initial commit of using censored_pmf

Author: SamuelBrand1

EpiAware/docs/Project.toml

@@ -8,11 +8,14 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855"
+FFMPEG = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
+TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f"

EpiAware/docs/src/getting-started/explainers/censored-obs.jl

@@ -0,0 +1,321 @@
+### A Pluto.jl notebook ###
+# v0.19.46
+
+using Markdown
+using InteractiveUtils
+
+# ╔═╡ a2624404-48b1-4faa-abbe-6d78b8e04f2b
+let
+    docs_dir = dirname(dirname(dirname(@__DIR__)))
+    pkg_dir = dirname(docs_dir)
+
+    using Pkg: Pkg
+    Pkg.activate(docs_dir)
+    Pkg.develop(; path = pkg_dir)
+	Pkg.add(["DataFramesMeta", "StatsBase", "TuringBenchmarking"])
+    Pkg.instantiate()
+end
+
+# ╔═╡ 5baa8d2e-bcf8-4e3b-b007-175ad3e2ca95
+begin
+	using EpiAware.EpiAwareUtils: censored_pmf
+	using Random, Distributions, StatsBase #utilities for random events
+	using DataFramesMeta #Data wrangling
+	using StatsPlots #plotting
+	using Turing, TuringBenchmarking #PPL
+end
+
+# ╔═╡ 8de5c5e0-6e95-11ef-1693-bfd465c8d919
+md"
+# Fitting distributions using `censored_pmf` and Turing PPL
+
+## Introduction
+
+### What are we going to do in this Vignette
+
+In this vignette, we'll demonstrate how to use `EpiAwareUtils.censored_pmf` in conjunction with the Turing PPL for Bayesian inference of epidemiological delay distributions. We'll cover the following key points:
+
+1. Simulating censored delay distribution data
+2. Fitting a naive model using Turing
+3. Evaluating the naive model's performance
+4. Fitting an improved model using `censored_pmf` functionality
+5. Comparing the `censored_pmf` model's performance to the naive model
+
+### What might I need to know before starting
+
+This note builds on the concepts introduced in the R/stan package [`primarycensoreddist`](https://github.com/epinowcast/primarycensoreddist), especially the [Getting Started with primarycensoreddist](https://primarycensoreddist.epinowcast.org/articles/fitting-dists-with-stan.html) vignette and assumes familiarity with using Turing tools as covered in the [Turing documentation](https://turinglang.org/).
+
+This note is generated using the `EpiAware` package locally via `Pkg.develop`, in the `EpiAware/docs` environment. It is also possible to install `EpiAware` using 
+
+```julia
+Pkg.add(url=\"https://github.com/CDCgov/Rt-without-renewal\", subdir=\"EpiAware\")
+```
+
+"
+
+# ╔═╡ 30dd9af4-b64f-42b1-8439-a890752f68e3
+md"
+The other dependencies are as follows:
+"
+
+# ╔═╡ c5704f67-208d-4c2e-8513-c07c6b94ca99
+md"
+## Simulating censored and truncated delay distribution data
+
+We'll start by simulating some censored and truncated delay distribution data.
