make.landscape: Make a simulation landscape

In sokole/MCSim: Metacommunity simulations for ecologists

Make a simulation landscape

Description

Define the attributes of a MCSim landscape, including number of sites, area, carrying capacity, and local immigration rates.

Usage

make.landscape(JM = 10000, m = 0.1)
make.landscape(site.coords = c(1:10), m = 0.1, JM = 10000)

Arguments

site.info	A data frame with site information
site.coords	A data.frame of site coordinates. Can be 1, 2, or more dimensions
dist.mat	Alternative to site.coords. Can be a distance matrix or a network map from the igraph package
JL	Scalar or vector number of individuals at each site, overrides JM
JM	Total number of individuals to include in a MCSim simulation.
m	Immigration rate paramter, from Hubbells neutral model. Overrides I.rate.m2.
I.rate.m2	Alternative to m, immigration rate in number of individuals / m2 / timestep. Default is 1.
area.m2	Area of each site in m2. Default is 1.
Ef.specificity	Vector of specificity values for environmental filters at each site. If 0 (default), site habitat value is modeled as a single point along an environmental gradient. If > 0, a site's habitat is modeled as a normal curve around a point on an environmental gradient.
Ef	Vector of habitat scores for each site.
guess.site.coords	Binary. If TRUE, Uses PCoA to extract site coordinates if given a distance matrix or network map. Useful to make a map to display sites. Not necessary if igraph input is used because igraph has a function to plot a network map. Default is FALSE.
list.of.stuff	A list that can be used to store other landscape attributes in the landscape object. Useful for storing igraph properties when igraph is used.

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

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