Error with Bayesian Model Normal distribution for omegas

Estimation bayesian
1

Hello

I have the following Bayesian Model

BAYESIAN_PKPD = @model begin
    @param begin
        tvKTV1 ~ LogNormal(log(0.4), 1.0)
        tvKTV2 ~ LogNormal(log(0.1), 1.0)
        tvecmo ~ Normal(-0.7, 1.0)
        tvCL1 ~ LogNormal(log(0.9), 1.0)
        tvCL2 ~ LogNormal(log(0.8), 1.0)
        tvcircuit ~ LogNormal(log(1.2), 1.0)
        tvVc1 ~ LogNormal(log(1.8), 0.1)
        tvVc2 ~ LogNormal(log(3.0), 0.1)
        σ_prop_1 ~ truncated(Cauchy(0, 0.18), 0.0, 1.0)
        σ_prop_2 ~ truncated(Cauchy(0, 0.02), 0.0, 1.0)
        σ_prop_3 ~ truncated(Cauchy(0, 0.04), 0.0, 1.0)
        σ_add ~ truncated(Cauchy(0, 5000.0), 0.0, Inf)
        ω²KTV ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 1.8)
        ω²CL ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 0.2)
        ω²Vc ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 0.9)
    end

    @random begin
        ηKTV ~ Normal(0.0, sqrt(ω²KTV))
        ηCL ~ Normal(0.0, sqrt(ω²CL))
        ηVc ~ Normal(0.0, sqrt(ω²Vc))
    end
    @covariates WT ECMO_DAYS IS_CIRCUIT_CHANGE site T
    @pre begin

        # PK parameters

        siteeffect_1 = if site==1 
            σ_prop_1 
        elseif site==2
            σ_prop_2
        else 
            σ_prop_3
        end 
        siteeffect_2 = site==2 ? σ_add : 0.0

        tvKTV = site == 1 ? tvKTV1 : tvKTV2*(ECMO_DAYS/6)^tvecmo
        KTV    = tvKTV*exp(ηKTV)
        TVCL = site == 1 ? tvCL1 * (WT/10)^0.75 : tvCL2* (WT/10)^0.75  * tvcircuit^IS_CIRCUIT_CHANGE  
        CL     = TVCL * exp(ηCL)*(1-exp(-KTV*T))
        TVVc = site == 1 ? tvVc1 * (WT/10)^1 : tvVc2 * (WT/10)^1
        Vc     = TVVc * exp(ηVc)
    end

    @dynamics begin
        Central' = -(CL/Vc) * Central
    end
    @derived begin
        CP = @. Central / Vc
        CONC = @. Normal(CP, sqrt(CP^2*siteeffect_1 + siteeffect_2))
    end
end

However, when I try to run it, I get the following error:

