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Submodels take kwargs variable splits rather than NamedTuples. #65

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Feb 23, 2024
Merged

Submodels take kwargs variable splits rather than NamedTuples. #65

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8035d60
Changed `Turing` models intended to be submodels into constructs taki…
SamuelBrand1 Feb 23, 2024
ee63f3d
Remove unnecessary `kwargs...`
SamuelBrand1 Feb 23, 2024
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6 changes: 3 additions & 3 deletions EpiAware/src/latent-processes.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@ function default_rw_priors()
)
end

@model function random_walk(n; latent_process_priors = default_rw_priors())
@model function random_walk(n; var_RW_dist, init_rw_value_dist)
ϵ_t ~ MvNormal(ones(n))
σ²_RW ~ latent_process_priors.var_RW_dist
init ~ latent_process_priors.init_rw_value_dist
σ²_RW ~ var_RW_dist
init ~ init_rw_value_dist
σ_RW = sqrt(σ²_RW)
rw = Vector{eltype(ϵ_t)}(undef, n)

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6 changes: 3 additions & 3 deletions EpiAware/src/models.jl
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Expand Up @@ -9,7 +9,7 @@
time_steps = epimodel.data.time_horizon
@submodel latent_process, init, latent_process_aux = latent_process_obj.latent_process(
time_steps;
latent_process_priors = latent_process_obj.latent_process_priors
latent_process_obj.latent_process_priors...
)

#Transform into infections
Expand All @@ -20,8 +20,8 @@
y_t,
I_t,
epimodel::AbstractEpiModel;
observation_process_priors = observation_process_obj.observation_model_priors,
pos_shift = pos_shift
pos_shift = pos_shift,
observation_process_obj.observation_model_priors...
)

#Generate quantities
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6 changes: 3 additions & 3 deletions EpiAware/src/observation-processes.jl
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Expand Up @@ -6,11 +6,11 @@ end
y_t,
I_t,
epimodel::AbstractEpiModel;
observation_process_priors = default_delay_obs_priors(),
pos_shift = 1e-6
neg_bin_cluster_factor_prior,
pos_shift
)
#Parameters
neg_bin_cluster_factor ~ observation_process_priors.neg_bin_cluster_factor_prior
neg_bin_cluster_factor ~ neg_bin_cluster_factor_prior

#Predictive distribution
case_pred_dists = (epimodel.data.delay_kernel * I_t) .+ pos_shift .|>
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3 changes: 2 additions & 1 deletion EpiAware/test/test_latent-processes.jl
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Expand Up @@ -2,7 +2,8 @@
@testitem "Testing random_walk against theoretical properties" begin
using DynamicPPL, Turing
n = 5
model = EpiAware.random_walk(n)
priors = EpiAware.default_rw_priors()
model = EpiAware.random_walk(n; priors...)
fixed_model = fix(model, (σ²_RW = 1.0, init_rw_value = 0.0)) #Fixing the standard deviation of the random walk process
n_samples = 1000
samples_day_5 = sample(fixed_model, Prior(), n_samples) |>
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5 changes: 3 additions & 2 deletions EpiAware/test/test_observation-processes.jl
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Expand Up @@ -8,14 +8,15 @@
data = EpiData([0.2, 0.3, 0.5], [1.0], 0.8, 3, exp)
epimodel = DirectInfections(data)
# Set up priors
observation_process_priors = default_delay_obs_priors()
priors = default_delay_obs_priors()

# Call the function
mdl = EpiAware.delay_observations(
missing,
I_t,
epimodel;
observation_process_priors = observation_process_priors
pos_shift = 1e-6,
priors...
)
fix_mdl = fix(mdl, neg_bin_cluster_factor = 0.00001) # Effectively Poisson sampling

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