Deprecated: use J.t0.initial
...	parameters sent to metasim()

Examples

## Not run: 
set.seed(1234) #set random seed

# make a landscapes
my.landscape.1 <- make.landscape(
  site.coords = data.frame(
    x = c(1, 2, 3, 4, 5),
    y = c(1, 3, 1, 5, 2)),
  Ef = c(-.8, -.6, 0, .25, .9),
  m = 0.5,
  JM = 10000)

my.landscape.2 <- make.landscape(
  site.coords = data.frame(
    x = c(1, 2, 3, 4, 5),
    y = c(1, 3, 1, 5, 2)),
  Ef = c(-.8, -.6, 0, 0, 0),
  m = 0.5,
  JM = 10000)

# niche positions, niche breadths, and relative abundances for three species
niche.positions <-  c(-.5, 0, .5)
niche.breadths <- c(.2, .2, 5)
regional.rel.abund <- c(.8, .1, .1)

sim.result <- metasim.disturbance(
  scenario.name = "niche_shift",
  landscape.list = list(my.landscape.1,my.landscape.2),
  time.interval.durations = c(10,10),
  trait.Ef = niche.positions,
  trait.Ef.sd = niche.breadths,
  gamma.abund = regional.rel.abund,
  W.r = 0,
  nu = 0.001,
  output.dir.path = "my_disturbance_sim_output_directory")

## End(Not run)

sokole/MCSim documentation built on April 2, 2022, 5:43 a.m.