Simulation

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:

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)

## id t comp y obs_type
## 1 1 0 1 0.00000 1
## 23 1 1 1 47.58129 1
## 45 1 2 1 90.63462 1
## 63 1 3 1 82.00960 1
## 65 1 4 1 74.20535 1
## 67 1 5 1 67.14378 1

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)

## id t comp y obs_type
## 1 1 0.5 1 24.38529 1
## 9 1 2.0 1 90.63462 1
## 11 1 4.0 1 74.20535 1
## 13 1 8.0 1 49.74134 1
## 3 1 12.0 1 33.34261 1
## 5 1 16.0 1 96.55558 1