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Improved tests for priors and add example dataset + parsing (#73)
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@ChrisRackauckas
ChrisRackauckas authored Jul 14, 2023
1 parent 61919b3 commit dea20aa
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Showing 4 changed files with 117 additions and 7 deletions.
91 changes: 91 additions & 0 deletions examples/dataset.csv
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18 changes: 13 additions & 5 deletions src/SimulationService.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -174,20 +174,28 @@ function amr_get(obj::Config, ::Type{ODESystem})
end

# priors
function amr_get(obj::Config, sys::ODESystem, ::Val{:priors})
paramlist = parameters(sys)
function amr_get(amr::Config, sys::ODESystem, ::Val{:priors})
paramlist = EasyModelAnalysis.ModelingToolkit.parameters(sys)
namelist = nameof.(paramlist)

map(amr.semantics.ode.parameters) do p
@assert p.distribution.type === "StandardUniform1"
dist = Uniform(p.distribution.parameters.minimum, p.distribution.parameters.maximum)
dist = EasyModelAnalysis.Distributions.Uniform(p.distribution.parameters.minimum, p.distribution.parameters.maximum)
paramlist[findfirst(x->x==Symbol(p.id),namelist)] => dist
end
end

# data
function amr_get(obj::Config, ::Val{:data})
error("TODO: amr_get for :data")
function amr_get(df::DataFrame, sys::ODESystem, ::Val{:data})
df = CSV.read(here("examples", "dataset.csv"), DataFrame)
statelist = states(sys)
statenames = string.(statelist)
statenames = map(statenames) do n; n[1:end-3]; end # there's a better way to do this
tvals = df[:,"timestamp"]

map(statelist, statenames) do s,n
s => (tvals,df[:,n])
end
end

#-----------------------------------------------------------------------------# job endpoints
Expand Down
4 changes: 2 additions & 2 deletions src/operations.jl
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Expand Up @@ -57,14 +57,14 @@ end
struct Calibrate <: Operation
sys::ODESystem
timespan::Tuple{Float64, Float64}
priors::Any # ???
priors::Vector{Pair{SymbolicUtils.BasicSymbolic{Real}, Uniform{Float64}}}
data::Any # ???
end

function Calibrate(o::OperationRequest)
sys = amr_get(o.model, ODESystem)
priors = amr_get(o.model, sys, Val(:priors))
data = o.df
data = amr_get(o.df, sys, Val(:data))
Calibrate(sys, o.timespan, priors, data)
end

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11 changes: 11 additions & 0 deletions test/runtests.jl
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Expand Up @@ -43,6 +43,17 @@ end
@test string.(states(sys)) == ["Susceptible(t)", "Diagnosed(t)", "Infected(t)", "Ailing(t)", "Recognized(t)", "Healed(t)", "Threatened(t)", "Extinct(t)"]
@test string.(parameters(sys)) == ["beta", "gamma", "delta", "alpha", "epsilon", "zeta", "lambda", "eta", "rho", "theta", "kappa", "mu", "nu", "xi", "tau", "sigma"]
@test map(x->string(x.lhs), observed(sys)) == ["Cases(t)", "Hospitalizations(t)", "Deaths(t)"]

priors = SimulationService.amr_get(amr, sys, Val(:priors))
@test priors isa Vector{Pair{SymbolicUtils.BasicSymbolic{Real}, Uniform{Float64}}}
@test string.(first.(priors)) == string.(parameters(sys))
@test last.(priors) isa Vector{Uniform{Float64}}

df = CSV.read(here("examples", "dataset.csv"), DataFrame)
data = SimulationService.amr_get(df, sys, Val(:data))
@test data isa Vector{Pair{SymbolicUtils.BasicSymbolic{Real}, Tuple{Vector{Int64}, Vector{Float64}}}}
@test string.(first.(data)) == string.(states(sys))
@test all(all.(map(first.(last.(data))) do x; x .== 0:89; end))
end

#-----------------------------------------------------------# DataServiceModel and OperationRequest
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