CNsim: A function to simulate the dynamics over time wrapping getPARAMS and foodwebode

Description

A function to simulate the dynamics over time wrapping getPARAMS and foodwebode

Usage

CNsim(
  usin,
  DIETLIMTS = NA,
  diet_correct = TRUE,
  Conly = FALSE,
  userdefinedinputs = NA,
  start_mod = NA,
  TIMES = 1:100,
  keepallnitrogen = TRUE,
  has_inorganic_nitrogen = FALSE,
  densitydependence = NA,
  inorganic_nitrogen_properties = list(INN = NA, q = NA, eqmN = NA),
  DETEXPT = NA,
  DETEXPTSTART = NA,
  rtn_only_state = TRUE
)

Value

The output of the simulation.

Arguments

usin: The community you want to simulate.
DIETLIMTS: The diet limits matrix for the stoichiometry correction (proportion of diet)?
diet_correct: Boolean: Does the organism correct it's diet?
Conly: Boolean: Is the model meant for carbon only?
userdefinedinputs: Do you want to input a user defined vector of input functions? If NA the input values that keep the system at equilibrium are calculated. If not, put in a vector of input rates for each node.
start_mod: A vector of modifications to the starting conditions, which default to the biomass vector in the community. This vector is multiplied by the biomass vector.
TIMES: The vector of times that you want to run the model. Defaults to 1 to 100 by 1.
keepallnitrogen: Boolean: Keep all the nitrogen pools in the model output? Will be set to FALSE if you are running a stability analysis using the function stability2().
has_inorganic_nitrogen: Boolean: Is there an inorganic nitrogen pool?
densitydependence: Which nodes have density dependence? NA default means none of them do. Should be a vector of 0 (no DD) and 1 (DD) for each node.
inorganic_nitrogen_properties: A list of state variables for the inorganic nitrogen pool (INN = inputs, q = per capita loss of N, eqmN = equilibrium N). Must include a value for two of the three variables and has the final one as NA.
DETEXPT: The pool that should be used for the detritus experiment by name or position in the vector usin$prop$ID.
DETEXPTSTART: The start of the detritus experiment. Defaults to 100.
rtn_only_state: Boolean: Do you want to only return the model state variables? If FALSE then the consumption rates and production efficiency at each time step are also returned.

Details

A function that simulates the food web over the user defined times. If you do not modify the starting state using start_mod or add a detritus experiment using DETEXPT, then the result will just be a flat line if the food web is stable.

Examples

Run this code

# Basic example with a 5% reduction in predator biomass:
CNsim(intro_comm, start_mod = c(0.95, 1,1,1,1,1,1))

# Simulate a decomposition experiment:
CNsim(intro_comm, DETEXPT = c("Detritus1"), DETEXPTSTART = 100)