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dMod (version 0.1)

variableTransformation: Do a variable transformation in the ODE

Description

Do a variable transformation in the ODE

Usage

variableTransformation(observables, f = NULL, dynvar = NULL, stoi = NULL,
  flows = NULL, conserved = TRUE)

Arguments

observables
Named character vector. The names are the new variable names, the vector entries define the new variables in terms of the old ones.
f
An object of class eqnList, see generateEquations.
dynvar
Character vector with the old variable names
stoi
The stoichiometric matrix
flows
Character vector with the rate expressions
conserved
Logical. If true, the conserved quantities derived from the stoichiometric matrix are automatically used for extending the vector of observables. See details.

Value

  • Named character vector with the ODE expressed in the new variables. In addition, attributes "variables" (the variable transformation) and "inverse" (the inverse transformation) are returned.

Details

Usually, the function is called by either using the f argument and leaving the other arguments NULL or by leaving f NULL and defining the ODE by the arguments dynvar, stoi and flows. The observables vector can have less entries than the vector dynvar. In this case, the observables are automatically extended by old variables to generate a full rank variable transformation. If conserved is TRUE, the conserved quantities are preferentially used to extend the observables vector. Consequently, the transformed equations will return a certain number of zero-equation.