diff --git a/EpiAware/Project.toml b/EpiAware/Project.toml index 1e6e5d220..972b66b99 100644 --- a/EpiAware/Project.toml +++ b/EpiAware/Project.toml @@ -36,7 +36,7 @@ FillArrays = "1.11" LinearAlgebra = ">= 1.9" LogExpFunctions = "0.3" MCMCChains = "6.0" -Pathfinder = "0.8, 0.9" +Pathfinder = "0.8" QuadGK = "2.9" Random = ">= 1.9" Reexport = "1.2" diff --git a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl index 553a3973a..0ab0bc1d1 100644 --- a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl +++ b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.43 +# v0.19.46 using Markdown using InteractiveUtils @@ -408,7 +408,9 @@ inference_method = EpiMethod( sampler = NUTSampler(adtype = AutoReverseDiff(), ndraws = 2000, nchains = num_threads, - mcmc_parallel = MCMCThreads()) + mcmc_parallel = MCMCThreads(), + nadapts = 500 + ) ) # ╔═╡ 92333a96-5c9b-46e1-9a8f-f1890831066b @@ -474,6 +476,11 @@ let hcat, generated_quantities(mdl_unconditional, inference_results.samples)) do gen gen.generated_y_t end + + if any(predicted_y_t .> 5_000) + throw("Sampled y_t badly") + end + predicted_I_t = mapreduce( hcat, gens) do gen gen.I_t @@ -483,6 +490,10 @@ let exp.(gen.Z_t) end + if any(predicted_R_t .> 250) + throw("Sampled R_t badly") + end + p1 = plot(D, predicted_y_t, c = :grey, alpha = 0.05, lab = "") scatter!(p1, D, C, lab = "Actual cases",