metasim: A metacommunity simulation for ecologists

In sokole/MCSim: Metacommunity simulations for ecologists

A metacommunity simulation for ecologists

Description

metasim() initiates a metacommunity simulation based on a landscape created by the make.landscape() function.

Usage

metasim(landscape, ...)

Arguments

landscape	Landscape object created by function make.landscape()
scenario.ID	A name for the simulation scenario. All simulations with the same scenario name will have metadata collated in a single .csv file. Default is NA
sim.ID	A name for this particular simulation. Default will provide a random ID.
alpha.fisher	User can use Fisher's alpha to seed a simulation's initial regional source pool.
nu	Probability a novel species will appear in a single recruitment event
speciation.limit	Set's a limit on the number of novel taxa that can appear in a simulation
JM.limit	set's an upper limit for the number of individuals in a simulation
n.timestep	Number of generations in a simulation
W.r	Dispersal kernel slope
save.sim	Binary, will save the simulation as a .rda file if TRUE. Default is FALSE.
output.dir.path	Name of directory to save simulation results and metadata. Default is "SIM_OUTPUT". Simulation will create a sub-directory in the working directory if none exists.
trait.dispersal	Vector of dispersal traits. Default is NULL
trait.dispersal.median	Scalar value for dispersal applied to all species if no vector is provided. Default is 1.
trait.dispersal.range	Range of dispersal values given to species if dispersal traits are randomly assigned.
trait.Ef	Vector of species' niche positions
trait.Ef.sd	Vector of species' niche breadths
gamma.abund	Vector of regional abundances, can be used to seed a simulation
J.t0	Site by species data.table or matrix that can be used to seed a simulation
taxa.list	A character vector of names for species

Details

There are two steps to creating a metacommunity simulation in MCSim: 1. Make a "landscape" – The landscape is the “game board” on which the simulation plays out, and it is created using the make.landscape function. 2. Run the simulation – Once the landscape is created, you can pass the landscape object to metaSIM along with parameter settings that define the rules for how metacommunity dynamics will play out in the metacommunity simulation. Note that the current version of MCSim is zero sum, which means there will always be JM individuals in the simulation during each generation. For a tutorial, see http://rpubs.com/sokole/159425

Note that a user can choose to save simulation output to a directory set by output.dir.path by setting save.sim = TRUE

Examples

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

# make a landscape
my.landscape <- 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)

# 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)

# run a simulation with 10 generations
sim.result <- metasim(
  landscape = my.landscape,
  trait.Ef = niche.positions,
  trait.Ef.sd = niche.breadths,
  gamma.abund = regional.rel.abund,
  W.r = 0,
  nu = 0.001,
  n.timestep = 10,
  sim.ID = "my_test_sim",
  output.dir.path = "my_sim_output_directory"
)


# plot coenoclines to view niches
plot.coenoclines(sim.result)

# plot dispersal kernal
plot.standardized.disp.kernel(sim.result)

# plot dot plots
plot.dot.plots(sim.result)

## End(Not run)

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