change default LatentDelay constructor to right truncation at 99th pe…

…rc (#265)

* change default LatentDelay constructor to right truncation at 99th perc

* update docstring

EpiAware/src/EpiObsModels/LatentDelay.jl

@@ -9,7 +9,13 @@ observed data.
 - `pmf::T`: The probability mass function (PMF) representing the delay distribution.
 
 ## Constructors
-- `LatentDelay(model::M, distribution::C; D = 15, Δd = 1.0) where {M <: AbstractTuringObservationModel, C <: ContinuousDistribution}`: Constructs a `LatentDelay` object with the given underlying observation model and continuous distribution. The `D` parameter specifies the number of discrete delay intervals, and the `Δd` parameter specifies the width of each delay interval.
+- `LatentDelay(model::M, distribution::C; D = nothing, Δd = 1.0)
+    where {M <: AbstractTuringObservationModel, C <: ContinuousDistribution}`: Constructs
+    a `LatentDelay` object with the given underlying observation model and continuous
+    distribution. The `D` parameter specifies the right truncation of the distribution,
+    with default `D = nothing` indicating that the distribution should be truncated at its
+    99th percentile rounded to nearest integer. The `Δd` parameter specifies the
+    width of each delay interval.
 
 - `LatentDelay(model::M, pmf::T) where {M <: AbstractTuringObservationModel, T <: AbstractVector{<:Real}}`: Constructs a `LatentDelay` object with the given underlying observation model and delay PMF.
 
@@ -26,9 +32,12 @@ struct LatentDelay{M <: AbstractTuringObservationModel, T <: AbstractVector{<:Re
     model::M
     pmf::T
 
-    function LatentDelay(model::M, distribution::C; D = 15,
+    function LatentDelay(model::M, distribution::C; D = nothing,
             Δd = 1.0) where {
             M <: AbstractTuringObservationModel, C <: ContinuousDistribution}
+        if isnothing(D)
+            D = invlogcdf(distribution, log(0.99)) |> round
+        end
         pmf = censored_pmf(distribution; Δd = Δd, D = D)
         return LatentDelay(model, pmf)
     end

EpiAware/test/EpiObsModels/LatentDelay.jl

@@ -21,6 +21,16 @@
 
     @test obs_model.model == dummy_model
     @test length(obs_model.pmf) == D_delay
+
+    # Test case 3: check default right truncation
+    delay_distribution = Gamma(3, 15 / 3)
+    D_delay = nothing
+    Δd = 1.0
+
+    obs_model = LatentDelay(dummy_model, delay_distribution, D = D_delay, Δd = Δd)
+
+    nn_perc_rounded = invlogcdf(delay_distribution, log(0.99)) |> x -> round(Int64, x)
+    @test length(obs_model.pmf) == nn_perc_rounded
 end
 
 @testitem "Testing delay obs against theoretical properties" begin