mkin (version 0.9-31)

mkinmod: Function to set up a kinetic model with one or more state variables.

Description

The function takes a specification, consisting of a list of the observed variables in the data. Each observed variable is again represented by a list, specifying the kinetic model type and reaction or transfer to other observed compartments.

Usage

mkinmod(..., use_of_ff = "min", speclist = NULL)

Arguments

...

For each observed variable, a list has to be specified as an argument, containing at least a component type, specifying the type of kinetics to use for the variable. Currently, single first order kinetics "SFO" or single first

use_of_ff

Specification of the use of formation fractions in the model equations and, if applicable, the coefficient matrix. If "min", a minimum use of formation fractions is made in order to avoid fitting the product of formation fractions and ra

speclist

The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL.

Value

• A list of class mkinmod for use with mkinfit, containing
• diffs
  A vector of string representations of differential equations, one for each modelling variable.
• parms
  A vector of parameter names occurring in the differential equations.
• map
  A list containing named character vectors for each observed variable, specifying the modelling variables by which it is represented.
• use_of_ff
  The content of use_of_ff is passed on in this list component.
• coefmat
  The coefficient matrix, if the system of differential equations can be represented by one.

Examples

# Specify the SFO model
SFO <- mkinmod(parent = list(type = "SFO"))

# One parent compound, one metabolite, both single first order.
SFO_SFO <- mkinmod(
  parent = list(type = "SFO", to = "m1"),
  m1 = list(type = "SFO"))