Add chatzilena et al as a replication example (#464)

* Plots to Makie Remove Statsplots and convert all plots to CairoMakie in Mishra replication * get_data script for English boarding school flu * fixed broken inference * Update index.jl * Update index.jl * Update index.jl * fix initialisation process for stochastic model * Update EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl Co-authored-by: Sam Abbott <[email protected]> * add StatsBase to doc env * add chatzilena replication to pages and build step * reformat * redo lines * link to `EpiProblem` * Small changes and prior pred plot for AR * reformat * implement xexpy and log1pexp * reformat --------- Co-authored-by: Sam Abbott <[email protected]>
CDCgov · Oct 3, 2024 · 4c29532 · 4c29532
1 parent f1f3571
commit 4c29532
Show file tree

Hide file tree

Showing 6 changed files with 708 additions and 4 deletions.
diff --git a/EpiAware/docs/Project.toml b/EpiAware/docs/Project.toml
@@ -9,16 +9,16 @@ 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"
+LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PairPlots = "43a3c2be-4208-490b-832a-a21dcd55d7da"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 TimeSeries = "9e3dc215-6440-5c97-bce1-76c03772f85e"
 Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f"
diff --git a/EpiAware/docs/make.jl b/EpiAware/docs/make.jl
@@ -15,6 +15,7 @@ include("build.jl")
 
 build("getting-started")
 build("getting-started/tutorials")
+build("showcase/replications/chatzilena-2019")
 build("showcase/replications/mishra-2020")
 
 DocMeta.setdocmeta!(EpiAware, :DocTestSetup, :(using EpiAware); recursive = true)

diff --git a/EpiAware/docs/pages.jl b/EpiAware/docs/pages.jl
@@ -26,7 +26,8 @@ getting_started_pages = Any[
 showcase_pages = Any[
     "Overview" => "showcase/index.md",
     "Replication" => [
-        "On the derivation of the renewal equation from an age-dependent branching process: an epidemic modelling perspective" => "showcase/replications/mishra-2020/index.md"
+        "On the derivation of the renewal equation from an age-dependent branching process: an epidemic modelling perspective" => "showcase/replications/mishra-2020/index.md",
+        "Statistical inference for ODE-based infectious disease models" => "showcase/replications/chatzilena-2019/index.md"
     ]
 ]
 

diff --git a/EpiAware/docs/src/showcase/replications/chatzilena-2019/get_data.R b/EpiAware/docs/src/showcase/replications/chatzilena-2019/get_data.R
@@ -0,0 +1,8 @@
+install.packages("outbreaks")
+library(outbreaks)
+
+# Get data
+
+data <- outbreaks::influenza_england_1978_school
+write.csv(data,
+          "EpiAware/docs/src/showcase/replications/chatzilena-2019/influenza_england_1978_school.csv2")