hi
i am trying to write one compartment first order absorption model with lag time . i have a doubt on how to write lag time in model. here i am showing the model which i have written , this model worked but did not give the exact result. please review it once and suggest me the changed where it is needed
model = @model begin
@param begin
tvcl ∈ RealDomain(lower=0, init = 1.0)
tvv ∈ RealDomain(lower=0, init = 100)
tvka ∈ RealDomain(lower = 0, init= 0.5)
tvlag ∈ RealDomain(lower = 0, init = 0.5)
Ω ∈ PDiagDomain(init=[0.04])
σ ∈ RealDomain(lower=0,init=0.01)
end
@random begin
η ~ MvNormal(Ω)
end
@pre begin
CL = tvcl * exp(η[1])
V = tvv
ka = tvka
lag = tvlag
end
@dynamics begin
Depot' = - ka * Depot
Central' = ka * Depot - (CL/V) * Central
end
@vars begin
Depot = Depot
Cent = Central/V
end
@derived begin
cp = Cent
dv ~ @. Normal(cp, abs(cp)*σ)
end
end
lags, bioav, rate and duration come under what are called as Dose Control Parameters
you can read the docs to understand more. But in your example, this is how it is done
using Pumas
using Plots
model = @model begin
@param begin
tvcl ∈ RealDomain(lower=0, init = 1.0)
tvv ∈ RealDomain(lower=0, init = 100)
tvka ∈ RealDomain(lower = 0, init= 0.5)
tvlag ∈ RealDomain(lower = 0, init = 0.5)
Ω ∈ PDiagDomain(init=[0.04])
σ ∈ RealDomain(lower=0,init=0.01)
end
@random begin
η ~ MvNormal(Ω)
end
@pre begin
CL = tvcl * exp(η[1])
V = tvv
ka = tvka
lags = (Depot = tvlag,)
end
@dynamics begin
Depot' = - ka * Depot
Central' = ka * Depot - (CL/V) * Central
end
@derived begin
cp = Central/V
dv ~ @. Normal(cp, abs(cp)*σ)
end
end
ev1 = DosageRegimen(150, cmt=1)
pop = Population(map(i -> Subject(id=i,evs=ev1),1:10))
lagmodel_params = (tvcl = 1.5,
tvv = 25.0,
tvka = 1,
tvlag = 10,
Ω = Diagonal([0.05]),
σ = 0.02)
sims = simobs(model, pop, lagmodel_params, obstimes = 0:1:48)
plot(sims)
Notice how I specified a parameter called lags (which is a reserved name). This is used to then create a list of compartments which are associated with a parameter that becomes the lag of that compartment. Same applies for bioav and other too. In the example I used an extreme lag of 10 hours just to illustrate
