In dlill/conveniencefunctions: Convenience Functions

library(conveniencefunctions)

 f <- NULL %>%
    addReaction("A", "B", "kcat*A*E/(Km + A)", "Activation") %>%
    addReaction("B",  "", "k2*B", "Degradation") %>%
    addReaction("E", "", "0", "Added Enzyme") %>%
    as.eqnvec()

  events <- eventlist(var = "E", time = 2, value = "E_add", method = "add")
  x <- odemodel(f, events = events) %>% Xs
  g <- Y(c(Bobs = "s1*B"), x)

  covtable <- data.frame(membrane = rep(1:2, each = 4), 
                         dose = rep(c(0,0.1,1,10), 2),
                         line = rep(paste0("line", 1:3), each = 8)) %>% as.condition.grid()
  parameters <- getParameters(g,x)

  trafo <-
    parameters %>%
    setNames(.,.) %>%
    branch(covtable) %>%
    insert("x~0", x = c("E", "B")) %>%
    insert("par~par_line", par = c("A", "k2", "kcat", "Km"), line = line) %>% 
    insert("x~x_scale", x = "s1", scale = membrane) %>%
    insert("x~dose", x = "E_add", dose = dose) %>%
    insert("x~exp(log(10)*x)", x = getSymbols(mytrafo[[i]])) %>%
    {.}

  p <- P(trafo)

  pars0 <- 
    c(
      kcat_line1    =   0   , # 1
      Km_line1      =   2   , # 2
      k2_line1      =   -2  , # 3
      s1_1          =   0   , # 4
      A_line1       =   2   , # 5
      s1_2          =   1   , # 6
      kcat_line2    =   0   , # 7
      Km_line2      =   2.2 , # 8
      k2_line2      =   -1  , # 9
      A_line2       =   2.3 , # 10
      kcat_line3    =   0   , # 11
      Km_line3      =   2.2 , # 12
      k2_line3      =   -1  , # 13
      A_line3       =   3     # 14 
    )
getConditions(p)
covtable %>% rownames()

model <-
  dMod.frame("1", g,x,p, NULL, NULL, pars = list(pars0), covtable = list(covtable)) %>%
    simulate_data(timesD = c(0,3,5,10), seed_data = 1, seed_pars = 1) %>% 
    appendObj(pars = list(pars))

saveRDS(model, "model0.rds")
model <- readDMod.frame("model0.rds")
# checkout_hypothesis(model,1)