No method matching for time

Simulation
1

My program runs into a problem with the time variable when I try to run the simulation.
Can you spot the problem?

# Practice developing dissolution model using Pumas
using Random
using Pumas
using PumasUtilities
using CairoMakie
using AlgebraOfGraphics
using DataFramesMeta
using DataFrames

## Model definition
pk_44_cim_emax = @model begin
    @metadata begin
        desc = "Dissolution model"
        timeu = u"minute"
    end

    @param begin
        "Maximum % drug dissolved (%)"
        tvfdissmax ∈ RealDomain(lower=0)
        "Time required for 50% of the drug to dissolve (minutes)"
        tvtd50 ∈ RealDomain(lower=0)
        "Additive RUV"
        σ_add ∈ RealDomain(lower=0)
    end

    @covariates dtd50

    @pre begin
        fdissmax = tvfdissmax
        td50 = tvtd50*(1 + dtd50)
        _time = time
    end

    @derived begin
        fdiss = @. fdissmax * _time / (td50 + _time)
        """
        Fraction dissolved in vitro
        """
        dv_fdiss ~ @. Normal(fdiss, σ_add)
    end
end

param_emax = ( tvfdissmax = 100.0, tvtd50 = 10, σ_add = 0.01)

## Creating a Dataset
df_sub1_emax = map(i -> DataFrame(id = i, time = 1:1:1000, dv_fdiss = missing, dtd50=0), 1:6)
df = vcat(DataFrame.(df_sub1_emax)...)
df[!, :dtd50] = ifelse.(df.id .== 2, -0.75, df.dtd50)
df[!, :dtd50] = ifelse.(df.id .== 3, -0.5, df.dtd50)
df[!, :dtd50] = ifelse.(df.id .== 4, -0.25, df.dtd50)
df[!, :dtd50] = ifelse.(df.id .== 5, 0.25, df.dtd50)
df[!, :dtd50] = ifelse.(df.id .== 6, 0.5, df.dtd50)
df_sub1_emax = df
sub1_emax = read_pumas(df_sub1_emax, observations=[:dv_fdiss], covariates=[:dtd50], event_data=false)

##Simulation
Random.seed!(123)
sim_emax = simobs(pk_44_cim_emax, sub1_emax, param_emax)
df44_1_emax = DataFrame(sim_emax)


##Visualization
@chain df44_1_emax begin
    @rsubset :time ∈ [1,5,10,26,104,251,502,1000]
    data(_) *
    mapping(:time => "Time(minutes)",
        :fdiss => "Fraction dissolved",
        color = :dtd50 => nonnumeric => "Exposure") *
    visual(ScatterLines, linewidth = 4, markersize = 12)
    draw(axis = (;xticks = 0:100:1000, yticks = 0:10:100))
end
2

Hi Kevin - change

@pre begin
    fdissmax = tvfdissmax
    td50 = tvtd50*(1 + dtd50)
    _time = time
end

to this:

@pre begin
    fdissmax = tvfdissmax
    td50 = tvtd50*(1 + dtd50)
    _time = t
end

and it will work. Essentially, underlying Pumas uses t for time and not time

For the future, remember to post the full error message when posing a question along with the code and data (or data sample), it will better help to resolve the error. You can use the “Hide Details” option by clicking the gear icon in the message. :slight_smile:

1 Like
3

Thank you! That let it run, but now my fdiss is only simulated as zeros.

4

By mentioning _time = t it is only considering at the first time point which is time=0 for all time points for a single ID. Change the @derived block to:

@derived begin
    fdiss = @. fdissmax * t / (td50 + t)
    """
    Fraction dissolved in vitro
    """
    dv_fdiss ~ @. Normal(fdiss, σ_add)
end

it will work. I am unsure why this is happening though. May be others can let us know.

5

That worked! Thank you!