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‎compare-interventions.md‎

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::::::::::::::::::::::::::::::::::::: prereq
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## Prerequisites
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+ Complete tutorials [Simulating transmission](../episodes/simulating-transmission.md) and [Modelling interventions](../episodes/modelling-interventions.md)
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Learners should familiarise themselves with following concept dependencies before working through this tutorial:
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::::::::::::::::: solution
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### SOLUTION
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1. Run the model
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``` output
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scenario averted_median averted_lower averted_upper
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<int> <num> <num> <num>
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1: 1 31 2 119
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2: 2 20 -16 113
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1: 1 32 1 112
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2: 2 22 -17 112
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```
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‎fig/model-choices-rendered-unnamed-chunk-3-1.png‎

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‎fig/model-choices-rendered-unnamed-chunk-4-1.png‎

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‎md5sum.txt‎

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"config.yaml" "01ba2faa4b450855eba2fba32408867c" "site/built/config.yaml" "2024-11-04"
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"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2024-10-01"
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"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-10-01"
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"episodes/simulating-transmission.Rmd" "96a960983a0b9c17c299830bc42b1ae0" "site/built/simulating-transmission.md" "2024-10-01"
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"episodes/model-choices.Rmd" "d30a11c5547d221fa999a4648f812ad7" "site/built/model-choices.md" "2024-10-23"
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"episodes/modelling-interventions.Rmd" "c24d8bf7b881e058f0118d5b5cf99b22" "site/built/modelling-interventions.md" "2024-10-01"
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"episodes/compare-interventions.Rmd" "077add8024fd071891f3cb583c891c30" "site/built/compare-interventions.md" "2024-10-23"
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"episodes/simulating-transmission.Rmd" "946faeb2fbc86729c97e1e64bf66add2" "site/built/simulating-transmission.md" "2024-11-06"
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"episodes/model-choices.Rmd" "597b512fd487349fe19eeb1ce3b565dc" "site/built/model-choices.md" "2024-11-06"
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"episodes/modelling-interventions.Rmd" "92be2434ff4fd8fd79eb981fc45687a3" "site/built/modelling-interventions.md" "2024-11-06"
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"episodes/compare-interventions.Rmd" "2d9b19604352386139e3527d4a6e5918" "site/built/compare-interventions.md" "2024-11-06"
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"instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-10-01"
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"learners/setup.md" "84c16abddfc207bfb445fdd69d4f36a9" "site/built/setup.md" "2024-10-01"

‎model-choices.md‎

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::::::::::::::::::::::::::::::::::::: prereq
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## Prerequisites
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+ Complete tutorial [Simulating transmission](../episodes/simulating-transmission.md)
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### HINT
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Consider the following questions:
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### SOLUTION
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+ What is the infection/disease of interest? **Ebola**
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+ Do we need a deterministic or stochastic model? **A stochastic model would allow us to explore variation in the early stages of the outbreak**
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+ What is the outcome of interest? **Number of infections**
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A deterministic SEIR model with age specific direct transmission.
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<!--html_preserve--><div class="grViz html-widget html-fill-item" id="htmlwidget-de81f282fc7eeda36f0a" style="width:504px;height:504px;"></div>
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<script type="application/json" data-for="htmlwidget-de81f282fc7eeda36f0a">{"x":{"diagram":"digraph {\n\n # graph statement\n #################\n graph [layout = dot,\n rankdir = LR,\n overlap = true,\n fontsize = 10]\n\n # nodes\n #######\n node [shape = square,\n fixedsize = true\n width = 1.3]\n\n S\n E\n I\n R\n\n # edges\n #######\n S -> E [label = \" infection \n(transmissibility &beta;)\"]\n E -> I [label = \" onset of infectiousness \n(infectiousness rate &alpha;)\"]\n I -> R [label = \" recovery \n(recovery rate &gamma;)\"]\n\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
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<img src="fig/model-choices-rendered-diagram-1.png" style="display: block; margin: auto;" />
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The model is capable of simulating an Ebola type outbreak, but as the model is deterministic, we are not able to explore stochastic variation in the early stages of the outbreak.
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**Note: the functional relationship between the preinfectious period ($\rho^E$) and the transition rate between exposed and infectious ($\gamma^E$) is $\rho^E = k^E/\gamma^E$ where $k^E$ is the shape of the Erlang distribution. Similarly for the infectious period $\rho^I = k^I/\gamma^I$. For more detail on the stochastic model formulation refer to the section on [Discrete-time Ebola virus disease model](https://epiverse-trace.github.io/epidemics/articles/model_ebola.html#details-discrete-time-ebola-virus-disease-model) in the "Modelling responses to a stochastic Ebola virus epidemic" vignette. **
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<!--html_preserve--><div class="grViz html-widget html-fill-item" id="htmlwidget-da752f7cf7bda5d9def9" style="width:504px;height:504px;"></div>
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<script type="application/json" data-for="htmlwidget-da752f7cf7bda5d9def9">{"x":{"diagram":"digraph {\n\n # graph statement\n #################\n graph [layout = dot,\n rankdir = LR,\n overlap = true,\n fontsize = 10]\n\n # nodes\n #######\n node [shape = square,\n fixedsize = true\n width = 1.3]\n\n S\n E\n I\n H\n F\n R\n\n # edges\n #######\n S -> E [label = \" infection (&beta;)\"]\n E -> I [label = \" onset of \ninfectiousness (&gamma; E)\"]\n I -> F [label = \" death (funeral) \n(&gamma; I)\"]\n F -> R [label = \" safe burial (one timestep) \"]\n I -> H [label = \" hospitalisation (p hosp)\"]\n H -> R [label = \" recovery or safe burial \n (&gamma; I)\"]\n\n subgraph {\n rank = same; I; F;\n }\n subgraph {\n rank = same; H; R;\n }\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
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<img src="fig/model-choices-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" />
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The model has additional parameters describing the transmission risk in hospital and funeral settings:
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### SOLUTION
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‎modelling-interventions.md‎

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- How do I investigate the effect of interventions on disease trajectories?
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## Prerequisites
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+ Complete tutorial on [Simulating transmission](../episodes/simulating-transmission.md).
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``` r
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# create intervention_type column for plotting

‎simulating-transmission.md‎

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## Prerequisites
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Learners should familiarise themselves with following concept dependencies before working through this tutorial:
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**Mathematical Modelling** : [Introduction to infectious disease models](https://doi.org/10.1038/s41592-020-0856-2), [state variables](../learners/reference.md#state), [model parameters](../learners/reference.md#parsode), [initial conditions](../learners/reference.md#initial), [differential equations](../learners/reference.md#ordinary).
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``` output

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