Hello,
I’m running a dual absorption (fast zero-order and transmit compartment) model fit, and I’m getting the following error:
ERROR: UndefRefError: access to undefined reference
Stacktrace:
[1] getindex
@ ./array.jl:861 [inlined]
[2] iterate
@ ./array.jl:835 [inlined]
[3] foreach(f::Base.Fix2{typeof(fill!), Float64}, itr::Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}})
@ Base ./abstractarray.jl:2712
[4] _labelled_fill_inf!
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/model_api.jl:1812 [inlined]
[5] _adjust_failed_solution_doses!(sol::Pumas.PKPDAnalyticalSolution{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, 2, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Pumas.Returns{NamedTuple{(:CL, :Q, :Vp, :Vc, :ktr, Symbol("##A##"), Symbol("##b##")), Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Matrix{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, FillArrays.Zeros{Float64, 1, Tuple{Base.OneTo{Int64}}}}}}, Pumas.AnalyticalPKPDProblem{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Float64, false, Pumas.LinearODE, Vector{Pumas.Event{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Float64, Float64, Int64}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Pumas.Returns{NamedTuple{(:CL, :Q, :Vp, :Vc, :ktr, Symbol("##A##"), Symbol("##b##")), Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Matrix{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, FillArrays.Zeros{Float64, 1, Tuple{Base.OneTo{Int64}}}}}}}})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/model_api.jl:1845
[6] _adjust_failed_solution!(subject::Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, sol::Pumas.PKPDAnalyticalSolution{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, 2, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Vector{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, Pumas.Returns{NamedTuple{(:CL, :Q, :Vp, :Vc, :ktr, Symbol("##A##"), Symbol("##b##")), Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Matrix{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, FillArrays.Zeros{Float64, 1, Tuple{Base.OneTo{Int64}}}}}}, Pumas.AnalyticalPKPDProblem{Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Float64, false, Pumas.LinearODE, Vector{Pumas.Event{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Float64, Float64, Int64}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, Pumas.Returns{NamedTuple{(:CL, :Q, :Vp, :Vc, :ktr, Symbol("##A##"), Symbol("##b##")), Tuple{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}, Matrix{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}, FillArrays.Zeros{Float64, 1, Tuple{Base.OneTo{Int64}}}}}}}})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/model_api.jl:1838
[7] #_derived#317
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/models/model_api.jl:1276 [inlined]
[8] (::Pumas.var"#570#571"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, NamedTuple{(), Tuple{}}})(vηorth::Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:2552
[9] chunk_mode_jacobian(f::Pumas.var"#570#571"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, NamedTuple{(), Tuple{}}}, x::Vector{Float64}, cfg::ForwardDiff.JacobianConfig{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7, Vector{ForwardDiff.Dual{ForwardDiff.Tag{Pumas.Tag, Float64}, Float64, 7}}}, #unused#::Val{7})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:2485
[10] _derived_vηorth_gradient
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:2556 [inlined]
[11] _∂²l∂η²
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:2601 [inlined]
[12] (::Pumas.var"#498#499"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, FOCE, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:ηCL, :ηQ, :ηVp, :ηVc, :ηbio, :ηdur, :ηktr), NTuple{7, Pumas.NormalTransform{Normal{Float64}}}}}, ParamSet{NamedTuple{(:ηCL, :ηQ, :ηVp, :ηVc, :ηbio, :ηdur, :ηktr), NTuple{7, Normal{Float64}}}}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}})(F::Float64, G::Vector{Float64}, H::Matrix{Float64}, x::Vector{Float64})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:979
[13] (::NLSolversBase.var"#98#104"{NLSolversBase.InplaceObjective{Nothing, Nothing, Pumas.var"#498#499"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, FOCE, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:ηCL, :ηQ, :ηVp, :ηVc, :ηbio, :ηdur, :ηktr), NTuple{7, Pumas.NormalTransform{Normal{Float64}}}}}, ParamSet{NamedTuple{(:ηCL, :ηQ, :ηVp, :ηVc, :ηbio, :ηdur, :ηktr), NTuple{7, Normal{Float64}}}}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Nothing, Nothing}, Float64})(G::Vector{Float64}, H::Matrix{Float64}, x::Vector{Float64})
@ NLSolversBase /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:115
[14] value_gradient_hessian!!(obj::NLSolversBase.TwiceDifferentiable{Float64, Vector{Float64}, Matrix{Float64}, Vector{Float64}}, x::Vector{Float64})
@ NLSolversBase /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:138
[15] initial_state(method::Optim.NewtonTrustRegion{Float64}, options::Optim.Options{Float64, Nothing}, d::NLSolversBase.TwiceDifferentiable{Float64, Vector{Float64}, Matrix{Float64}, Vector{Float64}}, initial_x::Vector{Float64})
@ Optim /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/multivariate/solvers/second_order/newton_trust_region.jl:310
[16] optimize
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/multivariate/optimize/optimize.jl:36 [inlined]
[17] _orth_empirical_bayes!(vrandeffsorth::Vector{Float64}, m::PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, _subject::Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, param::NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, approx::FOCE, diffeq_options::NamedTuple{(), Tuple{}})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:1007
[18] _update_ebes_and_evaluate_marginal_nll!
