addReaction: Add reaction to reaction table

In dkaschek/dMod: Dynamic Modeling and Parameter Estimation in ODE Models

Add reaction to reaction table

Description

Add reaction to reaction table

Usage

addReaction(eqnlist, from, to, rate, description = names(rate))

Arguments

eqnlist	equation list, see eqnlist
from	character with the left hand side of the reaction, e.g. "2*A + B"
to	character with the right hand side of the reaction, e.g. "C + 2*D"
rate	character. The rate associated with the reaction. The name is employed as a description of the reaction.
description	Optional description instead of names(rate).

Value

An object of class eqnlist.

Examples

f <- eqnlist()
f <- addReaction(f, "2*A+B", "C + 2*D", "k1*B*A^2")
f <- addReaction(f, "C + A", "B + A", "k2*C*A")



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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)
    
    
  

dkaschek/dMod documentation built on July 27, 2023, 11:45 p.m.