Error while running working example

1

i have tried running a workshop example ( Problem 1: Simulate a first-order absorption model with linear elimination after a 100 mg oral dose in 24 subjects)

i am getting error in this part
Part 2: Perform a model fit

res = fit(mymodel,data,param,Pumas.FOCEI())
single_dose_regimen = DosageRegimen(100, time=0)
first(single_dose_regimen.data)

s1 = Subject(id=1, evs=single_dose_regimen,cvs=(Wt=70,))

choose_covariates() = (Wt = rand(55:80),)

pop = Population(map(i -> Subject(id = i,evs = single_dose_regimen, cvs =  choose_covariates()),1:24))

mymodel = @model begin
  @param   begin
    tvcl ∈ RealDomain(lower=0, init = 1.0)
    tvv ∈ RealDomain(lower=0, init = 20)
    tvka ∈ RealDomain(lower = 0, init= 1)
    Ω ∈ PDiagDomain(init=[0.09,0.09, 0.09])
    σ_prop ∈ RealDomain(lower=0,init=0.04)
  end

  @random begin
    η ~ MvNormal(Ω)
  end

  @pre begin
    CL = tvcl * (Wt/70)^0.75 * exp(η[1])
    V  = tvv * (Wt/70) * exp(η[2])
    Ka = tvka * exp(η[3])
  end
  @covariates Wt

  @dynamics OneCompartmentModel
    #@dynamics begin
    #    Depot' =  -Ka*Depot
    #    Central' =  Ka*Depot - (CL/V)*Central
    #end

  @derived begin
      cp = @. 1000*(Central / V)
      dv ~ @. Normal(cp, sqrt(cp^2*σ_prop))
    end
end

param = init_param(mymodel)

obs = simobs(mymodel, pop, param, obstimes=0:1:72)
plot(obs)

simdf = DataFrame(obs)
first(simdf, 6)

simdf.route = "ev"

timeu = u"hr"
concu = u"mg/L"
amtu  = u"mg"

ncadf = read_nca(simdf, id=:id, time=:time, conc=:cp, amt=:amt,
    route=:route,timeu=timeu, concu=concu, amtu=amtu, lloq=0.4concu)

plot(ncadf)


auc = NCA.auc(ncadf)

cmax = NCA.cmax(ncadf)

report = NCAReport(ncadf)
report = NCA.to_dataframe(report)
first(report,6)

simdf.cmt = ifelse.(ismissing.(simdf.cmt), 2, simdf.cmt)
est_df = simdf[.!((simdf.dv .== 0.0) .& (simdf.cmt .==2)),:]
first(est_df,6)

data = read_pumas(est_df ,cvs = [:Wt], dvs=[:dv])

res = fit(mymodel,data,param,Pumas.FOCEI())
2

Hi Sai,

Can you post what’s the error that you are getting?

Vijay

3

i am able to run fit …
now im got an error while running infer(res)infer(res)

4

I’m unable to reproduce this. Which version of Pumas and JuliaPro are you using. Also, does the error persist if you rerun the program?

5

itz juliapro1.2.0-1,
and and re run the program and got same error

6

Which version of Pumas are you using? You can see it if you write ] status or Pkg.status().

7 
(v1.2) pkg> status
    Status `C:\Users\Lenovo\.juliapro\JuliaPro_v1.2.0-1\environments\v1.2\Project.toml`
  [c52e3926] Atom v0.9.1
  [336ed68f] CSV v0.5.12
  [a93c6f00] DataFrames v0.19.4
  [7073ff75] IJulia v1.19.0
  [e5e0dc1b] Juno v0.7.1
  [91a5bcdd] Plots v0.26.3
  [4f2c3c20] Pumas v0.4.0
  [8bb1440f] DelimitedFiles
  [37e2e46d] LinearAlgebra
8

You are not using the latest version of Pumas. Could you please try ] up Pumas or Pkg.update("Pumas") and then restart Julia and rerun your code?

9

Sure. Thankyou very much