stability2 {soilfoodwebs}

A function to run the stability analysis using the numerical simulation of the Jacobain matrix.

Description

A function to run the stability analysis using the numerical simulation of the Jacobain matrix.

Usage

stability2(
  usin,
  DIETLIMTS = NA,
  diet_correct = TRUE,
  Conly = FALSE,
  userdefinedinputs = NA,
  has_inorganic_nitrogen = FALSE,
  inorganic_nitrogen_properties = list(INN = NA, q = NA, eqmN = NA),
  forstabilityonly = TRUE,
  densitydependence = NA
)

Arguments

usin

The community for which to calculate stability.

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.

has_inorganic_nitrogen

Boolean: Is there an inorganic nitrogen pool?

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.

forstabilityonly

Boolean: Do you only want to check the stability of the carbon equations and inorganic nitrogen? If FALSE then changes in detritus nitrogen are also included.

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.

Details

The stability as defined by the Jacobian is estimated using the ordinary differential equations. Consequenlty, the parameters are retrieved using getPARAMS and then added to the function jacobian.full using the ODE defined by foodwebode This stability function allows the user to define density-dependence by node as present or absent. If you want to apply a uniform level of density-dependence use the function 'stability' and choose the option Moorecobain.

Value

The stability calculated by the Jacobian as a list of the Jacobian, eigenvalues, and the maximum eigenvalue.

See Also

getPARAMS and foodwebode for functions which are called internally and jacobian.full for the method used.

Examples

# Basic stability calculation:
stability2(intro_comm)

# Stability calculation with density-dependence for the animals:
stability2(intro_comm, densitydependence = c(1, 1, 1, 0, 0, 0, 0))