Error with vpc() function

Diagnostics vpc
1

Hello I am trying to run the vpc function but I am getting the following error

julia> ufh_vpc = vpc(modfit, 500; observations = [:CONC],
                    ensemblealg=EnsembleThreads(), prediction_correction = true)
[ Info: Continuous VPC
ERROR: MethodError: Cannot `convert` an object of type Missing to an object of type Float64
Closest candidates are:
  convert(::Type{T}, ::Static.StaticFloat64{N}) where {N, T<:AbstractFloat} at /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Static/pkxBE/src/float.jl:26
  convert(::Type{T}, ::LLVM.GenericValue, ::LLVM.LLVMType) where T<:AbstractFloat at /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LLVM/WjSQG/src/execution.jl:39
  convert(::Type{T}, ::LLVM.ConstantFP) where T<:AbstractFloat at /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LLVM/WjSQG/src/core/value/constant.jl:111
  ...
Stacktrace:
  [1] setindex!(A::Vector{Float64}, x::Missing, i1::Int64)
    @ Base ./array.jl:903
  [2] DataFrame(subject::Subject{NamedTuple{(:CONC,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantInterpolationStructArray{Vector{Float64}, NamedTuple{(:logwt, :AGE_GROUP, :logecmo, :WT, :AGE_D, :ISMALE, :SCR, :GFR, :AGEYRS, :TYPE_MODELING, :IS_BLEEDING, :IS_CIRCUIT_CHANGE, :ECMO_DAYS, :Occassions, :IS_CIRCUIT_CHANGE_UPDATE, :IS_BLEEDING_UPDATE), Tuple{Vector{Float64}, Vector{String31}, Vector{Float64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Float64}, Vector{Int64}, Vector{Float64}, Vector{Int64}, Vector{Int64}, Vector{Int64}, Vector{Int64}, Vector{Int64}, Vector{Int64}, Vector{Int64}}}, Symbol}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}; include_covariates::Bool, include_observations::Bool, include_events::Bool, extra_time::Vector{Float64})
    @ Pumas /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/MxXdQ/src/data_parsing/io.jl:1180

Any idea why I am getting this error ?

Thanks

2

Unfortunately, it’s the same bug as Error with DataFrame function when using output from predict function since the vpc function is hitting that method. I’ll try to see if there is a workaround. In any case, this will be fixed in the upcoming release.

1 Like
3

Hello, I’m getting the same error when trying read_nca using data i got from the predict function. Would that be the same bug here?
Thank you.

4

Can you share the full error message please and the code you ran.

