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
## 3 1 1 1 47.58129 1
## 25 1 2 1 90.63462 1
## 47 1 3 1 82.00960 1
## 65 1 4 1 74.20535 1
## 67 1 5 1 67.14378 1By 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
## 7 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