set_g_p: Set global parameters

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

Description

Set the global parameters for the simulation, allowing for individual elements to be reassigned. Default parameters assume 8.1 hectare cells.

Usage

set_g_p(tmax = 100, dem.st = FALSE, sdd.st = TRUE, bank = TRUE,
  n.cores = 4, lc.r = Inf, lc.c = Inf, n.lc = 6, N.p.t0 = 10,
  p.f = c(0.45, 0, 0.291, 0.309, 0.309, 0.272), mu = c(1948, 0, 14, 41,
  41, 21), gamma = 2.48, m = c(3, 3, 7, 7, 7, 7), p.c = c(0.165,
  0.165, 0.296, 0.252, 0.252, 0.296), sdd.rate = 0.03775, sdd.max = 24,
  bird.hab = c(0.32, 0.36, 0.05, 0.09, 0.09, 0.09), n.ldd = 19,
  s.c = 0.585, s.B = 0.72, s.M = c(0.9, 0, 0.6, 0.6, 0.6, 0.6),
  s.N = c(1, 1, 1, 1, 1, 1), K = c(28205, 0, 4162, 4162, 4162, 4162),
  g.D = 0, g.B = 0.2, p = c(0.295, 0, 0.421, 0.082, 0.082, 0.23),
  edges = "wall", method = "wt.mn")

Arguments

tmax	100 Number of time steps per simulation
dem.st	FALSE Include stochasticity in demography?
sdd.st	TRUE Include stochasticity in short distance dispersal?
bank	TRUE Include seedbank?
n.cores	4 Number of cores for parallelizing sdd.pr calculation
lc.r	Inf Maximum number of rows (y) in landscape
lc.c	Inf Maximum number of columns (x) in landscape
n.lc	6 Number of land cover categories
N.p.t0	10 Number of cells with buckthorn at t=1
p.f	c(0.45, 0, 0.291, 0.309, 0.309, 0.272) Vector length=n.lc of fruiting probabilities
mu	c(1948, 0, 14, 41, 41, 21) Vector length=n.lc of mean fruit per adult
gamma	2.48 Scalar: mean number of seeds per fruit
m	c(3, 3, 7, 7, 7, 7) Vector length=n.lc or scalar of age at first fruiting. Individuals at this age are considered adults
p.c	c(0.165, 0.165, 0.296, 0.252, 0.252, 0.296) Vector length=n.lc of proportion of fruits eaten by birds, with 1-p.c assumed to drop directly below buckthorn individuals
sdd.rate	0.03775 1/mn for exponential dispersal kernel (units = cells); value assumes 20ac (8.1 ha) grid cells
sdd.max	24 Maximum dispersal distance in cells (units = cells); value assumes 20ac (8.1 ha) grid cells
bird.hab	c(0.32, 0.36, 0.05, 0.09, 0.09, 0.09) Vector length=n.lc of relative bird habitat preferences
n.ldd	19 Number of long distance dispersal events per year
s.c	0.585 Seed viability post-digestion
s.B	0.72 Probability of annual survival in seed bank
s.M	c(0.9, 0. 0.6, 0.6, 0.6, 0.6) Vector length=n.lc of annual juvenile survival rates
s.N	c(1, 1, 1, 1, 1, 1) Vector length=n.lc of annual adult survival rates
K	c(28205, 0, 4162, 4162, 4162, 4162) Vector (length=n.lc) of carrying capacities for adults; values assume 20ac (8.1 ha) grid cells
g.D	0 Probability of direct germination (i.e., a seed germinates in the same year it is produced)
g.B	0.2 Probability of germinating from the seed bank
p	c(0.295, 0, 0.421, 0.082, 0.082, 0.23) Vector length=n.lc of seedling establishment probabilities
edges	"wall" Boundary behavior, taking values of "wall", "sink", or "none". See boundary_behavior.Rmd for descriptions
method	"wt.mn" Method for calculating cell expectations, taking values of "wt.mn" or "lm". If "wt.mn", the expectation for each parameter is the weighted mean across land cover types proportional to their coverage, with the land cover specific values stored in the parameter vectors. If "lm", the expectation is calculated in a regression with the slopes contained in each parameter vector. Individuals cannot be assigned to specific land cover categories with "lm", so "m" must be scalar.

Value

Named list of global parameters including all arguments as elements

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