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3099 [inlined]
[19] _update_ebes_and_evaluate_marginal_nll_threads!(m::PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, vvrandeffs::Vector{Vector{Float64}}, vvrandeffs_tmp::Vector{Vector{Float64}}, approx::FOCE, diffeq_options::NamedTuple{(), Tuple{}})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3148
[20] #613
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3967 [inlined]
[21] (::Pumas.OptimSafeFunction{true, Pumas.var"#613#615"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, FOCE, EnsembleThreads, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, TransformVariables.ShiftedExp{true, Float64}}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{Float64}}})(F::Float64, g::Nothing, x::Vector{Float64})
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3856
[22] (::NLSolversBase.var"#55#56"{NLSolversBase.InplaceObjective{Nothing, Pumas.OptimSafeFunction{true, Pumas.var"#613#615"{PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, FOCE, EnsembleThreads, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, TransformVariables.ShiftedExp{true, Float64}}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{Float64}}}, Nothing, Nothing, Nothing}, Float64})(x::Vector{Float64})
@ NLSolversBase /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:44
[23] value!!(obj::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, x::Vector{Float64})
@ NLSolversBase /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NLSolversBase/cfJrN/src/interface.jl:9
[24] value!(obj::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, x::Vector{Float64})
@ NLSolversBase /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NLSolversBase/cfJrN/src/interface.jl:28
[25] value!(obj::Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, x::Vector{Float64})
@ Optim /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/Manifolds.jl:31
[26] (::LineSearches.var"#ϕ#1"{Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, Vector{Float64}, Vector{Float64}, Vector{Float64}})(α::Float64)
@ LineSearches /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/LineSearches/G1LRk/src/LineSearches.jl:25
[27] (::LineSearches.BackTracking{Float64, Int64})(ϕ::LineSearches.var"#ϕ#1"{Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, Vector{Float64}, Vector{Float64}, Vector{Float64}}, αinitial::Float64, ϕ_0::Float64, dϕ_0::Float64)
@ LineSearches /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/LineSearches/G1LRk/src/backtracking.jl:60
[28] BackTracking
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/LineSearches/G1LRk/src/backtracking.jl:33 [inlined]
[29] BackTracking
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/LineSearches/G1LRk/src/backtracking.jl:23 [inlined]
[30] perform_linesearch!(state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}, d::Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}})
@ Optim /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/utilities/perform_linesearch.jl:59
[31] update_state!(d::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat})
@ Optim /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/multivariate/solvers/first_order/bfgs.jl:139
[32] optimize(d::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, initial_x::Vector{Float64}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}, options::Optim.Options{Float64, Pumas.var"#585#587"{Pumas.DefaultOptimizeFN{Nothing, NamedTuple{(:show_trace, :store_trace, :extended_trace, :g_tol, :allow_f_increases), Tuple{Bool, Bool, Bool, Float64, Bool}}}, Pumas.var"#614#616"{FOCE, Bool, NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, TransformVariables.TransformTuple{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, TransformVariables.ShiftedExp{true, Float64}}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}}}}, state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}})