+"
+
+# ╔═╡ aed124c7-b4ba-4c97-a01f-ff553f376c86
+Random.seed!(123) # For reproducibility
+
+# ╔═╡ 105b9594-36ce-4ae8-87a8-5c81867b1ce3
+# Define the true distribution parameters
+n = 1000
+
+# ╔═╡ 8aa9f9c1-d3c4-49f3-be18-a400fc71e8f7
+meanlog = 1.5
+
+# ╔═╡ 84bb3999-9f2b-4eaa-9c2d-776a86677eaf
+sdlog = 0.75
+
+# ╔═╡ 2bf6677e-ebe9-4aa8-aa91-f631e99669bb
+true_dist = LogNormal(meanlog, sdlog)
+
+# ╔═╡ aea8b28e-fffe-4aa6-b51e-8199a7c7975c
+# Generate varying pwindow, swindow, and obs_time lengths
+pwindows = rand(1:1, n)
+
+# ╔═╡ d231bd0c-165f-4973-a46f-f66991813ea7
+swindows = rand(1:1, n)
+
+# ╔═╡ 7522f05b-1750-4983-8947-ef70f4298d06
+obs_times = fill(10.0,n)
+
+# ╔═╡ a4f5e9b6-ff3a-48fa-aa51-0abccb9c7bed
+#Sample secondary time relative to beginning of primary censor window respecting the right-truncation
+samples = map(pwindows, swindows, obs_times) do pw, sw, ot
+	P = rand() * pw # Primary event time 
+	T = rand(truncated(true_dist; upper= ot - P))
+end
+
+# ╔═╡ 0b5e96eb-9312-472e-8a88-d4509a4f25d0
+# Generate samples
+delay_counts = mapreduce(vcat, samples, pwindows, swindows, obs_times) do T, pw, sw, ot
+	DataFrame(
+		pwindow = pw, 
+		swindow = sw, 
+		obs_time = ot, 
+		observed_delay = T ÷ sw .|> Int,
+		observed_delay_upper = (T ÷ sw) + sw |> Int,
+	)
+end |> # Aggregate to unique combinations and count occurrences
+	df -> @groupby(df, :pwindow, :swindow, :obs_time, :observed_delay, :observed_delay_upper) |>
+	gd -> @combine(gd, :n = length(:pwindow))
+
+# ╔═╡ a7bff47d-b61f-499e-8631-206661c2bdc0
+empirical_cdf = ecdf(samples)
+
+# ╔═╡ 16bcb80a-970f-4633-aca2-261fa04172f7
+empirical_cdf_obs = ecdf(delay_counts.observed_delay, weights=delay_counts.n)
+
+# ╔═╡ 60711c3c-266e-42b5-acc6-6624db294f24
+x_seq = range(minimum(samples), maximum(samples), 100)
+
+# ╔═╡ c6fe3c52-af87-4a84-b280-bc9a8532e269
+#plot
+let
+	plot(; title = "Comparison of Observed vs Theoretical CDF",
+		ylabel = "Cumulative Probability",
+		xlabel = "Delay",
+		xticks = 0:obs_times[1],
+		xlims = (-0.1, obs_times[1] + 0.5)
+	)
+	plot!(x_seq, x_seq .|> x->empirical_cdf(x), 
+		lab = "Observed secondary times",
+		c = :blue,
+		lw = 3,
+	)
+	plot!(x_seq, x_seq .|> x->empirical_cdf_obs(x), 
+		lab = "Observed censored secondary times",
+		c = :green,
+		lw = 3,
+	)
+	plot!(x_seq, x_seq .|> x -> cdf(true_dist, x),
+		lab = "Theoretical",
+		c = :black,
+		lw = 3,
+	)
+	vline!([mean(samples)], ls = :dash, c= :blue, lw = 3, lab = "")
+	vline!([mean(true_dist)], ls = :dash, c= :black, lw = 3, lab = "")
+end
+
+# ╔═╡ f66d4b2e-ed66-423e-9cba-62bff712862b
+md"
+We've aggregated the data to unique combinations of `pwindow`, `swindow`, and `obs_time` and counted the number of occurrences of each `observed_delay` for each combination. This is the data we will use to fit our model.
+"
+
+# ╔═╡ 010ebe37-782b-4a35-bf5c-dca6dc0fee45
+md"
+## Fitting a naive model using Turing
+
+We'll start by fitting a naive model using Turing.
+"
+
+# ╔═╡ d9d14c48-8700-42b5-89b4-7fc51d0f577c
+@model function naive_model(N, y, n)
+	mu ~ Normal(1., 1.)
