inst/examples/steadystates.R

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

\dontrun{
  library(dMod)
  setwd(tempdir())
  
  reactions <- eqnlist()
  reactions <-   addReaction(reactions, "Tca_buffer", "Tca_cyto", 
                             "import_Tca*Tca_buffer", "Basolateral uptake")
  reactions <-   addReaction(reactions, "Tca_cyto", "Tca_buffer", 
                             "export_Tca_baso*Tca_cyto", "Basolateral efflux")
  reactions <-   addReaction(reactions, "Tca_cyto", "Tca_canalicular", 
                             "export_Tca_cana*Tca_cyto", "Canalicular efflux")
  reactions <-   addReaction(reactions, "Tca_canalicular", "Tca_buffer", 
                             "transport_Tca*Tca_canalicular", "Transport bile")
  
  mysteadies <- steadyStates(reactions)
  print(mysteadies)
  
  x <- Xs(odemodel(reactions))
  
  parameters <- getParameters(x)
  trafo <- `names<-`(parameters, parameters)
  trafo <- repar("inner~steadyEqn", trafo, inner = names(mysteadies), steadyEqn = mysteadies)
  
  pSS <- P(trafo, condition = "steady")
  
  set.seed(2)
  pars <- structure(runif( length(getParameters(pSS)), 0,1), names = getParameters(pSS))
  
  prediction <- (x*pSS)(seq(0,10, 0.1), pars, deriv = F)
  plot(prediction)
}