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‎CODE_OF_CONDUCT.md

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---
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title: "Contributor Code of Conduct"
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---
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As contributors and maintainers of this project,
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we pledge to follow the [The Epiverse-TRACE Code of Conduct][coc].
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<!--
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Instances of abusive, harassing, or otherwise unacceptable behavior
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may be reported by following our [reporting guidelines][coc-reporting].
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-->
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[coc-reporting]: https://forms.gle/guKqVXPk6K43jPn59
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[coc]: https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md
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‎LICENSE.md

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---
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title: "Licenses"
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---
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## Instructional Material
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The tutorials in this repository are developed by Epiverse-TRACE, based on the [lesson template from the Carpentries](https://github.com/carpentries/workbench-template-rmd) (template under CC BY license).
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All Epiverse-TRACE
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instructional material is made available under the [Creative Commons
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Attribution license][cc-by-human]. The following is a human-readable summary of
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(and not a substitute for) the [full legal text of the CC BY 4.0
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license][cc-by-legal].
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You are free:
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- to **Share**---copy and redistribute the material in any medium or format
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- to **Adapt**---remix, transform, and build upon the material
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for any purpose, even commercially.
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The licensor cannot revoke these freedoms as long as you follow the license
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terms.
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Under the following terms:
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- **Attribution**---You must give appropriate credit (mentioning that your work
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is derived from work that is Copyright (c) Epiverse-TRACE, where
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practical, linking to <https://epiverse-trace.github.io/>), provide a [link to the
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license][cc-by-human], and indicate if changes were made. You may do so in
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any reasonable manner, but not in any way that suggests the licensor endorses
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you or your use.
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- **No additional restrictions**---You may not apply legal terms or
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technological measures that legally restrict others from doing anything the
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license permits. With the understanding that:
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Notices:
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* You do not have to comply with the license for elements of the material in
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the public domain or where your use is permitted by an applicable exception
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or limitation.
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* No warranties are given. The license may not give you all of the permissions
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necessary for your intended use. For example, other rights such as publicity,
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privacy, or moral rights may limit how you use the material.
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## Software
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Except where otherwise noted, the example programs and other software provided
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by Epiverse-TRACE are made available under the [OSI][osi]-approved [MIT
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license][mit-license].
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
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of the Software, and to permit persons to whom the Software is furnished to do
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so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
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[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
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[mit-license]: https://opensource.org/licenses/mit-license.html
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[osi]: https://opensource.org

