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Auto-generated via {sandpaper} Source : 5c76e4e Branch : main Author : Amanda Minter <[email protected]> Time : 2023-12-21 14:05:03 +0000 Message : update late tasks from feedback (#85) * Extend challenge in 'Choosing an appropriate model' * Edit to accounting for uncertainty example Store all results and then extract infectious compartment for plotting * Add detail to Ebola case study challenge * update glossary entries * Add callout on ODE solver * clarify purpose of concept dependencies * Updates from review * Remove infection object * Update simulating-transmission.Rmd * Update model-choices.Rmd * Add exercise to `compare_interventions.Rmd` * update modelling interventions after review * Update renv.lock * update plots * make uncertainty plots consistent across episodes * fix broken link * making plots consistent across tutorials * update summary and key points * update plots and add challenge * update introduction * move contact matrix callout and clarify reduction is performed within the model functions * add callout on intervention types * update introduction and reorder text in other sections * update PI section * style code * spell check * Update compare-interventions.Rmd * Apply suggestions from code review Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * add dropdown menus to make section more interactive * add reminder about transmissibility calculation * link to latent period * update model terms * add note on flow diagram * add callout on model rates * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * update tutorial objectives * distinguish parameter definitions from process descriptions in flow diagram * Update model-choices.Rmd * remove pak call from set up * Update renv.lock --------- Co-authored-by: Andree Valle Campos <[email protected]>
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diff --git a/compare-interventions.md b/compare-interventions.md
@@ -16,7 +16,7 @@ exercises: 30 # exercise time in minutes
 
 ::::::::::::::::::::::::::::::::::::: objectives
 
-- Understand how to compare intervention scenarios
+- Compare intervention scenarios
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -25,7 +25,7 @@ exercises: 30 # exercise time in minutes
 ## Prerequisites
 + Complete tutorials [Simulating transmission](../episodes/simulating-transmission.md) and [Modelling interventions](../episodes/modelling-interventions.md)
 
-This tutorial has the following concept dependencies:
+Learners should familiarise themselves with following concept dependencies before working through this tutorial: 
 
 **Outbreak response** : [Intervention types](https://www.cdc.gov/nonpharmaceutical-interventions/).
 :::::::::::::::::::::::::::::::::
@@ -50,7 +50,7 @@ In this tutorial we introduce the concept of the counter factual and how to comp
 
 ## Vacamole model
 
-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:
+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) to describe the effect of vaccination on COVID-19 dynamics. The model consists of 11 compartments, individuals are classed as one of the following:
 
 + susceptible, $S$,
 + partial vaccination ($V_1$), fully vaccination ($V_2$),
@@ -64,42 +64,174 @@ The diagram below describes the flow of individuals through the different compar
 
 <img src="fig/compare-interventions-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" />
 
-See `?epidemics::model_vacamole_cpp` for detail on how to run the model. 
 
-## Comparing scenarios
+::::::::::::::::::::::::::::::::::::: challenge
 
-*Coming soon*
+## Running a counterfactual scenario using the Vacamole model 
 
-## Challenge
+1. Run the model with the default parameter values for the UK population assuming that :
 
-*Coming soon*
++ 1 in a million individual are infectious (and not vaccinated) at the start of the simulation
++ The contact matrix for the United Kingdom has age bins:
+  + age between 0 and 20 years,
+  + age between 20 and 40,
+  + 40 years and over.
++ There is no vaccination scheme in place
+
+2. Using the output, plot the number of deaths through time
+
+
+::::::::::::::::: hint
+
+### Vaccination code 
+
+To run the model with no vaccination in place we can *either* create two vaccination objects (one for each dose) using `vaccination()` with the time start, time end and vaccination rate all set to 0, or we can use the `no_vaccination()` function to create a vaccination object for two doses with all values set to 0.
+
+
+```r
+no_vaccination <- no_vaccination(population = uk_population, doses = 2)
+```
+::::::::::::::::::::::
+
+::::::::::::::::: hint
+
+### HINT : Running the model with default parameter values
+
+We can run the Vacamole model with [default parameter values](https://epiverse-trace.github.io/epidemics/articles/vacamole.html#model-epidemic-using-vacamole) by just specifying the population object and number of time steps to run the model for: 
+
+
+
+```r
+output <- model_vacamole_cpp(
+  population = uk_population,
+  vaccination = no_vaccination,
+  time_end = 300
+)
+```
+
+::::::::::::::::::::::
 
