Description Usage Arguments Value Examples
Generate list of fluxes from equation list
1 |
eqnlist |
object of class eqnlist. |
type |
"conc." or "amount" for fluxes in units of concentrations or number of molecules. |
list of named characters, the in- and out-fluxes for each state.
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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)
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