@ Optim /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/multivariate/optimize/optimize.jl:54
[33] optimize
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Optim/Zq1jM/src/multivariate/optimize/optimize.jl:36 [inlined]
[34] DefaultOptimizeFN
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:2993 [inlined]
[35] _fit(m::PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, approx::FOCE, ensemblealg::EnsembleThreads, optimize_fn::Pumas.DefaultOptimizeFN{Nothing, NamedTuple{(:show_trace, :store_trace, :extended_trace, :g_tol, :allow_f_increases), Tuple{Bool, Bool, Bool, Float64, Bool}}}, fixedparamset::ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, fixedparam::NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, checkidentification::Bool, diffeq_options::NamedTuple{(), Tuple{}}, init_vrandeffsorth::Vector{Vector{Float64}}, verbose::Bool)
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:4062
[36] __fit
@ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3804 [inlined]
[37] fit(m::PumasModel{(tvCL = 1, tvQ = 1, tvVp = 1, tvVc = 1, tvbio = 1, tvdur = 1, tvktr = 1, ωCL = 1, ωQ = 1, ωVp = 1, ωVc = 1, ωbio = 1, ωdur = 1, ωktr = 1, σ_prop = 1), 7, (:Depot, :Transit1, :Transit2, :Transit3, :Transit4, :Central, :Peripheral), ParamSet{NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#235#241", var"#236#242", var"#237#243", var"#238#244", Pumas.LinearODE, var"#239#245", var"#240#246", ModelingToolkit.ODESystem}, _population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:STUDY,), Tuple{Int64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvCL, :tvQ, :tvVp, :tvVc, :tvbio, :tvdur, :tvktr, :ωCL, :ωQ, :ωVp, :ωVc, :ωbio, :ωdur, :ωktr, :σ_prop), NTuple{15, Float64}}, approx::FOCE; optim_alg::Nothing, optim_options::Nothing, optimize_fn::Nothing, constantcoef::NamedTuple{(), Tuple{}}, omegas::Tuple{}, ensemblealg::EnsembleThreads, checkidentification::Bool, diffeq_options::NamedTuple{(), Tuple{}}, init_randeffs::Nothing, init_vrandeffsorth::Nothing, verbose::Bool)
@ Pumas /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Pumas/Td3Jp/src/estimation/likelihoods.jl:3768
[38] top-level scope
@ ~/data/code/padagis_mibe/modeling/pilot1_3_estimation_RT_separated (dual absorption) copy.jl:170
It’s giving me the error after Iteration 6. I have 4 transit compartments, so I sent my 2nd dosing row in the data set to CMT=6, rate=-2 for the dual absorption. Previously, when I ran the fit with CMT=2 by mistake, it errored prior to any iterations.
Does anyone know what may cause this error?
The following is my model:
cmt2_dual_abs_prop_model = @model begin
@param begin
tvCL ∈ RealDomain(lower = 0.0001)
tvQ ∈ RealDomain(lower = 0.0001)
tvVp ∈ RealDomain(lower = 0.0001)
tvVc ∈ RealDomain(lower = 0.0001)
tvbio ∈ RealDomain(lower = 0.0001)
tvdur ∈ RealDomain(lower = 0.0001)
tvktr ∈ RealDomain(lower = 0.0001)
ωCL ∈ RealDomain(lower = 0.0001)
ωQ ∈ RealDomain(lower = 0.0001)
ωVp ∈ RealDomain(lower = 0.0001)
ωVc ∈ RealDomain(lower = 0.0001)
ωbio ∈ RealDomain(lower = 0.0001)
ωdur ∈ RealDomain(lower = 0.0001)
ωktr ∈ RealDomain(lower = 0.0001)
σ_prop ∈ RealDomain(lower = 0.0001)
end
@random begin
ηCL ~ Normal(0., ωCL)
ηQ ~ Normal(0., ωQ)
ηVp ~ Normal(0., ωVp)
ηVc ~ Normal(0., ωVc)
ηbio ~ Normal(0., ωbio)
ηdur ~ Normal(0., ωdur)
ηktr ~ Normal(0., ωktr)
end
@pre begin
CL = tvCL*exp(ηCL)
Q = tvQ*exp(ηQ)
Vp = tvVp*exp(ηVp)
Vc = tvVc*exp(ηVc)
ktr = tvktr*exp(ηktr)
end
@dosecontrol begin
duration = (Central = tvdur*exp(ηdur),)
bioav = (Depot = tvbio*exp(ηbio),
Central = 1 - tvbio*exp(ηbio)
)
end
@dynamics begin
Depot' = -ktr * Depot
Transit1' = ktr * Depot - ktr * Transit1
Transit2' = ktr * Transit1 - ktr * Transit2
Transit3' = ktr * Transit2 - ktr * Transit3
Transit4' = ktr * Transit3 - ktr * Transit4
Central' = ktr * Transit4 - Q/Vc * Central + Q/Vp * Peripheral - CL/Vc * Central
Peripheral' = Q/Vc * Central - Q/Vp * Peripheral
end
@derived begin
CP = @. Central/Vc
DV ~ @. Normal(CP, abs(CP)*σ_prop)
end
end