-<!-- ::::::::::::::::::::::::::::::::::::: challenge -->
 
-<!-- ## The effect of vaccination on COVID-19 hospitalisations   -->
 
+::::::::::::::::: solution
 
+### SOLUTION
 
-<!-- ::::::::::::::::: hint -->
+1.  Run the model
 
-<!-- ### HINT -->
 
+```r
+polymod <- socialmixr::polymod
+contact_data <- socialmixr::contact_matrix(
+  survey = polymod,
+  countries = "United Kingdom",
+  age.limits = c(0, 20, 40),
+  symmetric = TRUE
+)
+```
 
-<!-- :::::::::::::::::::::: -->
+```{.output}
+Using POLYMOD social contact data. To cite this in a publication, use the 'get_citation()' function
+```
 
+```{.output}
+Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
+```
 
-<!-- ::::::::::::::::: solution -->
+```r
+# prepare contact matrix
+contact_matrix <- t(contact_data$matrix)
 
-<!-- ### SOLUTION -->
+# extract demography vector
+demography_vector <- contact_data$demography$population
+names(demography_vector) <- rownames(contact_matrix)
 
+# prepare initial conditions
+initial_i <- 1e-6
 
+initial_conditions <- c(
+  S = 1 - initial_i,
+  V1 = 0, V2 = 0,
+  E = 0, EV = 0,
+  I = initial_i, IV = 0,
+  H = 0, HV = 0, D = 0, R = 0
+)
 
+initial_conditions <- rbind(
+  initial_conditions,
+  initial_conditions,
+  initial_conditions
+)
+rownames(initial_conditions) <- rownames(contact_matrix)
 
+# prepare population object
+uk_population <- population(
+  name = "UK",
+  contact_matrix = contact_matrix,
+  demography_vector = demography_vector,
+  initial_conditions = initial_conditions
+)
 
-<!-- ::::::::::::::::::::::::::: -->
+no_vaccination <- no_vaccination(population = uk_population, doses = 2)
 
+# run model
+output <- model_vacamole_cpp(
+  population = uk_population,
+  vaccination = no_vaccination,
+  time_end = 300
+)
+```
+
+2. Plot the number of deaths through time
+
+
+```r
+ggplot(output[output$compartment == "dead", ]) +
+  geom_line(
+    aes(time, value, colour = demography_group),
+    linewidth = 1
+  ) +
+  scale_colour_brewer(
+    palette = "Dark2",
+    labels = rownames(contact_matrix),
+    name = "Age group"
+  ) +
+  scale_y_continuous(
+    labels = scales::comma
+  ) +
+  labs(
+    x = "Simulation time (days)",
+    y = "Individuals"
+  ) +
+  theme(
+    legend.position = "top"
+  ) +
+  theme_bw(
+    base_size = 15
+  )
+```
+
+<img src="fig/compare-interventions-rendered-unnamed-chunk-5-1.png" style="display: block; margin: auto;" />
+
+
+
+:::::::::::::::::::::::::::
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+
+## Comparing scenarios
+
+*Coming soon*
+
+
+
+## Challenge : Ebola outbreak analysis 
+
+*Coming soon*
 
-<!-- :::::::::::::::::::::::::::::::::::::::::::::::: -->
 
 
 

diff --git a/fig/compare-interventions-rendered-unnamed-chunk-5-1.png b/fig/compare-interventions-rendered-unnamed-chunk-5-1.png
diff --git a/fig/model-choices-rendered-diagram-1.png b/fig/model-choices-rendered-diagram-1.png
diff --git a/fig/model-choices-rendered-unnamed-chunk-1-1.png b/fig/model-choices-rendered-unnamed-chunk-1-1.png
diff --git a/fig/model-choices-rendered-unnamed-chunk-3-1.png b/fig/model-choices-rendered-unnamed-chunk-3-1.png
diff --git a/fig/modelling-interventions-rendered-baseline-1.png b/fig/modelling-interventions-rendered-baseline-1.png
diff --git a/fig/modelling-interventions-rendered-plot_masks-1.png b/fig/modelling-interventions-rendered-plot_masks-1.png
diff --git a/fig/modelling-interventions-rendered-plot_vaccinate-1.png b/fig/modelling-interventions-rendered-plot_vaccinate-1.png
diff --git a/fig/simulating-transmission-rendered-diagram-1.png b/fig/simulating-transmission-rendered-diagram-1.png
diff --git a/fig/simulating-transmission-rendered-plot-1.png b/fig/simulating-transmission-rendered-plot-1.png
diff --git a/fig/simulating-transmission-rendered-traj-1.png b/fig/simulating-transmission-rendered-traj-1.png
diff --git a/fig/simulating-transmission-rendered-visualise-1.png b/fig/simulating-transmission-rendered-visualise-1.png
diff --git a/md5sum.txt b/md5sum.txt
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