setup.matrices: Set up model matrices

In akeyel/spatialdemography: A Spatially Explicit Metacommunity Model

Description

This function sets up the core matrices for the matrix diagnostics and the simulation model.

Usage

setup.matrices(K_g, spe, SpTraits, p, S, landscape, landscape.identifiers,
  distances, B1.template, B2.template, P, M_sub, DispPath, vdb.data,
  change.count, outpath.base, num.sim, run.times = NA, run.lbl = NA,
  multi.species.K = 0, edge.type = "TORUS")

Arguments

K_g	Carrying capacity in grams
spe	Total number of species in the species pool
SpTraits	A dataframe containing species traits
p	The number of cells in a square landscape
S	The number of stages in the matrix model
landscape	a list of environmental layers, each with a value for each cell in the landscape
landscape.identifiers	A list of single-letter identifiers for each environmental layer
distances	Distances between each cell in the landscape
B1.template	A template for the B1 demography matrix
B2.template	A template for the B2 demography matrix
P	The vec-permutation matrix
M_sub	The M matrix template
DispPath	The path to the dispersal tables
vdb.data	An indicator for whether or not to create visual debugger data
change.count	The change step
outpath.base	The base output path.
num.sim	The number of simulations to use in creating dispersal probabilities
run.times	(optional, defaults to NA) For timing the function
run.lbl	= (optional, defaults to NA) For labeling the timing of the function
multi.species.K	(default is 0) An indicator for whether a multispecies carrying capacity is desired
edge.type	(default is "TORUS") An indicator for what type of landscape edge is desired.

akeyel/spatialdemography documentation built on May 12, 2019, 4:43 a.m.