Download tutorial code

Background

• Structural model - Two compartment linear elimination with first order elimination

• Route of administration - IV bolus,

• Dosage Regimen - 100 μg IV or 0.1 mg IV

• Number of Subjects - 1

Learning Outcome

This exercise explains simulating single IV bolus dose kinetics from a two compartment model.

Objectives

To build a two compartment model and to simulate the model for a single subject given a single IV bolus dose.

Libraries

call the "necessary" libraries to get started.

using Random
using Pumas
using PumasUtilities
using CairoMakie

Model

pk_08_05        = @model begin
  @metadata begin
    desc = "Two Compartment Model"
    timeu = u"hr"
  end

  @param begin
    "Clearance (L/hr)"
    tvcl        ∈ RealDomain(lower=0)
    "Volume of Distribution (L)"
    tvvc        ∈ RealDomain(lower=0)
    "Intercompartmental Clearance (L/hr)"
    tvq         ∈ RealDomain(lower=0)
    "Peripheral Volume of Distribution (L)"
    tvvp        ∈ RealDomain(lower=0)
    Ω           ∈ PDiagDomain(4)
    "Proportional RUV"
    σ²_prop     ∈ RealDomain(lower=0)
  end

  @random begin
    η           ~ MvNormal(Ω)
  end

  @pre begin
    Cl          = tvcl * exp(η[1])
    Vc          = tvvc * exp(η[2])
    Vp          = tvvp * exp(η[3])
    Q           = tvq * exp(η[4])
  end

  @dynamics begin
    Central'    = -(Cl/Vc)*Central - (Q/Vc)*Central + (Q/Vp)*Peripheral
    Peripheral' =  (Q/Vc)*Central  - (Q/Vp)*Peripheral
  end

  @derived begin
    """
    PK08 Concentration (ug/L)
    """
    cp          = @. Central/Vc
    """
    PK08 Concentration (ug/L)
    """
    dv          ~ @. Normal(cp, sqrt(cp^2*σ²_prop))
  end
end

PumasModel
  Parameters: tvcl, tvvc, tvq, tvvp, Ω, σ²_prop
  Random effects: η
  Covariates: 
  Dynamical variables: Central, Peripheral
  Derived: cp, dv
  Observed: cp, dv

Parameters

• $C$L - Clearance(L/hr),

• $V$c - Volume of Central Compartment(L),

• $V$p - Volume of Peripheral Compartment(L),

• $Q$ - Inter-departmental clearance(L/hr),

• $Ω$ - Between Subject Variability,

• $σ$ - Residual error

param  = (tvcl    = 6.6,
          tvvc    = 53.09,
          tvvp    = 57.22,
          tvq     = 51.5,
          Ω       = Diagonal([0.0,0.0,0.0,0.0]),
          σ²_prop = 0.047)

(tvcl = 6.6, tvvc = 53.09, tvvp = 57.22, tvq = 51.5, Ω = [0.0 0.0 0.0 0.0; 
0.0 0.0 0.0 0.0; 0.0 0.0 0.0 0.0; 0.0 0.0 0.0 0.0], σ²_prop = 0.047)

Dosage Regimen

Dosage Regimen - 100 μg or 0.1mg of IV bolus was given to the single subject.

ev1   = DosageRegimen(100, time = 0, cmt = 1, evid = 1, addl = 0, ii = 0)
sub1  = Subject(id = 1, events = ev1)

Subject
  ID: 1
  Events: 1

Simulation

To simulate the plasma concentration with given observation time-points for single subject.

Random.seed!(123)
sim_s1 = simobs(pk_08_05,sub1,param,
                obstimes=[0.08,0.25,0.5,0.75,1,1.33,1.67,2,2.5,3.07,3.5,4.03,5,7,11,23,29,35,47.25]);

Visualize results

f, a, p = sim_plot(pk_08_05, [sim_s1], 
        observations = :cp, 
        color = :redsblues, linewidth = 4,
        axis = (xlabel = "Time (hours)", 
        ylabel = "PK08 Concentrations (ug/L)",
        xticks = 0:5:50, yscale = log10))
axislegend(a)
f

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