Simulation

In PKPDsim: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

The sim() function will combine the model, the parameters, and the regimen, and simulate out the ODE system. It will return a data.frame in the long format, i.e. one observation per row, and split by compartment and individual. The command for sim() looks e.g. like this:

library("PKPDsim")

dat <- sim(
  ode = model,              # created using new_ode_model()
  parameters = parameters,  # a named list of parameter values
  regimen = regimen         # created using new_regimen
)

Here is a minimal example using real code:

model <- new_ode_model("pk_1cmt_iv")
parameters <- list(CL = 5, V = 50)
regimen <- new_regimen(
  amt = 100,
  n = 3,
  interval = 12,
  type = "infusion",
  t_inf = 2
)

dat1 <- sim(
  ode = model,
  parameters = parameters,
  regimen = regimen
)
head(dat1)

By default, the observation times will include an observation every 1 hour. However, you can specify a vector of observation times to get only those observations:

dat2 <- sim(
  ode = model,
  parameters = parameters,
  regimen = regimen,
  t_obs = c(0.5, 2, 4, 8, 12, 16, 24)
)
head(dat2)

PKPDsim documentation built on March 7, 2023, 5:40 p.m.