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video resources pre-workshop instructions
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‎diagrams/measles-mike.svg‎

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‎video-resources.md‎

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Please watch the following videos to prepare for the workshop (links are
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to Google Drive).
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1. [Background and motivation for
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1. 5:06 minutes – [Background and motivation for
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`macpan2`](https://drive.google.com/file/d/1GPNZX59sJyfcIvScgnY78BBYlPO1fyOE)
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2. [Specifying simple
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2. 8:46 minutes – [Specifying simple
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models](https://drive.google.com/file/d/1BwAYWPi6e3PDn4AhqVsM14KkHie6Vx26)
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3. [Simulating from
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3. 8:28 minutes – [Simulating from
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models](https://drive.google.com/file/d/1x3BTWenFmKokCG3IS4JcI5h8kj8J24y6)
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| <img src="images/tip.svg" width="120" /> |
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|:-------------------------------------------------------------------------------------------------------------------------|
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| Code that is discussed in the videos is [here](https://github.com/canmod/macpan-workshop/blob/main/code/intro-videos.R). |
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If you are not familiar with R or the
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[tidyverse](https://www.tidyverse.org/) suite of packages, please
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consider watching the following videos from [this video
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series](https://www.youtube.com/playlist?list=PL9qLtkRkGWLeh9UNptt_734t0u1zXz5wy).
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1. [R Programming: How to get
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started](https://www.youtube.com/watch?v=Ld_JZNNahbQ&list=PL9qLtkRkGWLeh9UNptt_734t0u1zXz5wy&index=3&pp=iAQB)
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2. [How to Install R
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Packages](https://www.youtube.com/watch?v=2bjeUV_ySyM&list=PL9qLtkRkGWLeh9UNptt_734t0u1zXz5wy&index=4)
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3. [Data Science with the Tidyverse in
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R](https://www.youtube.com/watch?v=q0uGggl3RbM&list=PL9qLtkRkGWLeh9UNptt_734t0u1zXz5wy&index=6)
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4. [Introduction to the Pipe
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Operator](https://www.youtube.com/watch?v=Stt3qEuIeso&list=PL9qLtkRkGWLeh9UNptt_734t0u1zXz5wy&index=6&pp=iAQB)
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These videos give you the background to do the following exercises. It
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would be great if you did some of these before the workshop, but it is
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not required.
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| <img src="images/exercise.svg" width="120" /> |
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|:------------------------------------------------------------------------------------------------------------------------------------|
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| Create a model specification of an [SEIR model](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology#The_SEIR_model). |
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| <img src="images/exercise.svg" width="120" /> |
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|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Create a model specification of an elaboration of an SEIR model that has been modified for measles (diagram immediately following this box). This modified SEIR model includes a box for vaccinated individuals, $V$, and isolated infectious individuals, $I_\text{iso}$. The force of infection, $\Lambda$, is given by $\frac{\beta I}{N}$, where $N$ is the total number of individuals in the population. The vaccine efficacy is $\epsilon$ and the proportion of exposed individuals who isolate is $\theta$. |
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<img src="diagrams/measles-mike.svg" width="700" />
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| <img src="images/exercise.svg" width="120" /> |
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|:---------------------------------------------------------------------------|
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| Create a model specification of a model that you use or are interested in. |
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| <img src="images/exercise.svg" width="120" /> |
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|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Simulate one or more of the state variables in one of the above models. A big challenge here will be in choosing default numerical values of the parameters and initial conditions. |
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| <img src="images/tip.svg" width="120" /> |
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|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| In doing these exercises you might find it helpful to use the `macpan2` [website](https://canmod.github.io/macpan2) as a reference. Pages that could be particularly useful are the [quick start guide](https://canmod.github.io/macpan2/articles/quickstart) and documentation for the [`mp_tmb_model_spec`](https://canmod.github.io/macpan2/reference/mp_tmb_model_spec), [`mp_per_capita_flow`](https://canmod.github.io/macpan2/reference/mp_per_capita_flow), [`mp_simulator`](https://canmod.github.io/macpan2/reference/mp_simulator), and [`mp_trajectory`](https://canmod.github.io/macpan2/reference/mp_trajectory). |
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| <img src="images/tip.svg" width="120" /> |
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|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| If you are not familIn doing these exercises you might find it helpful to use the `macpan2` [website](https://canmod.github.io/macpan2) as a reference. Pages that could be particularly useful are the [quick start guide](https://canmod.github.io/macpan2/articles/quickstart) and documentation for the [`mp_tmb_model_spec`](https://canmod.github.io/macpan2/reference/mp_tmb_model_spec), [`mp_per_capita_flow`](https://canmod.github.io/macpan2/reference/mp_per_capita_flow), [`mp_simulator`](https://canmod.github.io/macpan2/reference/mp_simulator), and [`mp_trajectory`](https://canmod.github.io/macpan2/reference/mp_trajectory). |
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## Additional Videos
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I might populate this section with additional videos as the workshop
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draws nearer.
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I might populate this section with additional videos either before or
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after the workshop.

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