PlantSim: Simulate a plant community

In xl0418/PlantSim: Simulating a plant community and estimating the interaction matrix

Simulate a plant community

Description

Simulate a plant community

Usage

plantsim(
  nplot,
  nspe,
  nt,
  ini_abundance,
  growth_rate,
  interaction_matrix,
  st_portion,
  filesave = NULL,
  vary_k = FALSE,
  distribution = "uniform",
  model = "Ricker",
  sig_disp = 1,
  boundary = FALSE,
  cell_kill_rate = 0,
  seed = FALSE
)

Arguments

nplot	The number of the plots in the community
nspe	The number of the species
nt	The total time steps
ini_abundance	The initial abundance of the species
growth_rate	The growth rate for each plot and each species. It could be universally same.
interaction_matrix	The interaction matrix among species
st_portion	The portion of the seedlings that stay at the parental plot.
filesave	The file name to be saved.
vary_k	Set vary_k be a vector of two entries providing the mean and the sd. Otherwise, it is FALSE giving the same k = 1 to all plots.
distribution	Distribution mode. "uniform" stands for the uniform dispersal; "random" stands for the random dispersal; "Gaussian" stands for the Gaussian dispersal.
model	Specify local population models, i.e. Ricker, BH, PL, for the Ricker model, the Beverton-Holt model and the power law model.
sig_disp	The variance of the dispersal for the Gaussian dispersal kernel.
boundary	If TRUE, the boundary effect is considered. Otherwise, the grid is a torus.
cell_kill_rate	The percentage of cells eliminates plant individuals.
seed	Set the seed for reproducibility of simulation.

Value

The abundance matrix for all plots and species through time.

Examples

plantsim(nplot = 5, nspe = 2, nt = 10, ini_abundance = matrix(1:10, 5, 2),
 growth_rate = 1, interaction_matrix = matrix(0.001, 2, 2), st_portion = 0.7)

xl0418/PlantSim documentation built on June 13, 2022, 4:38 a.m.