simulate_MC: Simulate Metacommunity Dynamics

In plthompson/mcomsimr: Simulates Metacommunity Dynamics in R

Simulate Metacommunity Dynamics

Description

Simulate Metacommunity Dynamics

Usage

simulate_MC(
  patches,
  species,
  dispersal = 0.01,
  plot = TRUE,
  torus = FALSE,
  kernel_exp = 0.1,
  env1Scale = 500,
  timesteps = 1200,
  burn_in = 800,
  initialization = 200,
  max_r = 5,
  min_env = 0,
  max_env = 1,
  env_niche_breadth = 0.5,
  optima_spacing = "random",
  intra = 1,
  min_inter = 0,
  max_inter = 1,
  comp_scaler = 0.05,
  extirp_prob = 0,
  landscape,
  disp_mat,
  env.df,
  env_optima,
  int_mat
)

Arguments

patches	number of patches to simulate
species	number of species to simulate
dispersal	dispersal probability between 0 and 1
plot	option to show plot of landscape
torus	whether to model the landscape as a torus
kernel_exp	the exponential rate at which dispersal decreases as a function of the distance between patches
env1Scale	scale of temporal environmental autocorrelation between -2 (anticorrelated) and 2 (correlated), default is 2
timesteps	number of timesteps to simulate
burn_in	length of burn in period
initialization	length of initial period before environmental change begins
max_r	intrinsic growth rate in optimal environment, can be single value or vector of length species
min_env	minium environmental optima
max_env	minium environmental optima
env_niche_breadth	standard deviation of environmental niche breadth, can be single value or vector of length species
optima_spacing	"even" or "random" to specify how optima should be distributed
intra	intraspecific competition coefficient, single value or vector of length species
min_inter	min interspecific comp. coefficient
max_inter	max interspecific comp. coefficient
comp_scaler	value to multiply all competition coefficients by
extirp_prob	probability of local extirpation for each population in each time step (should be a very small value, e.g. 0 or 0.002)
landscape	optional dataframe with x and y columns for patch coordinates
disp_mat	optional matrix with each column specifying the probability that an individual disperses to each other patch (row)
env.df	optional dataframe with environmental conditions with columns: env1, patch, time
env_optima	optional values of environmental optima, should be a vector of length species
int_mat	optional externally generated competition matrix

Value

list that includes metacommunity dynamics, landscape coordinates, environmental conditions, species environmental traits, dispersal matrix, and the competition matrix

Author(s)

Patrick L. Thompson, [e-mail]

Examples

simulate_MC(patches = 6, species = 10, dispersal = 0.001, min_inter = 1, max_inter = 1, env_niche_breadth = 10)

plthompson/mcomsimr documentation built on Feb. 6, 2023, 8:20 a.m.