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

Run this code

# NOT RUN {
  # Write your example here. You can also add more Start..End blocks if needed.
  # Please mask all output such as print() with the special tag
  #    
  # such that the test is not littered. Statements guarded by  are enabled
  # in the example file which is extracted from this test file. To extract the
  # example run
  #    extractExamples()
  # on the R command line.
    
    ## 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)
    
    
  
# }