dot {dMod} | R Documentation |
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 |
Details
Observables are translated into an ODE
Value
An object of class eqnvec
Examples
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## 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, "2*pA", "pA_pA", "form_complex_pA * pA^2", "Complex formation of pA")
eq <- addReaction(eq, "B", "pB", "act_B * B * pA_pA", "Phosphorylation of B")
eq <- addReaction(eq, "pB", "B", "deact_B * pB", "Deposphorylation of pB")
## Extract data.frame of reactions
reactions <- getReactions(eq)
print(reactions)
## Get conserved quantities
cq <- conservedQuantities(eq$smatrix)
print(cq)
## Get fluxes
fluxes <- getFluxes(eq)
print(fluxes)
## Subsetting of equation list
subeq1 <- subset(eq, "pB" %in% Product)
print(subeq1)
subeq2 <- subset(eq, grepl("not_available", Description))
print(subeq2)
## 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)
[Package dMod version 1.0.2 Index]