Add documentation of evid 5

[billdenney]

Docs needed here: https://nlmixr2.github.io/rxode2/articles/rxode2-event-types.html#rxode2-event-tables

[billdenney]

Something like this could be used:

library(tidyverse)
library(nlmixr2)

one.compartment <- function() {
  ini({
    tka <- log(1.57); label("Absorption rate (1/hr)")
    tcl <- log(2.72); label("Clearance (L/hr)")
    tq <- log(1.5); label("Intercompartmental clearance (L/hr)")
    tv <- log(31.5); label("Central volume (L)")
    tv2 <- log(60); label("Peripheral volume (L)")
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    q <- exp(tq)
    v <- exp(tv + eta.v)
    v2 <- exp(tv2)
    
    kel <- cl/v
    k12 <- q/v
    k21 <- q/v2
    
    d/dt(depot) <- -ka * depot
    d/dt(center) <- ka * depot - kel * center - k12 * center + k21 * peripheral
    d/dt(peripheral) <- k12 * center - k21 * peripheral
    cp <- center / v
    cp ~ add(add.sd)
  })
}

d_sim_prep <-
  bind_rows(
    # dosing
    data.frame(
      ID = 1,
      EVID = 1,
      CMT = "depot",
      AMT = 1,
      TIME = 0
    ),
    # reset
    data.frame(
      ID = 1,
      EVID = 5,
      CMT = "peripheral",
      AMT = 0,
      TIME = 5
    ),
    # observations
    data.frame(
      ID = 1,
      EVID = 0,
      CMT = "center",
      AMT = 0,
      TIME = seq(0, 24, by = 0.1)
    )
  ) |>
  arrange(ID, TIME, EVID)

sim <- nlmixr2(one.compartment, d_sim_prep, est="rxSolve")
ggplot(as.data.frame(sim), aes(x = time)) +
  geom_line(aes(y = center), colour = "blue") +
  geom_line(aes(y = peripheral), colour = "red")