stability2 {soilfoodwebs} | R Documentation |
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))