+	sigma ~ truncated(Normal(0.5, 1.0); lower= 0.0)
+	d = LogNormal(mu, sigma)
+	
+	for i in eachindex(y)
+		Turing.@addlogprob! n[i] * logpdf(d, y[i])
+	end
+end
+
+# ╔═╡ 8a7cd9ec-5640-4f5f-84c3-ae3f465ca68b
+md"
+Now lets instantiate this model with data
+"
+
+# ╔═╡ 028ade5c-17bd-4dfc-8433-23aaff02c181
+naive_mdl = naive_model(
+	size(delay_counts,1), 
+	delay_counts.observed_delay .+ 1e-6, # Add a small constant to avoid log(0)
+	delay_counts.n)
+
+# ╔═╡ 04b4eefb-f0f9-4887-8db0-7cbb7f3b169b
+md"
+and now let's fit the compiled model.
+"
+
+# ╔═╡ 21655344-d12b-4e47-a9a9-d06bd909f6ea
+naive_fit = sample(naive_mdl, NUTS(), MCMCThreads(), 500, 4)
+
+# ╔═╡ 3b89fe00-6aaf-4764-8b29-e71479f1e641
+summarize(naive_fit)
+
+# ╔═╡ 43eac8dd-8f1d-440e-b1e8-85db9e740651
+md"
+We see that the model has converged and the diagnostics look good. However, just from the model posterior summary we see that we might not be very happy with the fit. `mu` is smaller than the target $(meanlog) and `sigma` is larger than the target $(sdlog).
+
+"
+
+# ╔═╡ b2efafab-8849-4a7a-bb64-ac9ce126ca75
+md"
+## Fitting an improved model using primarycensoreddist
+
+We'll now fit an improved model using the `censored_pmf` function from the `EpiAware.EpiAwareUtils` submodule. This accounts for the primary and secondary censoring windows as well as the truncation.
+
+"
+
+# ╔═╡ ef40112b-f23e-4d4b-8a7d-3793b786f472
+@model function primarycensoreddist_model(N, y, y_upper, n, pwindow, D)
+	try
+		mu ~ Normal(1., 1.)
+		sigma ~ truncated(Normal(0.5, 0.5); lower= 0.1,)
+		d = LogNormal(mu, sigma)
+		log_pmf = censored_pmf(d; Δd = pwindow, D = D) .|> log
+	
+		for i in eachindex(y)
+			Turing.@addlogprob! n[i] * log_pmf[y[i] + 1] #0 obs is first element of array
+		end
+		return log_pmf
+	catch
+		Turing.@addlogprob! -Inf
+	end
+end
+
+# ╔═╡ b823d824-419d-41e9-9ac9-2c45ef190acf
+md"
+Lets instantiate this model with data
+"
+
+# ╔═╡ 93bca93a-5484-47fa-8424-7315eef15e37
+primarycensoreddist_mdl = primarycensoreddist_model(
+	size(delay_counts,1), 
+	delay_counts.observed_delay, # Add a small constant to avoid log(0)
+	delay_counts.observed_delay_upper, # Add a small constant to avoid log(0)
+	delay_counts.n,
+	delay_counts.pwindow[1],
+	delay_counts.obs_time[1]
+)
+
+# ╔═╡ 8f1d32fd-f54b-4f69-8c93-8f0786366cef
+# ╠═╡ disabled = true
+#=╠═╡
+benchmark_model(
+           primarycensoreddist_mdl;
+           # Check correctness of computations
+           check=true,
+           # Automatic differentiation backends to check and benchmark
+           adbackends=[:forwarddiff, :reversediff, :reversediff_compiled]
+       )
