Equilibrium: An R6 class to calculate the equilibrium of a model

In junlingm/REpiSim: Mathematical Epidemiological Model Simulations in R

An R6 class to calculate the equilibrium of a model

Description

An R6 class to calculate the equilibrium of a model

An R6 class to calculate the equilibrium of a model

Details

Calculate the equilibrium of the model with a given initial condition

Super classes

REpiSim::Simulator -> REpiSim::ODE -> Equilibrium

Methods

Public methods

• Equilibrium$new()

• Equilibrium$simulate()

• Equilibrium$clone()

---

Method new()

constructor

Usage

Equilibrium$new(
  model,
  vary = NULL,
  range = NULL,
  max.iter = 100,
  error = 1e-06
)

Arguments

model

the model to simulate. It must be an object of a subclass of 'Model'.

vary

the name of a parameter to value, a character

range

the range of the varying parameter, a numerical vector

max.iter

the maximum iterations to search for the equilibrium

error

a numeric value giving the 2-norm of the tolerance

---

Method simulate()

simulate the model

Usage

Equilibrium$simulate(t, y0, parms = NULL, vars = names(y0), ...)

Arguments

t

a numeric vector of times.

y0

a numeric vector of initial conditions.

parms

a numeric vector of parameter values.

vars

a character vector specifying the variable names to be returned. A variable can be either a compartment or a substitution

...

extra arguments to be passed to the 'ode' method substitutions that depend on the compartments are calculated and returned

Returns

a data frame which rows correspond to each time in 't', and columns correspond to the variables specified in vars.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Equilibrium$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## an SIR model
SIR = Model$new(title="SIR")
SIR$compartment(S ~ -beta*S*I/N)$
  compartment(I ~ beta*S*I/N - gamma*I)$
  compartment(R ~ gamma*I)$
  where(N = S + I + R)
eq = Equilibrium$new(SIR, vary="beta", range=seq(0, 0.4, by=0.01))
ode$simulate(
  time=0:40, 
  y0=c(S=10000, I=1, R=0), 
  parms=c(beta=0.4, gamma=0.2), 
  alias = FALSE) # N is not returned.

junlingm/REpiSim documentation built on Nov. 28, 2023, 2:35 a.m.