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Add chatzilena et al as a replication example #464

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merged 18 commits into from
Oct 3, 2024
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Merged

Add chatzilena et al as a replication example #464

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11b9034
Plots to Makie
SamuelBrand1 Sep 27, 2024
a1763f1
get_data script for English boarding school flu
SamuelBrand1 Sep 27, 2024
422b8d9
fixed broken inference
SamuelBrand1 Oct 1, 2024
0aaba4b
Update index.jl
SamuelBrand1 Oct 1, 2024
ff9c3dc
Update index.jl
SamuelBrand1 Oct 2, 2024
32b176b
Update index.jl
SamuelBrand1 Oct 2, 2024
b2fae2d
fix initialisation process for stochastic model
SamuelBrand1 Oct 2, 2024
cae03e3
Merge branch 'main' into 446-add-chatzilena-et-al-as-a-replication-ex…
SamuelBrand1 Oct 2, 2024
615d7e9
Update EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl
SamuelBrand1 Oct 2, 2024
813a166
add StatsBase to doc env
SamuelBrand1 Oct 2, 2024
3ba8106
add chatzilena replication to pages and build step
SamuelBrand1 Oct 2, 2024
1b50d1d
reformat
SamuelBrand1 Oct 2, 2024
86479f0
redo lines
SamuelBrand1 Oct 2, 2024
3b75af5
link to `EpiProblem`
SamuelBrand1 Oct 2, 2024
1b9b943
Small changes and prior pred plot for AR
SamuelBrand1 Oct 3, 2024
8c35483
reformat
SamuelBrand1 Oct 3, 2024
e5cb99e
implement xexpy and log1pexp
SamuelBrand1 Oct 3, 2024
e27927f
reformat
SamuelBrand1 Oct 3, 2024
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6 changes: 3 additions & 3 deletions EpiAware/docs/Project.toml
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Expand Up @@ -9,16 +9,16 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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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"
1 change: 1 addition & 0 deletions EpiAware/docs/make.jl
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Expand Up @@ -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)
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3 changes: 2 additions & 1 deletion EpiAware/docs/pages.jl
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Expand Up @@ -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"
]
]

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8 changes: 8 additions & 0 deletions EpiAware/docs/src/showcase/replications/chatzilena-2019/get_data.R
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@@ -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")
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