+  ╠═╡ =#
+
+# ╔═╡ 44132e2e-5a1a-49ad-9e57-cec24f981f52
+map_estimate = [maximum_a_posteriori(primarycensoreddist_mdl) for _ in 1:10] |>
+	opts -> (opts, findmax([o.lp for o in opts])[2]) |>
+	opts_i -> opts_i[1][opts_i[2]]
+
+# ╔═╡ a34c19e8-ba9e-4276-a17e-c853bb3341cf
+# ╠═╡ disabled = true
+#=╠═╡
+primarycensoreddist_fit = sample(primarycensoreddist_mdl, NUTS(), MCMCThreads(), 500, 4)
+  ╠═╡ =#
+
+# ╔═╡ 1210443f-480f-4e9f-b195-d557e9e1fc31
+summarize(primarycensoreddist_fit)
+
+# ╔═╡ 46711233-f680-4962-9e3e-60c747db4d2c
+censored_pmf(true_dist; D = obs_times[1] )
+
+# ╔═╡ 604458a6-7b6f-4b5c-b2e7-09be1908c0f9
+# ╠═╡ disabled = true
+#=╠═╡
+primarycensoreddist_fit = sample(primarycensoreddist_mdl, MH(), 100_000; initial_params=map_estimate.values.array) |>
+	chn -> chn[50_000:end, :, :]
+  ╠═╡ =#
+
+# ╔═╡ 7ae6c61d-0e33-4af8-b8d2-e31223a15a7c
+primarycensoreddist_fit = sample(primarycensoreddist_mdl, NUTS(), 1000; initial_params=map_estimate.values.array)
+
+# ╔═╡ Cell order:
+# ╟─8de5c5e0-6e95-11ef-1693-bfd465c8d919
+# ╠═a2624404-48b1-4faa-abbe-6d78b8e04f2b
+# ╟─30dd9af4-b64f-42b1-8439-a890752f68e3
+# ╠═5baa8d2e-bcf8-4e3b-b007-175ad3e2ca95
+# ╟─c5704f67-208d-4c2e-8513-c07c6b94ca99
+# ╠═aed124c7-b4ba-4c97-a01f-ff553f376c86
+# ╠═105b9594-36ce-4ae8-87a8-5c81867b1ce3
+# ╠═8aa9f9c1-d3c4-49f3-be18-a400fc71e8f7
+# ╠═84bb3999-9f2b-4eaa-9c2d-776a86677eaf
+# ╠═2bf6677e-ebe9-4aa8-aa91-f631e99669bb
+# ╠═aea8b28e-fffe-4aa6-b51e-8199a7c7975c
+# ╠═d231bd0c-165f-4973-a46f-f66991813ea7
+# ╠═7522f05b-1750-4983-8947-ef70f4298d06
+# ╠═a4f5e9b6-ff3a-48fa-aa51-0abccb9c7bed
+# ╠═0b5e96eb-9312-472e-8a88-d4509a4f25d0
+# ╠═a7bff47d-b61f-499e-8631-206661c2bdc0
+# ╠═16bcb80a-970f-4633-aca2-261fa04172f7
+# ╠═60711c3c-266e-42b5-acc6-6624db294f24
+# ╠═c6fe3c52-af87-4a84-b280-bc9a8532e269
+# ╟─f66d4b2e-ed66-423e-9cba-62bff712862b
+# ╟─010ebe37-782b-4a35-bf5c-dca6dc0fee45
+# ╠═d9d14c48-8700-42b5-89b4-7fc51d0f577c
+# ╟─8a7cd9ec-5640-4f5f-84c3-ae3f465ca68b
+# ╠═028ade5c-17bd-4dfc-8433-23aaff02c181
+# ╟─04b4eefb-f0f9-4887-8db0-7cbb7f3b169b
+# ╠═21655344-d12b-4e47-a9a9-d06bd909f6ea
+# ╠═3b89fe00-6aaf-4764-8b29-e71479f1e641
+# ╟─43eac8dd-8f1d-440e-b1e8-85db9e740651
+# ╠═b2efafab-8849-4a7a-bb64-ac9ce126ca75
+# ╠═ef40112b-f23e-4d4b-8a7d-3793b786f472
+# ╟─b823d824-419d-41e9-9ac9-2c45ef190acf
+# ╠═93bca93a-5484-47fa-8424-7315eef15e37
+# ╠═8f1d32fd-f54b-4f69-8c93-8f0786366cef
+# ╠═44132e2e-5a1a-49ad-9e57-cec24f981f52
+# ╠═604458a6-7b6f-4b5c-b2e7-09be1908c0f9
+# ╠═a34c19e8-ba9e-4276-a17e-c853bb3341cf
+# ╠═7ae6c61d-0e33-4af8-b8d2-e31223a15a7c
+# ╠═1210443f-480f-4e9f-b195-d557e9e1fc31
+# ╠═46711233-f680-4962-9e3e-60c747db4d2c