dMod (version 0.3.1)

dot: Symbolic time derivative of equation vector given an equation list

Description

The time evolution of the internal states is defined in the equation list. Time derivatives of observation functions are expressed in terms of the rates of the internal states.

Usage

dot(observable, eqnlist)

Arguments

observable

named character vector or object of type eqnvec

eqnlist

equation list

Value

An object of class eqnvec

Details

Observables are translated into an ODE

Examples

## Generate another equation list
eq <- eqnlist()
eq <- addReaction(eq, "A", "pA", "act_A * A * stimulus", "Phosphorylation of A")
eq <- addReaction(eq, "pA", "A", "deact_A * pA", "Deposphorylation of pA")
eq <- addReaction(eq, "B", "pB", "act_B * B * pA", "Phosphorylation of B")
eq <- addReaction(eq, "pB", "B", "deact_B * pB", "Deposphorylation of pB")

## Extract data.frame of reactions
getReactions(eq)

## Get conserved quantities
conservedQuantities(eq$smatrix)

## Get fluxes
getFluxes(eq)

## Subsetting of equation list
subset(eq, "pB" %in% Product)
subset(eq, grepl("Phosphorylation", Description))

## Time derivatives of observables
observables <- eqnvec(pA_obs = "s1*pA", tA_obs = "s2*(A + pA)")
dobs <- dot(observables, eq)

## Combined equation vector for ODE and observables
f <- c(as.eqnvec(eq), dobs)
print(f)