result_PKPD   = @time fit(BAYESIAN_PKPD, estimation, init_params(BAYESIAN_PKPD), Pumas.BayesMCMC(nsamples=2000, nadapts=1000,nchains =4,target_accept = 0.8,ensemblealg = EnsembleThreads()))
ERROR: MethodError: no method matching iterate(::TransformVariables.Infinity{true})
Closest candidates are:
  iterate(::Union{LinRange, StepRangeLen}) at /opt/julia-1.7.3/share/julia/base/range.jl:826
  iterate(::Union{LinRange, StepRangeLen}, ::Integer) at /opt/julia-1.7.3/share/julia/base/range.jl:826
  iterate(::T) where T<:Union{Base.KeySet{<:Any, <:Dict}, Base.ValueIterator{<:Dict}} at /opt/julia-1.7.3/share/julia/base/dict.jl:695
  ...
Stacktrace:
  [1] _zip_iterate_some
    @ ./iterators.jl:358 [inlined]
  [2] _zip_iterate_some (repeats 2 times)
    @ ./iterators.jl:360 [inlined]
  [3] _zip_iterate_all
    @ ./iterators.jl:350 [inlined]
  [4] iterate
    @ ./iterators.jl:340 [inlined]
  [5] _all(f::Pumas.var"#176#177", itr::Base.Iterators.Zip{Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}, Float64, TransformVariables.Infinity{true}}}, #unused#::Colon)
    @ Base ./reduce.jl:1156
  [6] all(f::Function, itr::Base.Iterators.Zip{Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}, Float64, TransformVariables.Infinity{true}}})
    @ Base ./reduce.jl:1152
  [7] logpdf(d::Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, x::ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/params.jl:561
  [8] _lpdf(d::Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, x::ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:555
  [9] macro expansion
    @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:0 [inlined]
 [10] _core_lpdf(lpdf::typeof(Pumas._lpdf), reduce::typeof(+), ds::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, xs::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:578
 [11] _lpdf(ds::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, xs::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:575
 [12] (::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}})(u::Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/bayes/logdensity.jl:203
 [13] chunk_mode_gradient!(result::DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}, f::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}}, x::Vector{Float64}, cfg::ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ ForwardDiff /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ForwardDiff/pDtsf/src/gradient.jl:150
 [14] gradient!(result::DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}, f::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}}, x::Vector{Float64}, cfg::ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}, ::Val{false})
    @ ForwardDiff /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ForwardDiff/pDtsf/src/gradient.jl:39
 [15] _logdensitygrad(b::Pumas.ThreadedBayesLogDensity{PumasModel{(tvKTV1 = 1, tvKTV2 = 1, tvecmo = 1, tvCL1 = 1, tvCL2 = 1, tvcircuit = 1, tvVc1 = 1, tvVc2 = 1, σ_prop_1 = 1, σ_prop_2 = 1, σ_prop_3 = 1, σ_add = 1, ω²KTV = 1, ω²CL = 1, ω²Vc = 1), 3, (:Central,), ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}, var"#747#754", Pumas.TimeDispatcher{var"#748#755", var"#749#756"}, Nothing, var"#751#758", Pumas.LinearODE, var"#752#759", var"#753#760", ModelingToolkit.ODESystem}, NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, Float64}}, Vector{Subject{NamedTuple{(:CONC,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantInterpolationStructArray{Vector{Float64}, NamedTuple{(:WT, :ECMO_DAYS, :IS_CIRCUIT_CHANGE, :site, :T), Tuple{Vector{Float64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Float64}}}, Symbol}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}}, Vector{DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}}, NamedTuple{(), Tuple{}}}, v::Vector{Float64})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/bayes/logdensity.jl:359
 [16] logdensitygrad(b::Pumas.ThreadedBayesLogDensity{PumasModel{(tvKTV1 = 1, tvKTV2 = 1, tvecmo = 1, tvCL1 = 1, tvCL2 = 1, tvcircuit = 1, tvVc1 = 1, tvVc2 = 1, σ_prop_1 = 1, σ_prop_2 = 1, σ_prop_3 = 1, σ_add = 1, ω²KTV = 1, ω²CL = 1, ω²Vc = 1), 3, (:Central,), ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}, var"#747#754", Pumas.TimeDispatcher{var"#748#755", var"#749#756"}, Nothing, var"#751#758", Pumas.LinearODE, var"#752#759", var"#753#760", ModelingToolkit.ODESystem}, NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, Float64}}, Vector{Subject{NamedTuple{(:CONC,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantInterpolationStructArray{Vector{Float64}, NamedTuple{(:WT, :ECMO_DAYS, :IS_CIRCUIT_CHANGE, :site, :T), Tuple{Vector{Float64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Float64}}}, Symbol}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}}, Vector{DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}}, NamedTuple{(), Tuple{}}}, v::Vector{Float64})

The model runs when I define the omegas in @param block as following:

        ω ∈ Constrained(
            MvNormal(zeros(3), Diagonal([1.0,0.2,1.0])),
            lower=zeros(3),
            upper=fill(Inf, 3),
            init=ones(3),
        )

I am not able to interpret the error. I appreciate your help.

Thanks!

2

You are using the ∈ notation in the @param as in:

       ω ∈ Constrained(
            MvNormal(zeros(3), Diagonal([1.0,0.2,1.0])),
            lower=zeros(3),
            upper=fill(Inf, 3),
            init=ones(3),
        )

I think it is overriding the prior something.

What if you do:

ω ~ Constrained(
            MvNormal(zeros(3), Diagonal([1.0,0.2,1.0])),
            lower=zeros(3),
            upper=fill(Inf, 3),
            init=ones(3),
        )

Does it error?

Cc @mohamed82008 .

3

Hi @storopoli, Thanks for the reply. The model is running fine when the priors for omegas are defined as multivariate normal distribution. The above error message appears when I define the prior for each omega term separately. or do you mean to use ~ instead of ∈ in the @param block ?

Thanks

4

Ok, but with ω ~ Constrained(...) or ω ∈ Constrained(...)?

5

It is running with both ~ and ∈ if I specified ω as MvNormal(). The error appears if I defined omega separately as

        ω²KTV ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 1.8)
        ω²CL ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 0.2)
        ω²Vc ~ Constrained(Normal(0.0, 1.0); lower = 0.0, init = 0.9)

