run_sim: Run demographic simulation

In Sz-Tim/gbPopMod: Mechanistic species distribution model for glossy buckthorn (*Frangula alnus*)

Description

Run the simulation. Currently, it runs all time steps, but for the economic model, the structure will need to be slightly adjusted to run a single time step. The initialization is separated from this function for that reason.

Usage

run_sim(ngrid, ncell, g.p, lc.df, sdd, N.init, control.p, verbose = TRUE,
  save_yrs = NULL, K_max = NULL, dem_out = TRUE,
  collapse_LCs = TRUE)

Arguments

ngrid	Number of grid cells in entire map
ncell	Number of inbound grid cells
g.p	Named list of global parameters set with set_g_p
lc.df	Dataframe or tibble with xy coords, land cover proportions, and cell id info
sdd	Output with short distance dispersal neighborhoods created by sdd_set_probs
N.init	Matrix or array with initial population sizes created by pop_init
control.p	NULL or named list of buckthorn control treatment parameters set with set_control_p
verbose	TRUE Show progress bar?
save_yrs	NULL Vector of years to save; if NULL, all years are returned
K_max	NULL Maximum carrying capacity to avoid memory overloads
dem_out	TRUE Store nFl, nSd, nSdStay, D?
collapse_LCs	TRUE Sum abundances within each cell?

Value

Array N of abundances for each cell and age group, matrix B of seed bank abundances, matrix nFl with number of flowering individuals, matrix nSd of total seeds produced in each cell, matrix nSdStay of total seeds remaining in each cell, and matrix D of immigrants into each cell.

Sz-Tim/gbPopMod documentation built on Dec. 7, 2020, 1:07 p.m.