Description Usage Arguments Details Value Examples
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.
1 |
observable |
named character vector or object of type eqnvec |
eqnlist |
equation list |
Observables are translated into an ODE
An object of class eqnvec
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | # 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.