# Symbolic time derivative of equation vector given an equation list 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. ```r dot(observable, eqnlist) ``` ## Arguments - `observable`: named character vector or object of type eqnvec - `eqnlist`: equation list ## Returns An object of class eqnvec ## Details Observables are translated into an ODE ## Examples ```r # 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) ```

dot function