inst/shiny-examples/catalytic.R

In deBif: Bifurcation Analysis of Ordinary Differential Equation Systems

# Catalytic oscillator model, see Matcont manual (september 2012, section 10.1.5)
# -------------------------------------------------------------------------------

# Equations:
# ----------
#
# dx
# -- = 2 q1 (1 - x - y - s)^2 - 2 q5 x^2 -q3 x y
# dt
#
# dy
# -- = q2 (1 - x - y - s) - q6 y -q3 x y
# dt
#
# ds
# -- = q4 (1 - x - y - s) - k q4 s
# dt
#

# The model has to be specified as a function that returns
# the derivatives as a list. You can adapt the body below
# to represent your model

# The initial state of the system has to be specified as a named vector of state values.
state <- c(x = 0.0029538, y = 0.76211, s = 0.16781)

# Parameters have to be specified as a named vector of parameters.
parms <- c(q1 = 2.5, q2 = 1.4707, q3 = 10, q4 = 0.0675, q5 = 1, q6 = 0.1, k = 0.4)

# The model has to be specified as a function that returns
# the derivatives as a list. You can adapt the body below
# to represent your model
catalytic <- function(t, state, parms) {
  with(as.list(c(state,parms)), {

    z <- (1 - x - y - s)
    dx <- 2*q1*(z^2) - 2*q5*(x^2) - q3*x*y
    dy <- q2*z - q6*y - q3*x*y
    ds <- q4*z - k*q4*s

    # The order of the derivatives in the returned list has to be
    # identical to the order of the state variables contained in 
    # the argument `state`
    return(list(c(dx, dy, ds)))
  })
}

bifurcation(catalytic, state, parms)