with either ~ or ∈

This is the error

result_PKPD   = @time fit(BAYESIAN_PKPD, estimation, init_params(BAYESIAN_PKPD), Pumas.BayesMCMC(nsamples=2000, nadapts=1000,nchains =4,target_accept = 0.8,ensemblealg = EnsembleThreads()))
ERROR: MethodError: no method matching iterate(::TransformVariables.Infinity{true})
Closest candidates are:
  iterate(::Union{LinRange, StepRangeLen}) at /opt/julia-1.7.3/share/julia/base/range.jl:826
  iterate(::Union{LinRange, StepRangeLen}, ::Integer) at /opt/julia-1.7.3/share/julia/base/range.jl:826
  iterate(::T) where T<:Union{Base.KeySet{<:Any, <:Dict}, Base.ValueIterator{<:Dict}} at /opt/julia-1.7.3/share/julia/base/dict.jl:695
  ...
Stacktrace:
  [1] _zip_iterate_some
    @ ./iterators.jl:358 [inlined]
  [2] _zip_iterate_some (repeats 2 times)
    @ ./iterators.jl:360 [inlined]
  [3] _zip_iterate_all
    @ ./iterators.jl:350 [inlined]
  [4] iterate
    @ ./iterators.jl:340 [inlined]
  [5] _all(f::Pumas.var"#176#177", itr::Base.Iterators.Zip{Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}, Float64, TransformVariables.Infinity{true}}}, #unused#::Colon)
    @ Base ./reduce.jl:1156
  [6] all(f::Function, itr::Base.Iterators.Zip{Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}, Float64, TransformVariables.Infinity{true}}})
    @ Base ./reduce.jl:1152
  [7] logpdf(d::Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, x::ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/params.jl:561
  [8] _lpdf(d::Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, x::ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:555
  [9] macro expansion
    @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:0 [inlined]
 [10] _core_lpdf(lpdf::typeof(Pumas._lpdf), reduce::typeof(+), ds::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, xs::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:578
 [11] _lpdf(ds::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, xs::NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:575
 [12] (::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}})(u::Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/bayes/logdensity.jl:203
 [13] chunk_mode_gradient!(result::DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}, f::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}}, x::Vector{Float64}, cfg::ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}})
    @ ForwardDiff /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ForwardDiff/pDtsf/src/gradient.jl:150
 [14] gradient!(result::DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}, f::Pumas._L_param{TransformVariables.TransformTuple{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.NormalTransform{Normal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, Pumas.LogNormalTransform{LogNormal{Float64}}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ScaledShiftedLogistic{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}}}}, ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}}, x::Vector{Float64}, cfg::ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}, ::Val{false})
    @ ForwardDiff /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ForwardDiff/pDtsf/src/gradient.jl:39
 [15] _logdensitygrad(b::Pumas.ThreadedBayesLogDensity{PumasModel{(tvKTV1 = 1, tvKTV2 = 1, tvecmo = 1, tvCL1 = 1, tvCL2 = 1, tvcircuit = 1, tvVc1 = 1, tvVc2 = 1, σ_prop_1 = 1, σ_prop_2 = 1, σ_prop_3 = 1, σ_add = 1, ω²KTV = 1, ω²CL = 1, ω²Vc = 1), 3, (:Central,), ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}, var"#747#754", Pumas.TimeDispatcher{var"#748#755", var"#749#756"}, Nothing, var"#751#758", Pumas.LinearODE, var"#752#759", var"#753#760", ModelingToolkit.ODESystem}, NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, Float64}}, Vector{Subject{NamedTuple{(:CONC,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantInterpolationStructArray{Vector{Float64}, NamedTuple{(:WT, :ECMO_DAYS, :IS_CIRCUIT_CHANGE, :site, :T), Tuple{Vector{Float64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Float64}}}, Symbol}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}}, Vector{DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}}, NamedTuple{(), Tuple{}}}, v::Vector{Float64})
    @ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/bayes/logdensity.jl:359
 [16] logdensitygrad(b::Pumas.ThreadedBayesLogDensity{PumasModel{(tvKTV1 = 1, tvKTV2 = 1, tvecmo = 1, tvCL1 = 1, tvCL2 = 1, tvcircuit = 1, tvVc1 = 1, tvVc2 = 1, σ_prop_1 = 1, σ_prop_2 = 1, σ_prop_3 = 1, σ_add = 1, ω²KTV = 1, ω²CL = 1, ω²Vc = 1), 3, (:Central,), ParamSet{NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), Tuple{LogNormal{Float64}, LogNormal{Float64}, Normal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, LogNormal{Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Truncated{Cauchy{Float64}, Continuous, Float64}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}, Constrained{Normal{Float64}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}}, var"#747#754", Pumas.TimeDispatcher{var"#748#755", var"#749#756"}, Nothing, var"#751#758", Pumas.LinearODE, var"#752#759", var"#753#760", ModelingToolkit.ODESystem}, NamedTuple{(:tvKTV1, :tvKTV2, :tvecmo, :tvCL1, :tvCL2, :tvcircuit, :tvVc1, :tvVc2, :σ_prop_1, :σ_prop_2, :σ_prop_3, :σ_add, :ω²KTV, :ω²CL, :ω²Vc), NTuple{15, Float64}}, Vector{Subject{NamedTuple{(:CONC,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantInterpolationStructArray{Vector{Float64}, NamedTuple{(:WT, :ECMO_DAYS, :IS_CIRCUIT_CHANGE, :site, :T), Tuple{Vector{Float64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Float64}}}, Symbol}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{ForwardDiff.GradientConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 6}}}}, Vector{DiffResults.MutableDiffResult{1, Float64, Tuple{Vector{Float64}}}}, NamedTuple{(), Tuple{}}}, v::Vector{Float64})

And this is my fit function

result_PKPD   = @time fit(BAYESIAN_PKPD, estimation, init_params(BAYESIAN_PKPD), Pumas.BayesMCMC(nsamples=2000, nadapts=1000,nchains =4,target_accept =0.8, ensemblealg = EnsembleThreads()))
6

@ahmed.salem this is a bug. Please use truncated for now for univariate variables.

2 Likes
7

@mohamed82008, thanks it works after changing to truncated