Description Usage Arguments Details Value See Also Examples
This function creates an object of class ratmak
(subclass of ode
), which holds the basic information of the Rational Mass Action Kinetics system in question.
1 2 
A 
The matrix of powers (bxd). Here d the number of species. 
C 
The stoichiometric coefficient matrix (rxd). Here r is the number of reactions. 
s 

r1 
An object of class 
r2 
An object of class 
rx0 
An object of class 
Rational Mass Action Kinetics is a class of ODE systems, having the following vector field:
\frac{dx}{dt} = C^T * (θ_1 * x^A) / (1 + θ_2 * x^A)
with x^A = (∏_{i=1}^dx_i^{A_{ji}})_{j=1}^b, θ_1 and θ_2 estimatable parameter matrices of dimension rxb. θ_2 is restricted to nonnegative values. The fraction is entrywise. By convention the theta's will only be reported as vectors (concatinated columnwise).
An object with S3 class "ratmak" and "ode".
ode, numsolve, field
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19  # Rational mass action kinetics
A < matrix(
c(1, 0, 0, 0,
0, 1, 2, 0,
1, 0, 0, 1), ncol = 4, byrow = TRUE)
x0 < c(X = 1, Y = 4, Z = 0.1, W = 0.1)
time < seq(0, 1, by = .1)
rmak < ratmak(A, diag(4))
# Solve system
numsolve(o = rmak, time = time, x0 = x0,
param = list(theta1 = t(A * 1:3),
theta2 = t((A + 1) * 3:1)))
# Evaluate field
field(rmak, x0,
param = list(theta1 = t(A * 1:3),
theta2 = t((A + 1) * 3:1)))

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