5 
julia> pop = read_nca(dfNCA,
                       id      = :id,
                       ii      = :ii,
                       ss      = :ss,
                       time    = :time,
                       observations = :Cparent_ipred,
                       amt          = :amt,
                       route        = :route,
                       group         = [:id, :DOSE_N] )
ERROR: MethodError: Cannot `convert` an object of type Missing to an object of type Float64
Closest candidates are:
  convert(::Type{T}, ::ColorTypes.Gray24) where T<:Real at /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ColorTypes/1dGw6/src/conversions.jl:114
  convert(::Type{T}, ::ColorTypes.Gray) where T<:Real at /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/ColorTypes/1dGw6/src/conversions.jl:113
  convert(::Type{T}, ::Gain) where T<:Real at /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/Unitful/ApCuY/src/logarithm.jl:62
  ...
Stacktrace:
  [1] NCADose(time::Float64, amt::Float64, duration::Missing, route::NCA.Route, ii::Int64, ss::Bool)
    @ NCA /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NCA/CDayS/src/type.jl:37
  [2] _broadcast_getindex_evalf
    @ ./broadcast.jl:670 [inlined]
  [3] _broadcast_getindex
    @ ./broadcast.jl:643 [inlined]
  [4] getindex
    @ ./broadcast.jl:597 [inlined]
  [5] copy
    @ ./broadcast.jl:875 [inlined]
  [6] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{0}, Nothing, Type{NCADose}, Tuple{Float64, Float64, Base.RefValue{Missing}, Base.RefValue{NCA.Route}, Int64, Bool}})
    @ Base.Broadcast ./broadcast.jl:860
  [7] (::NCA.var"#292#303"{Nothing, Symbol, Symbol, Symbol, Symbol, Vector{Pair{String, String}}, Bool, Bool, Bool, Bool, Bool, Nothing, Nothing, Nothing, Nothing, Vector{Union{Missing, Float64}}, Vector{Union{Missing, Int64}}, Vector{Int64}, Bool})(::Tuple{Int64, String})
    @ NCA /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NCA/CDayS/src/data_parsing.jl:287
  [8] iterate
    @ ./generator.jl:47 [inlined]
  [9] collect(itr::Base.Generator{Base.Iterators.Enumerate{Vector{String}}, NCA.var"#292#303"{Nothing, Symbol, Symbol, Symbol, Symbol, Vector{Pair{String, String}}, Bool, Bool, Bool, Bool, Bool, Nothing, Nothing, Nothing, Nothing, Vector{Union{Missing, Float64}}, Vector{Union{Missing, Int64}}, Vector{Int64}, Bool}})
    @ Base ./array.jl:724
 [10] map(f::Function, A::Base.Iterators.Enumerate{Vector{String}})
    @ Base ./abstractarray.jl:2896
 [11] ___read_nca(df::DataFrame; id::Symbol, time::Symbol, observations::Symbol, nominal_time::Symbol, start_time::Symbol, end_time::Symbol, volume::Symbol, amt::Symbol, route::Symbol, duration::Symbol, blq::Symbol, ii::Symbol, ss::Symbol, group::Vector{Pair{String, String}}, concu::Bool, timeu::Bool, amtu::Bool, volumeu::Bool, verbose::Bool, sparse::Bool, lambdazidxs::Nothing, lambdazslopetimes::Nothing, concblq::Nothing, llq::Nothing, missingconc::Nothing, missingvolume::Nothing)
    @ NCA /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NCA/CDayS/src/data_parsing.jl:230
 [12] (::NCA.var"#284#286"{Vector{Symbol}, Base.Pairs{Symbol, Symbol, NTuple{7, Symbol}, NamedTuple{(:id, :ii, :ss, :time, :observations, :amt, :route), NTuple{7, Symbol}}}})(df::SubDataFrame{DataFrame, DataFrames.Index, Vector{Int64}})
    @ NCA /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NCA/CDayS/src/data_parsing.jl:68
 [13] mapreduce_impl(f::NCA.var"#284#286"{Vector{Symbol}, Base.Pairs{Symbol, Symbol, NTuple{7, Symbol}, NamedTuple{(:id, :ii, :ss, :time, :observations, :amt, :route), NTuple{7, Symbol}}}}, op::typeof(vcat), A::Vector{Any}, ifirst::Int64, ilast::Int64, blksize::Int64)
    @ Base ./reduce.jl:244
 [14] mapreduce_impl
    @ ./reduce.jl:259 [inlined]
 [15] _mapreduce(f::NCA.var"#284#286"{Vector{Symbol}, Base.Pairs{Symbol, Symbol, NTuple{7, Symbol}, NamedTuple{(:id, :ii, :ss, :time, :observations, :amt, :route), NTuple{7, Symbol}}}}, op::typeof(vcat), #unused#::IndexLinear, A::Vector{Any})
    @ Base ./reduce.jl:417
 [16] _mapreduce_dim
    @ ./reducedim.jl:330 [inlined]
 [17] #mapreduce#731
    @ ./reducedim.jl:322 [inlined]
 [18] mapreduce
    @ ./reducedim.jl:322 [inlined]
 [19] read_nca(df::DataFrame; group::Vector{Symbol}, kwargs::Base.Pairs{Symbol, Symbol, NTuple{7, Symbol}, NamedTuple{(:id, :ii, :ss, :time, :observations, :amt, :route), NTuple{7, Symbol}}})
    @ NCA /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/NCA/CDayS/src/data_parsing.jl:62
 [20] top-level scope
    @ ~/data/code/SEL/SEL_pumas.jl:33