‎compare-interventions.md

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---
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title: 'Comparing public health outcomes of interventions'
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teaching: 45 # teaching time in minutes
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exercises: 30 # exercise time in minutes
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---
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:::::::::::::::::::::::::::::::::::::: questions
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- How can I quantify the effect of an intervention?
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::::::::::::::::::::::::::::::::::::::::::::::::
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::::::::::::::::::::::::::::::::::::: objectives
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- Understand how to compare intervention scenarios
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::::::::::::::::::::::::::::::::::::::::::::::::
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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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This tutorial has the following concept dependencies:
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**Outbreak response** : [Intervention types](https://www.cdc.gov/nonpharmaceutical-interventions/).
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:::::::::::::::::::::::::::::::::
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## Introduction
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In this tutorial we will compare intervention scenarios against each other. To quantify the effect of the intervention we need to compare our intervention scenario to a counter factual scenario. The *counter factual* is the scenario in which nothing changes, often referred to as the 'do nothing' scenario. The counter factual scenario may include no interventions, or if we are investigating the potential impact of an additional intervention in the later stages of an outbreak there may be existing interventions in place.
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We must also decide what our *outcome of interest* is to make comparisons between intervention and counter factual scenarios. The outcome of interest can be:
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+ a model outcome, e.g. number of infections or hospitalisations,
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+ a metric such as the epidemic peak time or size,
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+ a measure that uses the model outcomes such as QALY/DALYs.
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:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: instructor
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In this tutorial we introduce the concept of the counter factual and how to compare scenarios (counter factual versus intervention) against each other.
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::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
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## Vacamole model
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The Vacamole model is a deterministic model based on a system of ODEs in [Ainslie et al. 2022]( https://doi.org/10.2807/1560-7917.ES.2022.27.44.2101090). The model consists of 11 compartments, individuals are classed as one of the following:
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+ susceptible, $S$,
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+ partial vaccination ($V_1$), fully vaccination ($V_2$),
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+ exposed, $E$ and exposed while vaccinated, $E_V$,
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+ infectious, $I$ and infectious while vaccinated, $I_V$,
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+ hospitalised, $H$ and hospitalised while vaccinated, $H_V$,
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+ dead, $D$,
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+ recovered, $R$.
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The diagram below describes the flow of individuals through the different compartments.
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<img src="fig/compare-interventions-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" />
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See `?epidemics::model_vacamole_cpp` for detail on how to run the model.
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## Comparing scenarios
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*Coming soon*
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## Challenge
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*Coming soon*
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<!-- ::::::::::::::::::::::::::::::::::::: challenge -->
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<!-- ## The effect of vaccination on COVID-19 hospitalisations -->
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<!-- ::::::::::::::::: hint -->
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<!-- ### HINT -->
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<!-- :::::::::::::::::::::: -->
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<!-- ::::::::::::::::: solution -->
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<!-- ### SOLUTION -->
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<!-- ::::::::::::::::::::::::::: -->
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<!-- :::::::::::::::::::::::::::::::::::::::::::::::: -->
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::::::::::::::::::::::::::::::::::::: keypoints
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- The counter factual scenario must be defined to make comparisons
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::::::::::::::::::::::::::::::::::::::::::::::::

‎config.yaml

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#------------------------------------------------------------
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# Values for this lesson.
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#------------------------------------------------------------
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# Which carpentry is this (swc, dc, lc, or cp)?
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# swc: Software Carpentry
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# dc: Data Carpentry
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# lc: Library Carpentry
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# cp: Carpentries (to use for instructor training for instance)
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# incubator: The Carpentries Incubator
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carpentry: 'incubator'
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# Overall title for pages.
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title: 'Outbreak analytics with R'
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# Date the lesson was created (YYYY-MM-DD, this is empty by default)
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created: ~
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# Comma-separated list of keywords for the lesson
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keywords: 'forecasts, epidemic models, interventions' #FIXME
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# Life cycle stage of the lesson
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# possible values: pre-alpha, alpha, beta, stable
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life_cycle: 'pre-alpha'
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# License of the lesson
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license: 'CC-BY 4.0' #FIXME
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# Link to the source repository for this lesson
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source: 'https://github.com/epiverse-trace/tutorials'
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# Default branch of your lesson
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branch: 'main'
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# Who to contact if there are any issues
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contact: '[email protected]' #FIXME
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# Navigation ------------------------------------------------
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#
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# Use the following menu items to specify the order of
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# individual pages in each dropdown section. Leave blank to
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# include all pages in the folder.
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#
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# Example -------------
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#
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# episodes:
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# - introduction.md
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# - first-steps.md
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#
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# learners:
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# - setup.md
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#
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# instructors:
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# - instructor-notes.md
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#
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# profiles:
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# - one-learner.md
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# - another-learner.md
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# Order of episodes in your lesson
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episodes:
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- simulating-transmission.Rmd
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- model-choices.Rmd
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- modelling-interventions.Rmd
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- compare-interventions.Rmd
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# Information for Learners
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learners:
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# Information for Instructors
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instructors:
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# Learner Profiles
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profiles:
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# Customisation ---------------------------------------------
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#
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# This space below is where custom yaml items (e.g. pinning
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# sandpaper and varnish versions) should live
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varnish: epiverse-trace/varnish@epiversetheme
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sandpaper: 'carpentries/sandpaper#533'

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